Starting phenix.real_space_refine on Sat Aug 8 08:18:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebt_27997/08_2026/8ebt_27997.cif" } resolution = 3.9 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= 0.001 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 6 6.06 5 P 89 5.49 5 S 157 5.16 5 C 16949 2.51 5 N 4682 2.21 5 O 5137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27026 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4874 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 24, 'TRANS': 578} Chain breaks: 2 Chain: "B" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5457 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 29, 'TRANS': 647} Chain breaks: 1 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1547 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3499 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 1 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2989 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 361} Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2034 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2224 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 2 Chain: "J" Number of atoms: 573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 558 Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1450 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "L" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 328 Unusual residues: {'VM6': 1} Classifications: {'DNA': 14, 'undetermined': 1} Link IDs: {'rna3p': 13, None: 1} Not linked: pdbres="VM6 L 30 " pdbres=" DT L 31 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 911 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5817 SG CYS B 116 54.366 31.067 50.625 1.00268.67 S ATOM 6126 SG CYS B 155 50.626 27.269 46.607 1.00326.40 S ATOM 5957 SG CYS B 134 52.156 33.156 44.782 1.00320.89 S ATOM 6415 SG CYS B 190 48.172 32.558 49.078 1.00265.74 S ATOM 18044 SG CYS E 345 42.931 60.325 139.758 1.00129.10 S ATOM 18066 SG CYS E 348 44.762 63.560 140.546 1.00125.11 S ATOM 18223 SG CYS E 368 42.938 63.196 137.209 1.00135.96 S ATOM 18244 SG CYS E 371 46.080 61.213 137.874 1.00133.75 S ATOM 18164 SG CYS E 360 41.639 48.885 134.861 1.00139.08 S ATOM 18182 SG CYS E 363 42.326 49.102 138.598 1.00142.19 S ATOM 18331 SG CYS E 382 44.630 50.832 136.215 1.00131.40 S ATOM 18348 SG CYS E 385 44.613 47.026 136.306 1.00137.03 S ATOM 17608 SG CYS E 291 81.228 37.439 129.165 1.00151.40 S ATOM 17630 SG CYS E 294 84.794 36.157 128.700 1.00160.52 S ATOM 17719 SG CYS E 305 83.329 38.463 126.109 1.00159.03 S ATOM 17742 SG CYS E 308 81.959 34.953 126.432 1.00162.98 S ATOM 20244 SG CYS F 268 61.071 35.857 120.706 1.00113.95 S ATOM 20263 SG CYS F 271 58.491 37.806 122.711 1.00115.58 S ATOM 20348 SG CYS F 282 58.619 34.052 123.029 1.00128.26 S ATOM 20368 SG CYS F 285 57.430 35.622 119.764 1.00133.59 S ATOM 20136 SG CYS F 255 62.814 33.187 132.988 1.00130.28 S ATOM 20153 SG CYS F 257 60.260 30.359 133.103 1.00131.84 S ATOM 20302 SG CYS F 276 64.046 29.583 133.502 1.00130.79 S ATOM 23752 SG CYS K 105 43.274 92.886 28.137 1.00249.87 S ATOM 23776 SG CYS K 108 42.636 92.325 24.430 1.00257.08 S ATOM 23924 SG CYS K 126 45.275 90.263 26.211 1.00230.55 S ATOM 23946 SG CYS K 129 45.854 93.947 25.488 1.00226.55 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 127 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS J 127 " occ=0.50 Time building chain proxies: 5.13, per 1000 atoms: 0.19 Number of scatterers: 27026 At special positions: 0 Unit cell: (153.272, 156.604, 184.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 Ca 2 19.99 S 157 16.00 P 89 15.00 O 5137 8.00 N 4682 7.00 C 16949 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " Number of angles added : 33 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 27 sheets defined 51.9% alpha, 10.6% beta 40 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.832A pdb=" N PHE A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 4.370A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 removed outlier: 4.776A pdb=" N LEU A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG A 200 " --> pdb=" O CYS A 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 202 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.583A pdb=" N LEU A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.562A pdb=" N VAL A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.128A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.529A pdb=" N LEU A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.847A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.579A pdb=" N ARG A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 4.217A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 4.340A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N HIS A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 642 removed outlier: 3.819A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 removed outlier: 4.053A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.561A pdb=" N ASP A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 removed outlier: 3.925A pdb=" N GLN