Starting phenix.real_space_refine on Mon May 4 02:17:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nb_75855/05_2026/11nb_75855.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nb_75855/05_2026/11nb_75855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nb_75855/05_2026/11nb_75855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nb_75855/05_2026/11nb_75855.map" model { file = "/net/cci-nas-00/data/ceres_data/11nb_75855/05_2026/11nb_75855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nb_75855/05_2026/11nb_75855.cif" } resolution = 2.46 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= 0.009 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 Mo 2 10.26 5 Fe 32 7.16 5 S 137 5.16 5 C 10166 2.51 5 N 2702 2.21 5 O 4009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17048 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 495} Chain: "C" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 456} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 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: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "B" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 322 Classifications: {'water': 322} Link IDs: {None: 321} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 187 Classifications: {'water': 187} Link IDs: {None: 186} Chain: "D" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 328 Classifications: {'water': 328} Link IDs: {None: 327} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 30.437 46.595 60.653 1.00 42.53 S ATOM 4549 SG CYS B 95 38.588 31.518 45.195 1.00 39.92 S ATOM 1170 SG CYS A 154 35.600 28.209 48.635 1.00 28.89 S ATOM 465 SG CYS A 62 36.510 34.706 50.434 1.00 28.88 S ATOM 652 SG CYS A 88 41.716 29.522 50.396 1.00 35.50 S ATOM 652 SG CYS A 88 41.716 29.522 50.396 1.00 35.50 S ATOM 5002 SG CYS B 153 39.793 26.209 46.489 1.00 53.13 S ATOM 4369 SG CYS B 70 45.300 30.410 45.235 1.00 27.24 S ATOM 4549 SG CYS B 95 38.588 31.518 45.195 1.00 39.92 S ATOM 10050 SG CYS C 275 104.766 57.404 60.803 1.00 50.72 S ATOM 12510 SG CYS D 95 96.586 72.890 45.156 1.00 37.39 S ATOM 9131 SG CYS C 154 99.643 76.211 48.665 1.00 27.76 S ATOM 8426 SG CYS C 62 98.718 69.681 50.596 1.00 30.01 S ATOM 8613 SG CYS C 88 93.524 74.822 50.330 1.00 34.29 S ATOM 8613 SG CYS C 88 93.524 74.822 50.330 1.00 34.29 S ATOM 12963 SG CYS D 153 95.317 78.179 46.459 1.00 46.26 S ATOM 12330 SG CYS D 70 90.039 73.805 45.140 1.00 31.97 S ATOM 12510 SG CYS D 95 96.586 72.890 45.156 1.00 37.39 S Time building chain proxies: 3.67, per 1000 atoms: 0.22 Number of scatterers: 17048 At special positions: 0 Unit cell: (135.24, 105.105, 100.695, 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) Mo 2 41.97 Fe 32 26.01 S 137 16.00 O 4009 8.00 N 2702 7.00 C 10166 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 701.1 milliseconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 12 sheets defined 58.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.931A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.550A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.560A pdb=" N SER A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.539A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.872A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.208A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.390A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.623A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.701A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 343 removed outlier: 3.502A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.737A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA A 366 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.516A pdb=" N TYR A 387 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.789A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.758A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 4.137A pdb=" N LEU A 475 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.768A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.916A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.788A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 removed outlier: 3.665A pdb=" N LYS B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.740A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.208A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.524A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.728A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.453A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.560A pdb=" N SER C 92 " --> pdb=" O CYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.725A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.018A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 207 through 210 removed outlier: 4.340A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.703A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 279 through 291 removed outlier: 3.525A pdb=" N HIS C 285 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.798A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.595A pdb=" N GLY C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 366 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.359A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 