A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.692A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 156 through 165 removed outlier: 4.639A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.625A pdb=" N ASP B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.941A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.959A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 272 removed outlier: 4.129A pdb=" N GLU B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.985A pdb=" N GLY B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.704A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 346 removed outlier: 3.543A pdb=" N ARG B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 removed outlier: 4.619A pdb=" N LEU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 4.065A pdb=" N ARG B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.556A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.639A pdb=" N ALA B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 513 through 528 removed outlier: 3.622A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 557 through 565 removed outlier: 3.583A pdb=" N ILE B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 590 Processing helix chain 'B' and resid 602 through 608 removed outlier: 4.162A pdb=" N GLU B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 631 removed outlier: 4.245A pdb=" N ARG B 631 " --> pdb=" O THR B 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 628 through 631' Processing helix chain 'B' and resid 632 through 644 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.801A pdb=" N GLU B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 725 removed outlier: 3.667A pdb=" N ALA B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.507A pdb=" N ASP C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.890A pdb=" N ALA C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.527A pdb=" N VAL C 421 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 422 " --> pdb=" O THR C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 422' Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 479 removed outlier: 3.583A pdb=" N GLU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 516 removed outlier: 3.722A pdb=" N GLU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 520 through 547 removed outlier: 4.152A pdb=" N HIS C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.702A pdb=" N GLY D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.558A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 207 through 227 removed outlier: 4.243A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 321 through 332 removed outlier: 4.082A pdb=" N PHE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 375 through 379 Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.518A pdb=" N THR D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 444 through 462 removed outlier: 4.227A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.640A pdb=" N LEU E 22 " --> pdb=" O TRP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.554A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 136 removed outlier: 3.678A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 158 removed outlier: 4.641A pdb=" N HIS E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 192 removed outlier: 4.110A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.709A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 4.272A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 321 through 326 removed outlier: 4.120A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 326' Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.847A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 3.851A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 Processing helix chain 'F' and resid 132 through 151 removed outlier: 3.586A pdb=" N GLU F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 222 through 228 Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.577A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 288 Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 49 through 64 removed outlier: 3.721A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 677 through 681 Processing helix chain 'H' and resid 686 through 693 Processing helix chain 'H' and resid 711 through 721 removed outlier: 3.854A pdb=" N LYS H 716 " --> pdb=" O ASN H 712 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU H 721 " --> pdb=" O ALA H 717 " (cutoff:3.500A) Processing helix chain 'H' and resid 722 through 728 removed outlier: 4.580A pdb=" N GLU H 726 " --> pdb=" O PRO H 722 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU H 727 " --> pdb=" O GLN H 723 " (cutoff:3.500A) Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 778 through 786 removed outlier: 3.772A pdb=" N VAL H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 865 removed outlier: 3.527A pdb=" N LEU H 822 " --> pdb=" O LYS H 818 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 902 Processing helix chain 'H' and resid 903 through 915 removed outlier: 4.179A pdb=" N ARG H 908 " --> pdb=" O TRP H 904 