3.858A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.896A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.860A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.119A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.029A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 removed outlier: 3.540A pdb=" N MET D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.727A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 3.631A pdb=" N THR D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.789A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.312A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 10.393A pdb=" N LEU A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 375 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N TYR A 401 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 349 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 375 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 351 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR A 377 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 353 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR A 379 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.924A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.947A pdb=" N VAL A 223 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN A 252 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 225 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP A 222 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU A 272 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA A 224 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.603A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.597A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.559A pdb=" N TYR C 401 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.184A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 253 removed outlier: 7.845A pdb=" N VAL C 223 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 252 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 225 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C 272 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA C 224 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN C 271 " --> pdb=" O MET C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 removed outlier: 8.615A pdb=" N VAL D 114 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.558A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.468A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 757 hydrogen bonds defined for protein. 2178 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: 2.55 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.83: 16339 1.83 - 2.46: 102 2.46 - 3.10: 20 3.10 - 3.74: 6 3.74 - 4.38: 8 Bond restraints: 16475 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.377 -2.177 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.374 -2.174 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.955 -1.755 2.00e-02 2.50e+03 7.70e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.951 -1.751 2.00e-02 2.50e+03 7.67e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.863 -1.663 2.00e-02 2.50e+03 6.91e+03 ... (remaining 16470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 22209 6.89 - 13.78: 14 13.78 - 20.67: 2 20.67 - 27.56: 0 27.56 - 34.45: 4 Bond angle restraints: 22229 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.55 34.45 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 60.67 29.33 3.00e+00 1.11e-01 9.56e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.72 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE3 CLF B 602 " ideal model delta sigma weight residual 90.00 108.20 -18.20 3.00e+00 1.11e-01 3.68e+01 ... (remaining 22224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9164 17.83 - 35.67: 740 35.67 - 53.50: 126 53.50 - 71.34: 34 71.34 - 89.17: 27 Dihedral angle restraints: 10091 sinusoidal: 4357 harmonic: 5734 Sorted by residual: dihedral pdb=" C LYS C 330 " pdb=" N LYS C 330 " pdb=" CA LYS C 330 " pdb=" CB LYS C 330 " ideal model delta harmonic sigma weight residual -122.60 -112.79 -9.81 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C ASP C 204 " pdb=" N ASP C 204 " pdb=" CA ASP C 204 " pdb=" CB ASP C 204 " ideal model delta harmonic sigma weight residual -122.60 -132.19 9.59 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C PHE A 429 " pdb=" N PHE A 429 " pdb=" CA PHE A 429 " pdb=" CB PHE A 429 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 10088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2036 0.089 - 0.179: 269 0.179 - 0.268: 24 0.268 - 0.358: 3 0.358 - 0.447: 2 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CB VAL C 250 " pdb=" CA VAL C 250 " pdb=" CG1 VAL C 250 " pdb=" CG2 VAL C 250 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB VAL A 250 " pdb=" CA VAL A 250 " pdb=" CG1 VAL A 250 " pdb=" CG2 VAL A 250 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA PHE B 474 " pdb=" N PHE B 474 " pdb=" C PHE B 474 " pdb=" CB PHE B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2331 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 233 " -0.024 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C GLY C 233 " 0.080 2.00e-02 2.50e+03 pdb=" O GLY C 233 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP C 234 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 469 