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS H 915 " --> pdb=" O GLU H 911 " (cutoff:3.500A) Processing helix chain 'H' and resid 927 through 934 Processing helix chain 'H' and resid 935 through 939 Processing helix chain 'J' and resid 104 through 114 Processing helix chain 'J' and resid 122 through 134 Processing helix chain 'J' and resid 138 through 150 Processing helix chain 'J' and resid 158 through 168 Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 141 through 149 Processing helix chain 'K' and resid 151 through 157 Processing helix chain 'K' and resid 183 through 195 Processing helix chain 'K' and resid 196 through 233 removed outlier: 4.181A pdb=" N LEU K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER K 233 " --> pdb=" O ALA K 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.642A pdb=" N ARG D 337 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.663A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 105 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 171 removed outlier: 3.518A pdb=" N VAL A 268 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.604A pdb=" N ALA A 333 " --> pdb=" O TYR A 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 392 removed outlier: 4.429A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 337 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.860A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 659 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 663 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.793A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 455 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 231 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR B 457 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE B 233 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 107 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 251 removed outlier: 3.840A pdb=" N VAL B 249 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 433 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 432 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 417 " --> pdb=" O HIS B 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 495 removed outlier: 3.780A pdb=" N CYS B 491 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET B 677 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 536 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.538A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB5, first strand: chain 'D' and resid 431 through 435 Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 121 removed outlier: 6.806A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLU E 119 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE E 104 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG E 59 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY E 105 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 61 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE E 107 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR E 62 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE E 170 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N HIS E 220 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 198 " --> pdb=" O HIS E 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 311 through 312 removed outlier: 4.367A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 252 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY F 265 " --> pdb=" O MET E 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 257 through 258 removed outlier: 3.541A pdb=" N GLY E 288 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC1, first strand: chain 'F' and resid 67 through 69 removed outlier: 7.528A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 8 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LEU F 190 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU F 215 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA F 193 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AC3, first strand: chain 'H' and resid 669 through 670 Processing sheet with id=AC4, first strand: chain 'H' and resid 695 through 697 Processing sheet with id=AC5, first strand: chain 'H' and resid 705 through 707 removed outlier: 3.881A pdb=" N LYS H 705 " --> pdb=" O LEU H 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 759 through 760 removed outlier: 6.788A pdb=" N VAL H 759 " --> pdb=" O ILE H 794 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY H 796 " --> pdb=" O VAL H 759 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY H 810 " --> pdb=" O ALA H 793 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR H 795 " --> pdb=" O THR H 808 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR H 808 " --> pdb=" O THR H 795 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE H 797 " --> pdb=" O PRO H 806 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE H 799 " --> pdb=" O SER H 804 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER H 804 " --> pdb=" O PHE H 799 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AC8, first strand: chain 'K' and resid 138 through 140 Processing sheet with id=AC9, first strand: chain 