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ILE B 469 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE B 469 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY B 470 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 253 " -0.017 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C TRP A 253 " 0.063 2.00e-02 2.50e+03 pdb=" O TRP A 253 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 254 " -0.022 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 246 2.53 - 3.12: 13424 3.12 - 3.72: 29065 3.72 - 4.31: 44107 4.31 - 4.90: 69581 Nonbonded interactions: 156423 Sorted by model distance: nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 1.941 2.260 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.161 2.260 nonbonded pdb=" OD2 ASP B 353 " pdb="FE FE B 601 " model vdw 2.174 2.260 nonbonded pdb=" OD1 ASP D 353 " pdb="FE FE D 601 " model vdw 2.202 2.260 nonbonded pdb=" OD1 ASP C 136 " pdb=" NZ LYS C 170 " model vdw 2.298 3.120 ... (remaining 156418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 502)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.760 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.050 2.177 16490 Z= 2.542 Angle : 1.060 34.454 22229 Z= 0.640 Chirality : 0.059 0.447 2334 Planarity : 0.006 0.051 2856 Dihedral : 13.930 89.171 6427 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.93 % Allowed : 1.63 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 1990 helix: 0.71 (0.17), residues: 972 sheet: -0.76 (0.34), residues: 208 loop : -1.33 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 238 TYR 0.026 0.002 TYR A 446 PHE 0.024 0.002 PHE C 429 TRP 0.026 0.003 TRP A 335 HIS 0.016 0.003 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.05004 (16475) covalent geometry : angle 1.05988 (22229) hydrogen bonds : bond 0.15901 ( 757) hydrogen bonds : angle 6.87560 ( 2178) Misc. bond : bond 0.19572 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 0.637 Fit side-chains REVERT: A 352 MET cc_start: 0.5536 (mtp) cc_final: 0.5319 (mtp) REVERT: A 373 GLU cc_start: 0.5788 (mp0) cc_final: 0.4869 (tt0) REVERT: A 463 MET cc_start: 0.8068 (mmt) cc_final: 0.7797 (mmt) REVERT: B 38 ASP cc_start: 0.7973 (p0) cc_final: 0.7632 (m-30) REVERT: B 259 GLU cc_start: 0.7233 (tp30) cc_final: 0.7028 (tp30) REVERT: B 270 ARG cc_start: 0.6769 (mtt90) cc_final: 0.6373 (mtt180) REVERT: B 417 LYS cc_start: 0.7421 (tptm) cc_final: 0.7103 (mmtt) REVERT: C 289 LYS cc_start: 0.6627 (tttt) cc_final: 0.6230 (ttpm) REVERT: C 315 LYS cc_start: 0.5446 (mttm) cc_final: 0.4504 (tptp) REVERT: C 381 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5492 (p90) REVERT: C 394 MET cc_start: 0.3122 (mmm) cc_final: 0.2609 (mmt) REVERT: C 456 PHE cc_start: 0.7538 (t80) cc_final: 0.7319 (t80) REVERT: C 474 LYS cc_start: 0.7634 (mttt) cc_final: 0.7419 (mmtp) REVERT: D 7 LYS cc_start: 0.6779 (tttp) cc_final: 0.6131 (tptt) REVERT: D 38 ASP cc_start: 0.8069 (m-30) cc_final: 0.7866 (m-30) REVERT: D 41 ASP cc_start: 0.8121 (m-30) cc_final: 0.7850 (m-30) REVERT: D 214 ASP cc_start: 0.7968 (m-30) cc_final: 0.7746 (m-30) REVERT: D 259 GLU cc_start: 0.7263 (tp30) cc_final: 0.7041 (tp30) REVERT: D 268 GLN cc_start: 0.6776 (mt0) cc_final: 0.6403 (tt0) outliers start: 16 outliers final: 4 residues processed: 332 average time/residue: 0.7166 time to fit residues: 260.3645 Evaluate side-chains 191 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 381 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 98 ASN A 468 ASN A 469 ASN B 128 GLN C 98 ASN C 191 GLN D 45 GLN D 128 GLN D 137 ASN ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.165251 restraints weight = 17713.282| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.47 r_work: 0.3819 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.301 16490 Z= 0.272 Angle : 0.752 30.218 22229 Z= 0.358 Chirality : 0.048 0.176 2334 Planarity : 0.005 0.054 2856 Dihedral : 5.552 55.469 2524 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.73 % Allowed : 9.94 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.19), residues: 1990 helix: 1.19 (0.16), residues: 992 sheet: -0.37 (0.34), residues: 212 loop : -1.17 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 28 TYR 0.021 0.002 TYR D 102 PHE 0.017 0.002 PHE C 429 TRP 0.023 0.002 TRP A 335 HIS 0.007 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00548 (16475) covalent geometry : angle 0.75207 (22229) hydrogen bonds : bond 0.05224 ( 757) hydrogen bonds : angle 5.47312 ( 2178) Misc. bond : bond 0.15736 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.545 Fit side-chains REVERT: A 355 ILE cc_start: 0.3713 (OUTLIER) cc_final: 0.3358 (mp) REVERT: A 373 GLU cc_start: 0.5638 (mp0) cc_final: 0.4793 (tt0) REVERT: A 394 MET cc_start: 0.4615 (mtp) cc_final: 0.2775 (tpt) REVERT: A 415 ARG cc_start: 0.4330 (OUTLIER) cc_final: 0.4107 (ptm160) REVERT: A 463 MET cc_start: 0.7801 (mmt) cc_final: 0.7554 (mmt) REVERT: B 258 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: B 417 LYS cc_start: 0.7440 (tptm) cc_final: 0.7237 (mmtt) REVERT: B 507 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: C 120 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6293 (mp0) REVERT: C 261 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6987 (mt-10) REVERT: C 315 LYS cc_start: 0.5195 (mttm) cc_final: 0.4120 (tptp) REVERT: C 372 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.3197 (mpt) REVERT: D 7 LYS cc_start: 0.6963 (tttp) cc_final: 0.6367 (tptt) REVERT: D 41 ASP cc_start: 0.8312 (m-30) cc_final: 0.7972 (m-30) REVERT: D 214 ASP cc_start: 0.7976 (m-30) cc_final: 0.7703 (m-30) REVERT: D 268 GLN cc_start: 0.6706 (mt0) cc_final: 0.6380 (tt0) outliers start: 47 outliers final: 15 residues processed: 224 average time/residue: 0.7016 time to fit residues: 172.7563 Evaluate side-chains 196 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 400 LYS Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 469 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 196 HIS C 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.192185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165284 restraints weight = 17963.212| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.48 r_work: 0.3816 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.268 16490 Z= 0.235 Angle : 0.713 30.614 22229 Z= 0.332 Chirality : 0.046 0.171 2334 Planarity : 0.005 0.057 2856 Dihedral : 5.098 52.970 2517 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.67 % Allowed : 11.97 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.19), residues: 1990 helix: 1.27 (0.16), residues: 1006 sheet: -0.35 (0.35), residues: 212 loop : -1.12 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 415 TYR 0.017 0.002 TYR D 102 PHE 0.013 0.002 PHE B 201 TRP 0.018 0.002 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00474 (16475) covalent geometry : angle 0.71316 (22229) hydrogen bonds : bond 0.04739 ( 757) hydrogen bonds : angle 5.24280 ( 2178) Misc. bond : bond 0.13156 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.648 Fit side-chains REVERT: A 279 MET cc_start: 0.5699 (mtp) cc_final: 0.5249 (mtt) REVERT: A 296 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 343 ARG cc_start: 0.7260 (ttt180) cc_final: 0.6840 (tpp80) REVERT: A 350 ARG cc_start: 0.5843 (mtt90) cc_final: 0.5555 (mtm180) REVERT: A 373 GLU cc_start: 0.5730 (mp0) cc_final: 0.4932 (tt0) REVERT: A 381 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6381 (p90) REVERT: A 394 MET cc_start: 0.4481 (mtp) cc_final: 0.2778 (tpt) REVERT: A 463 MET cc_start: 0.7770 (mmt) cc_final: 0.7525 (mmt) REVERT: B 38 ASP cc_start: 0.7947 (p0) cc_final: 0.7510 (p0) REVERT: B 258 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: B 400 LYS cc_start: 0.7636 (mtmm) cc_final: 0.7265 (mmtt) REVERT: B 417 LYS cc_start: 0.7430 (tptm) cc_final: 0.7230 (mmtt) REVERT: B 507 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: C 261 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6857 (mt-10) REVERT: C 289 LYS cc_start: 0.6575 (ttpt) cc_final: 0.6189 (ttpm) REVERT: C 345 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.4805 (mtp180) REVERT: C 372 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.3409 (mpt) REVERT: D 7 LYS cc_start: 0.6946 (tttp) cc_final: 0.6385 (tptt) REVERT: D 41 ASP cc_start: 0.8311 (m-30) cc_final: 0.8007 (m-30) REVERT: D 214 ASP cc_start: 0.7948 (m-30) cc_final: 0.7666 (m-30) REVERT: D 268 GLN cc_start: 0.6697 (mt0) cc_final: 0.6411 (tt0) outliers start: 46 outliers final: 14 residues processed: 218 average time/residue: 0.6823 time to fit residues: 163.9431 Evaluate side-chains 193 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 469 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 469 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165380 restraints weight = 17933.838| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.47 r_work: 0.3820 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 16490 Z= 0.222 Angle : 0.695 30.588 22229 Z= 0.321 Chirality : 0.045 0.174 2334 Planarity : 0.005 0.058 2856 Dihedral : 4.968 51.453 2517 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 2.96 % Allowed : 12.67 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.19), residues: 1990 helix: 1.31 (0.16), residues: 1020 sheet: -0.35 (0.35), residues: 212 loop : -1.13 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 28 TYR 0.015 0.001 TYR C 229 PHE 0.012 0.002 PHE B 201 TRP 0.015 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00446 (16475) covalent geometry : angle 0.69492 (22229) hydrogen bonds : bond 0.04461 ( 757) hydrogen bonds : angle 5.10013 ( 2178) Misc. bond : bond 0.11812 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.631 Fit side-chains REVERT: A 4 MET cc_start: -0.0890 (OUTLIER) cc_final: -0.2476 (ppp) REVERT: A 191 GLN cc_start: 0.6908 (mt0) cc_final: 0.6617 (mt0) REVERT: A 279 MET cc_start: 0.5944 (mtp) cc_final: 0.5567 (mtt) REVERT: A 281 TYR cc_start: 0.5283 (m-80) cc_final: 0.5054 (m-80) REVERT: A 289 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6712 (ptmt) REVERT: A 343 ARG cc_start: 0.7295 (ttt180) cc_final: 0.6895 (tpp80) REVERT: A 350 ARG cc_start: 0.5917 (mtt90) cc_final: 0.5589 (mtm180) REVERT: A 352 MET cc_start: 0.5462 (mtp) cc_final: 0.5249 (mtm) REVERT: A 373 GLU cc_start: 0.5713 (mp0) cc_final: 0.4890 (tt0) REVERT: A 394 MET cc_start: 0.4427 (mtp) cc_final: 0.2743 (tpt) REVERT: A 463 MET cc_start: 0.7755 (mmt) cc_final: 0.7526 (mmt) REVERT: B 38 ASP cc_start: 0.7885 (p0) cc_final: 0.7420 (p0) REVERT: B 258 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: B 400 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7270 (mmtt) REVERT: B 417 LYS cc_start: 0.7412 (tptm) cc_final: 0.7053 (mmpt) REVERT: B 507 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: C 261 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6745 (mt-10) REVERT: C 345 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.4822 (mtp180) REVERT: C 372 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.3329 (mpt) REVERT: C 401 TYR cc_start: 0.6261 (OUTLIER) cc_final: 0.5592 (p90) REVERT: C 415 ARG cc_start: 0.4513 (OUTLIER) cc_final: 0.3513 (mtt-85) REVERT: C 417 LYS cc_start: 0.5598 (ttmt) cc_final: 0.5093 (tptp) REVERT: C 474 LYS cc_start: 0.7995 (mmtp) cc_final: 0.7365 (mmtt) REVERT: D 7 LYS cc_start: 0.6981 (tttp) cc_final: 0.6408 (tptt) REVERT: D 41 ASP cc_start: 0.8315 (m-30) cc_final: 0.8005 (m-30) REVERT: D 214 ASP cc_start: 0.7946 (m-30) cc_final: 0.7681 (m-30) REVERT: D 222 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7396 (mppt) REVERT: D 268 GLN cc_start: 0.6544 (mt0) cc_final: 0.6270 (tt0) REVERT: D 280 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7801 (mt-10) outliers start: 51 outliers final: 17 residues processed: 218 average time/residue: 0.6545 time to fit residues: 157.5985 Evaluate side-chains 201 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 482 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 175 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.0020 chunk 68 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 469 ASN B 518 ASN C 98 ASN C 469 ASN D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.194947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168096 restraints weight = 17928.726| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.48 r_work: 0.3849 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 16490 Z= 0.199 Angle : 0.670 30.556 22229 Z= 0.306 Chirality : 0.043 0.194 2334 Planarity : 0.005 0.056 2856 Dihedral : 4.796 50.405 2517 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 2.32 % Allowed : 13.83 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.19), residues: 1990 helix: 1.56 (0.17), residues: 996 sheet: -0.43 (0.36), residues: 216 loop : -1.13 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 415 TYR 0.013 0.001 TYR D 88 PHE 0.010 0.001 PHE A 409 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00389 (16475) covalent geometry : angle 0.66992 (22229) hydrogen bonds : bond 0.03852 ( 757) hydrogen bonds : angle 4.97559 ( 2178) Misc. bond : bond 0.10843 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.632 Fit side-chains REVERT: A 4 MET cc_start: -0.0828 (OUTLIER) cc_final: -0.2459 (ppp) REVERT: A 279 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5556 (mtt) REVERT: A 289 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6653 (ptmm) REVERT: A 343 ARG cc_start: 0.7266 (ttt180) cc_final: 0.6978 (tpp80) REVERT: A 350 ARG cc_start: 0.5879 (mtt90) cc_final: 0.5525 (mtm180) REVERT: A 352 MET cc_start: 0.5337 (mtp) cc_final: 0.5133 (mtm) REVERT: A 373 GLU cc_start: 0.5672 (mp0) cc_final: 0.4785 (tt0) REVERT: A 394 MET cc_start: 0.4365 (mtp) cc_final: 0.2781 (tpt) REVERT: A 463 MET cc_start: 0.7722 (mmt) cc_final: 0.7375 (mmt) REVERT: B 38 ASP cc_start: 0.7846 (p0) cc_final: 0.7407 (p0) REVERT: B 258 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: B 400 LYS cc_start: 0.7594 (mtmm) cc_final: 0.7214 (mmtp) REVERT: B 417 LYS cc_start: 0.7399 (tptm) cc_final: 0.7018 (mmpt) REVERT: B 507 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: C 261 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6712 (mt-10) REVERT: C 345 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.4837 (mtp180) REVERT: C 401 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.5423 (p90) REVERT: C 415 ARG cc_start: 0.4469 (OUTLIER) cc_final: 0.3512 (mtt-85) REVERT: C 417 LYS cc_start: 0.5677 (ttmt) cc_final: 0.5107 (tptp) REVERT: D 7 LYS cc_start: 0.6892 (tttp) cc_final: 0.6311 (tptt) REVERT: D 41 ASP cc_start: 0.8317 (m-30) cc_final: 0.8026 (m-30) REVERT: D 214 ASP cc_start: 0.7951 (m-30) cc_final: 0.7665 (m-30) REVERT: D 268 GLN cc_start: 0.6497 (mt0) cc_final: 0.6255 (tt0) REVERT: D 315 LYS cc_start: 0.8269 (mtpt) cc_final: 0.8063 (mtpm) outliers start: 40 outliers final: 12 residues processed: 208 average time/residue: 0.6793 time to fit residues: 155.8906 Evaluate side-chains 191 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 152 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 451 HIS A 469 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.191937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.164986 restraints weight = 17902.137| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.48 r_work: 0.3817 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 16490 Z= 0.226 Angle : 0.701 30.570 22229 Z= 0.324 Chirality : 0.045 0.163 2334 Planarity : 0.005 0.057 2856 Dihedral : 4.712 50.651 2512 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 2.56 % Allowed : 13.71 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.19), residues: 1990 helix: 1.47 (0.17), residues: 1010 sheet: -0.47 (0.35), residues: 216 loop : -1.09 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 415 TYR 0.015 0.002 TYR B 207 PHE 0.011 0.002 PHE B 201 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00457 (16475) covalent geometry : angle 0.70054 (22229) hydrogen bonds : bond 0.04432 ( 757) hydrogen bonds : angle 5.00694 ( 2178) Misc. bond : bond 0.11931 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.692 Fit side-chains REVERT: A 4 MET cc_start: -0.0805 (OUTLIER) cc_final: -0.2448 (ppp) REVERT: A 191 GLN cc_start: 0.6843 (mt0) cc_final: 0.6445 (mt0) REVERT: A 279 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5693 (mtt) REVERT: A 289 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6666 (ptmm) REVERT: A 343 ARG cc_start: 0.7315 (ttt180) cc_final: 0.6989 (tpp80) REVERT: A 350 ARG cc_start: 0.6052 (mtt90) cc_final: 0.5491 (mtm180) REVERT: A 373 GLU cc_start: 0.5607 (mp0) cc_final: 0.4791 (tt0) REVERT: A 394 MET cc_start: 0.4455 (mtp) cc_final: 0.2862 (tpt) REVERT: A 463 MET cc_start: 0.7758 (mmt) cc_final: 0.7505 (mmt) REVERT: B 258 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: B 400 LYS cc_start: 0.7627 (mtmm) cc_final: 0.7251 (mmtp) REVERT: B 417 LYS cc_start: 0.7403 (tptm) cc_final: 0.7042 (mmpt) REVERT: B 507 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: C 261 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6757 (mt-10) REVERT: C 289 LYS cc_start: 0.6448 (ttpt) cc_final: 0.6219 (ptmt) REVERT: C 345 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.4840 (mtp180) REVERT: C 372 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.3642 (mpp) REVERT: C 401 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.5634 (p90) REVERT: C 415 ARG cc_start: 0.4539 (ptp90) cc_final: 0.3499 (mtt-85) REVERT: C 417 LYS cc_start: 0.5711 (ttmt) cc_final: 0.5182 (tptp) REVERT: D 7 LYS cc_start: 0.6988 (tttp) cc_final: 0.6411 (tptt) REVERT: D 41 ASP cc_start: 0.8335 (m-30) cc_final: 0.8039 (m-30) REVERT: D 214 ASP cc_start: 0.7967 (m-30) cc_final: 0.7665 (m-30) REVERT: D 268 GLN cc_start: 0.6485 (mt0) cc_final: 0.6240 (tt0) REVERT: D 315 LYS cc_start: 0.8241 (mtpt) cc_final: 0.8041 (mtpm) outliers start: 44 outliers final: 18 residues processed: 207 average time/residue: 0.6304 time to fit residues: 144.5758 Evaluate side-chains 199 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 190 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 469 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 469 ASN ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.187318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160235 restraints weight = 17856.802| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.46 r_work: 0.3765 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.296 16490 Z= 0.294 Angle : 0.778 30.791 22229 Z= 0.371 Chirality : 0.049 0.166 2334 Planarity : 0.006 0.061 2856 Dihedral : 5.086 53.410 2512 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.79 % Allowed : 13.65 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.18), residues: 1990 helix: 1.01 (0.16), residues: 1024 sheet: -0.56 (0.33), residues: 234 loop : -1.21 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 415 TYR 0.020 0.002 TYR A 229 PHE 0.017 0.002 PHE A 300 TRP 0.017 0.002 TRP D 296 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00625 (16475) covalent geometry : angle 0.77840 (22229) hydrogen bonds : bond 0.05717 ( 757) hydrogen bonds : angle 5.22756 ( 2178) Misc. bond : bond 0.14888 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.707 Fit side-chains REVERT: A 4 MET cc_start: -0.0768 (OUTLIER) cc_final: -0.2450 (ppp) REVERT: A 279 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5962 (mtt) REVERT: A 289 LYS cc_start: 0.6938 (ttpm) cc_final: 0.6674 (ptmm) REVERT: A 295 MET cc_start: 0.7283 (ptm) cc_final: 0.7045 (ttp) REVERT: A 343 ARG cc_start: 0.7294 (ttt180) cc_final: 0.6911 (tpp80) REVERT: A 350 ARG cc_start: 0.6223 (mtt90) cc_final: 0.5566 (mtm180) REVERT: A 373 GLU cc_start: 0.5760 (mp0) cc_final: 0.4941 (tt0) REVERT: A 381 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6635 (p90) REVERT: A 394 MET cc_start: 0.4434 (mtp) cc_final: 0.2839 (tpt) REVERT: A 463 MET cc_start: 0.7804 (mmt) cc_final: 0.7557 (mmt) REVERT: B 38 ASP cc_start: 0.7938 (p0) cc_final: 0.7459 (p0) REVERT: B 258 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: B 400 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7356 (mmtt) REVERT: B 417 LYS cc_start: 0.7493 (tptm) cc_final: 0.7286 (mmtt) REVERT: B 507 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: C 261 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6945 (mt-10) REVERT: C 282 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5922 (tp) REVERT: C 322 LYS cc_start: 0.5914 (tttt) cc_final: 0.5330 (mmpt) REVERT: C 345 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.4954 (mtp180) REVERT: C 372 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.3668 (mpp) REVERT: C 401 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5718 (p90) REVERT: C 417 LYS cc_start: 0.5692 (ttmt) cc_final: 0.5195 (tptp) REVERT: D 7 LYS cc_start: 0.7126 (tttp) cc_final: 0.6501 (tptt) REVERT: D 41 ASP cc_start: 0.8335 (m-30) cc_final: 0.7970 (m-30) REVERT: D 214 ASP cc_start: 0.8016 (m-30) cc_final: 0.7742 (m-30) REVERT: D 268 GLN cc_start: 0.6506 (mt0) cc_final: 0.6265 (tt0) REVERT: D 315 LYS cc_start: 0.8234 (mtpt) cc_final: 0.8025 (mtpm) outliers start: 48 outliers final: 22 residues processed: 217 average time/residue: 0.6663 time to fit residues: 159.8149 Evaluate side-chains 208 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 163 optimal weight: 0.0770 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 469 ASN C 98 ASN C 191 GLN C 469 ASN D 45 GLN D 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.193468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166645 restraints weight = 17947.653| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.48 r_work: 0.3833 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 16490 Z= 0.203 Angle : 0.685 30.586 22229 Z= 0.315 Chirality : 0.044 0.173 2334 Planarity : 0.005 0.059 2856 Dihedral : 4.757 52.888 2512 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 2.32 % Allowed : 14.06 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.19), residues: 1990 helix: 1.43 (0.17), residues: 1012 sheet: -0.53 (0.36), residues: 216 loop : -1.09 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 415 TYR 0.013 0.001 TYR D 142 PHE 0.013 0.001 PHE A 300 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (16475) covalent geometry : angle 0.68534 (22229) hydrogen bonds : bond 0.03957 ( 757) hydrogen bonds : angle 4.98278 ( 2178) Misc. bond : bond 0.11281 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.661 Fit side-chains REVERT: A 4 MET cc_start: -0.0703 (OUTLIER) cc_final: -0.2408 (ppp) REVERT: A 27 ASP cc_start: 0.4173 (OUTLIER) cc_final: 0.3555 (m-30) REVERT: A 50 LYS cc_start: 0.5287 (pptt) cc_final: 0.5067 (pptt) REVERT: A 279 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5633 (mtt) REVERT: A 295 MET cc_start: 0.7238 (ptm) cc_final: 0.6916 (ptm) REVERT: A 343 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6909 (tpp80) REVERT: A 350 ARG cc_start: 0.6169 (mtt90) cc_final: 0.5468 (mtm180) REVERT: A 373 GLU cc_start: 0.5550 (mp0) cc_final: 0.4708 (tt0) REVERT: A 394 MET cc_start: 0.4380 (mtp) cc_final: 0.2848 (tpt) REVERT: A 463 MET cc_start: 0.7724 (mmt) cc_final: 0.7412 (mmt) REVERT: B 38 ASP cc_start: 0.7968 (p0) cc_final: 0.7507 (p0) REVERT: B 258 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: B 400 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7265 (mmtp) REVERT: B 417 LYS cc_start: 0.7423 (tptm) cc_final: 0.7099 (mmpt) REVERT: B 507 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: C 261 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6862 (mt-10) REVERT: C 345 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.4835 (mtp180) REVERT: C 401 TYR cc_start: 0.6470 (OUTLIER) cc_final: 0.5494 (p90) REVERT: C 415 ARG cc_start: 0.4513 (ptp90) cc_final: 0.3507 (mtt-85) REVERT: C 417 LYS cc_start: 0.5630 (ttmt) cc_final: 0.5099 (tptp) REVERT: D 7 LYS cc_start: 0.6994 (tttp) cc_final: 0.6405 (tptt) REVERT: D 41 ASP cc_start: 0.8303 (m-30) cc_final: 0.8008 (m-30) REVERT: D 214 ASP cc_start: 0.8004 (m-30) cc_final: 0.7714 (m-30) REVERT: D 268 GLN cc_start: 0.6488 (mt0) cc_final: 0.6244 (tt0) REVERT: D 315 LYS cc_start: 0.8250 (mtpt) cc_final: 0.8042 (mtpm) outliers start: 40 outliers final: 15 residues processed: 213 average time/residue: 0.6556 time to fit residues: 154.3991 Evaluate side-chains 199 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 176 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 195 HIS A 196 HIS A 469 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN C 98 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.193842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.167178 restraints weight = 17832.289| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.46 r_work: 0.3840 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 16490 Z= 0.202 Angle : 0.687 30.571 22229 Z= 0.315 Chirality : 0.044 0.164 2334 Planarity : 0.005 0.058 2856 Dihedral : 4.652 52.803 2512 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 1.92 % Allowed : 15.05 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.19), residues: 1990 helix: 1.54 (0.17), residues: 1002 sheet: -0.43 (0.37), residues: 198 loop : -1.06 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 415 TYR 0.018 0.001 TYR B 207 PHE 0.012 0.001 PHE A 409 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00397 (16475) covalent geometry : angle 0.68664 (22229) hydrogen bonds : bond 0.03938 ( 757) hydrogen bonds : angle 4.92560 ( 2178) Misc. bond : bond 0.10977 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.634 Fit side-chains REVERT: A 4 MET cc_start: -0.0710 (OUTLIER) cc_final: -0.2345 (ppp) REVERT: A 27 ASP cc_start: 0.4231 (OUTLIER) cc_final: 0.3615 (m-30) REVERT: A 191 GLN cc_start: 0.6821 (mt0) cc_final: 0.6580 (mt0) REVERT: A 279 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5616 (mtt) REVERT: A 295 MET cc_start: 0.7189 (ptm) cc_final: 0.6835 (ptm) REVERT: A 343 ARG cc_start: 0.7290 (ttt180) cc_final: 0.6979 (tpp80) REVERT: A 350 ARG cc_start: 0.6159 (mtt90) cc_final: 0.5455 (mtm180) REVERT: A 373 GLU cc_start: 0.5520 (mp0) cc_final: 0.4729 (tt0) REVERT: A 394 MET cc_start: 0.4367 (mtp) cc_final: 0.2867 (tpt) REVERT: A 463 MET cc_start: 0.7747 (mmt) cc_final: 0.7413 (mmt) REVERT: B 38 ASP cc_start: 0.7943 (p0) cc_final: 0.7523 (p0) REVERT: B 258 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: B 400 LYS cc_start: 0.7633 (mtmm) cc_final: 0.7269 (mmtt) REVERT: B 417 LYS cc_start: 0.7408 (tptm) cc_final: 0.7068 (mmpt) REVERT: B 507 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: C 261 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6824 (mt-10) REVERT: C 345 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.4868 (mtp180) REVERT: C 401 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5505 (p90) REVERT: C 415 ARG cc_start: 0.4503 (ptp90) cc_final: 0.3541 (mtt-85) REVERT: C 417 LYS cc_start: 0.5661 (ttmt) cc_final: 0.5109 (tptp) REVERT: D 7 LYS cc_start: 0.6990 (tttp) cc_final: 0.6406 (tptt) REVERT: D 41 ASP cc_start: 0.8319 (m-30) cc_final: 0.8026 (m-30) REVERT: D 109 GLU cc_start: 0.7408 (tp30) cc_final: 0.7200 (tp30) REVERT: D 214 ASP cc_start: 0.7989 (m-30) cc_final: 0.7696 (m-30) REVERT: D 268 GLN cc_start: 0.6470 (mt0) cc_final: 0.6215 (tt0) REVERT: D 315 LYS cc_start: 0.8211 (mtpt) cc_final: 0.8008 (mtpm) outliers start: 33 outliers final: 16 residues processed: 205 average time/residue: 0.6543 time to fit residues: 148.4146 Evaluate side-chains 198 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 147 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 196 HIS A 432 GLN A 469 ASN C 98 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167441 restraints weight = 17846.515| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.47 r_work: 0.3844 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 16490 Z= 0.201 Angle : 0.689 30.559 22229 Z= 0.316 Chirality : 0.044 0.161 2334 Planarity : 0.005 0.060 2856 Dihedral : 4.616 52.240 2512 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 1.80 % Allowed : 15.51 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1990 helix: 1.56 (0.17), residues: 1004 sheet: -0.28 (0.35), residues: 218 loop : -1.08 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 415 TYR 0.018 0.001 TYR B 207 PHE 0.012 0.001 PHE A 409 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00396 (16475) covalent geometry : angle 0.68895 (22229) hydrogen bonds : bond 0.03871 ( 757) hydrogen bonds : angle 4.89500 ( 2178) Misc. bond : bond 0.10740 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.540 Fit side-chains REVERT: A 4 MET cc_start: -0.0682 (OUTLIER) cc_final: -0.2314 (ppp) REVERT: A 191 GLN cc_start: 0.6848 (mt0) cc_final: 0.6605 (mt0) REVERT: A 279 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.5617 (mtt) REVERT: A 289 LYS cc_start: 0.6165 (ptmt) cc_final: 0.5814 (ttpm) REVERT: A 295 MET cc_start: 0.7225 (ptm) cc_final: 0.6865 (ptm) REVERT: A 343 ARG cc_start: 0.7319 (ttt180) cc_final: 0.7010 (tpp80) REVERT: A 350 ARG cc_start: 0.6184 (mtt90) cc_final: 0.5457 (mtm110) REVERT: A 373 GLU cc_start: 0.5519 (mp0) cc_final: 0.4729 (tt0) REVERT: A 394 MET cc_start: 0.4363 (mtp) cc_final: 0.2880 (tpt) REVERT: A 463 MET cc_start: 0.7758 (mmt) cc_final: 0.7428 (mmt) REVERT: B 38 ASP cc_start: 0.7973 (p0) cc_final: 0.7510 (p0) REVERT: B 258 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: B 400 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7274 (mmtt) REVERT: B 417 LYS cc_start: 0.7407 (tptm) cc_final: 0.7074 (mmpt) REVERT: B 507 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: C 261 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6820 (mt-10) REVERT: C 345 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.4904 (mtp180) REVERT: C 372 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.3187 (mpt) REVERT: C 401 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5509 (p90) REVERT: C 415 ARG cc_start: 0.4529 (ptp90) cc_final: 0.3574 (mtt-85) REVERT: C 417 LYS cc_start: 0.5646 (ttmt) cc_final: 0.5090 (tptp) REVERT: D 7 LYS cc_start: 0.6971 (tttp) cc_final: 0.6387 (tptt) REVERT: D 41 ASP cc_start: 0.8318 (m-30) cc_final: 0.8033 (m-30) REVERT: D 109 GLU cc_start: 0.7450 (tp30) cc_final: 0.7222 (tp30) REVERT: D 214 ASP cc_start: 0.7980 (m-30) cc_final: 0.7689 (m-30) REVERT: D 268 GLN cc_start: 0.6474 (mt0) cc_final: 0.6191 (tt0) REVERT: D 315 LYS cc_start: 0.8235 (mtpt) cc_final: 0.8033 (mtpm) outliers start: 31 outliers final: 19 residues processed: 199 average time/residue: 0.6397 time to fit residues: 140.9277 Evaluate side-chains 202 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 ARG Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 182 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 196 HIS A 451 HIS A 469 ASN B 518 ASN C 98 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.164073 restraints weight = 17858.330| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.47 r_work: 0.3808 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.247 16490 Z= 0.233 Angle : 0.725 30.576 22229 Z= 0.338 Chirality : 0.045 0.151 2334 Planarity : 0.005 0.073 2856 Dihedral : 4.764 53.537 2512 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 15.28 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.19), residues: 1990 helix: 1.32 (0.16), residues: 1028 sheet: -0.43 (0.33), residues: 236 loop : -1.07 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 415 TYR 0.030 0.002 TYR C 290 PHE 0.012 0.002 PHE B 201 TRP 0.013 0.002 TRP B 296 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00477 (16475) covalent geometry : angle 0.72479 (22229) hydrogen bonds : bond 0.04589 ( 757) hydrogen bonds : angle 4.98591 ( 2178) Misc. bond : bond 0.12404 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6094.71 seconds wall clock time: 104 minutes 46.95 seconds (6286.95 seconds total)