'K' and resid 250 through 252 removed outlier: 3.733A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 11771 1.43 - 1.64: 15752 1.64 - 1.86: 234 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 27769 Sorted by residual: bond pdb=" OP1 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.527 1.658 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" OP2 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.528 1.658 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 1.504 1.375 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " ideal model delta sigma weight residual 1.502 1.395 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C5 VM6 L 30 " pdb=" C6 VM6 L 30 " ideal model delta sigma weight residual 1.448 1.359 0.089 2.00e-02 2.50e+03 1.98e+01 ... (remaining 27764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 37712 2.66 - 5.31: 183 5.31 - 7.97: 10 7.97 - 10.62: 1 10.62 - 13.28: 1 Bond angle restraints: 37907 Sorted by residual: angle pdb=" O4' DT L 31 " pdb=" C4' DT L 31 " pdb=" C3' DT L 31 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT L 37 " pdb=" C4 DT L 37 " pdb=" O4 DT L 37 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT M 52 " pdb=" C4 DT M 52 " pdb=" O4 DT M 52 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 112.29 108.10 4.19 9.40e-01 1.13e+00 1.98e+01 angle pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 112.55 125.83 -13.28 3.00e+00 1.11e-01 1.96e+01 ... (remaining 37902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 16193 34.36 - 68.71: 421 68.71 - 103.07: 7 103.07 - 137.42: 3 137.42 - 171.78: 1 Dihedral angle restraints: 16625 sinusoidal: 7461 harmonic: 9164 Sorted by residual: dihedral pdb=" C4' DT L 18 " pdb=" C3' DT L 18 " pdb=" O3' DT L 18 " pdb=" P DG L 19 " ideal model delta sinusoidal sigma weight residual -140.00 31.78 -171.78 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C13 VM6 L 30 " pdb=" C11 VM6 L 30 " pdb=" C12 VM6 L 30 " pdb=" N1 VM6 L 30 " ideal model delta sinusoidal sigma weight residual -178.91 -67.01 -111.90 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CA VAL B 5 " pdb=" C VAL B 5 " pdb=" N ASP B 6 " pdb=" CA ASP B 6 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 16622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2894 0.032 - 0.064: 909 0.064 - 0.096: 238 0.096 - 0.128: 168 0.128 - 0.161: 4 Chirality restraints: 4213 Sorted by residual: chirality pdb=" C3' DT L 18 " pdb=" C4' DT L 18 " pdb=" O3' DT L 18 " pdb=" C2' DT L 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" C3' DG L 38 " pdb=" C4' DG L 38 " pdb=" O3' DG L 38 " pdb=" C2' DG L 38 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CB VAL C 453 " pdb=" CA VAL C 453 " pdb=" CG1 VAL C 453 " pdb=" CG2 VAL C 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 4210 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 583 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO B 354 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT M 26 " -0.016 2.00e-02 2.50e+03 8.34e-03 1.74e+00 pdb=" N1 DT M 26 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DT M 26 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT M 26 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT M 26 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT M 26 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT M 26 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT M 26 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT M 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT M 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 694 2.71 - 3.25: 26507 3.25 - 3.80: 43996 3.80 - 4.35: 54855 4.35 - 4.90: 89261 Nonbonded interactions: 215313 Sorted by model distance: nonbonded pdb=" O LEU E 211 " pdb=" OG1 THR E 215 " model vdw 2.157 3.040 nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.170 3.040 nonbonded pdb=" O LEU E 30 " pdb=" OG1 THR E 33 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLN K 174 " pdb=" N2 DG L 24 " model vdw 2.257 3.120 nonbonded pdb=" OE1 GLU A 115 " pdb=" NH1 ARG D 314 " model vdw 2.258 3.120 ... (remaining 215308 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 32.100 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.003 0.131 27799 Z= 0.227 Angle : 0.513 13.281 37952 Z= 0.351 Chirality : 0.039 0.161 4213 Planarity : 0.003 0.060 4537 Dihedral : 13.112 171.781 10691 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.21 % Allowed : 5.32 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 3094 helix: 2.23 (0.15), residues: 1416 sheet: 0.56 (0.29), residues: 400 loop : -0.55 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 616 TYR 0.010 0.001 TYR E 95 PHE 0.007 0.001 PHE A 89 TRP 0.017 0.001 TRP K 175 HIS 0.002 0.000 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.23 (27769) covalent geometry : angle 0.49927 / 0.35 (37907) hydrogen bonds : bond 0.18622 / 12.39 ( 1245) hydrogen bonds : angle 5.59990 / 3.92 ( 3497) metal coordination : bond 0.00283 / 0.17 ( 28) metal coordination : angle 3.42120 / 1.61 ( 45) Misc. bond : bond 0.00147 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9146 (pp) REVERT: A 450 MET cc_start: 0.7762 (ptm) cc_final: 0.7168 (ttt) REVERT: A 644 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9133 (pp) REVERT: B 1 MET cc_start: 0.8449 (ppp) cc_final: 0.8056 (ppp) REVERT: B 57 MET cc_start: 0.8839 (mmt) cc_final: 0.8590 (mmm) REVERT: B 118 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.6303 (m-70) REVERT: H 764 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7621 (Cg_endo) REVERT: H 778 ASN cc_start: 0.8158 (m-40) cc_final: 0.7832 (t0) REVERT: H 795 THR cc_start: 0.7841 (m) cc_final: 0.7292 (p) REVERT: H 799 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5444 (p90) REVERT: H 823 THR cc_start: 0.9033 (t) cc_final: 0.8624 (p) REVERT: H 827 ASN cc_start: 0.9117 (t0) cc_final: 0.8801 (m-40) REVERT: H 904 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7726 (t-100) REVERT: J 147 ASP cc_start: 0.8631 (t0) cc_final: 0.8303 (m-30) outliers start: 61 outliers final: 11 residues processed: 252 average time/residue: 0.2002 time to fit residues: 77.0965 Evaluate side-chains 137 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN E 60 HIS F 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.046936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.032617 restraints weight = 270757.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.033375 restraints weight = 151562.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.033847 restraints weight = 107056.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.034154 restraints weight = 86958.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.034228 restraints weight = 77324.269| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 27799 Z= 0.220 Angle : 0.630 12.799 37952 Z= 0.326 Chirality : 0.042 0.271 4213 Planarity : 0.004 0.060 4537 Dihedral : 15.769 170.755 4464 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.81 % Allowed : 7.53 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 3094 helix: 2.05 (0.14), residues: 1480 sheet: 0.13 (0.27), residues: 423 loop : -0.71 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 128 TYR 0.019 0.001 TYR H 811 PHE 0.018 0.001 PHE B 720 TRP 0.018 0.001 TRP A 381 HIS 0.009 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (27769) covalent geometry : angle 0.61322 / 0.33 (37907) hydrogen bonds : bond 0.04998 / 3.39 ( 1245) hydrogen bonds : angle 4.69831 / 3.27 ( 3497) metal coordination : bond 0.00905 / 0.54 ( 28) metal coordination : angle 4.28677 / 2.22 ( 45) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9245 (pp) REVERT: A 276 MET cc_start: 0.8243 (ttt) cc_final: 0.7919 (ttp) REVERT: B 1 MET cc_start: 0.8378 (ppp) cc_final: 0.7969 (ppp) REVERT: B 25 MET cc_start: 0.9478 (mmm) cc_final: 0.9252 (mmm) REVERT: B 57 MET cc_start: 0.8907 (mmt) cc_final: 0.8661 (mmm) REVERT: B 118 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6408 (m-70) REVERT: B 724 MET cc_start: 0.8115 (tpp) cc_final: 0.7797 (tpp) REVERT: C 493 MET cc_start: 0.9217 (mmm) cc_final: 0.8747 (mmp) REVERT: D 441 MET cc_start: 0.8475 (ttm) cc_final: 0.8002 (mtt) REVERT: G 16 MET cc_start: 0.9369 (mmm) cc_final: 0.9162 (mmm) REVERT: H 649 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.6805 (mm) REVERT: H 799 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6208 (p90) REVERT: H 823 THR cc_start: 0.9034 (t) cc_final: 0.8696 (p) REVERT: H 827 ASN cc_start: 0.9134 (t0) cc_final: 0.8856 (m-40) REVERT: H 904 TRP cc_start: 0.8332 (OUTLIER) cc_final: 0.7147 (t-100) REVERT: J 147 ASP cc_start: 0.8649 (t0) cc_final: 0.8312 (m-30) REVERT: K 104 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9212 (tp) REVERT: K 118 MET cc_start: 0.9303 (tpt) cc_final: 0.8984 (mmm) outliers start: 50 outliers final: 23 residues processed: 173 average time/residue: 0.1768 time to fit residues: 48.8058 Evaluate side-chains 139 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 ASN ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.047230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032846 restraints weight = 268304.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.033630 restraints weight = 148320.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.034121 restraints weight = 103909.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.034311 restraints weight = 84476.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.034540 restraints weight = 76183.155| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27799 Z= 0.121 Angle : 0.553 11.580 37952 Z= 0.286 Chirality : 0.041 0.293 4213 Planarity : 0.003 0.060 4537 Dihedral : 15.839 169.672 4460 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.81 % Allowed : 8.04 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 3094 helix: 1.95 (0.14), residues: 1486 sheet: 0.18 (0.27), residues: 407 loop : -0.74 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 499 TYR 0.018 0.001 TYR A 534 PHE 0.013 0.001 PHE G 33 TRP 0.018 0.001 TRP A 421 HIS 0.006 0.001 HIS H 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (27769) covalent geometry : angle 0.53724 / 0.29 (37907) hydrogen bonds : bond 0.03897 / 2.64 ( 1245) hydrogen bonds : angle 4.40518 / 3.05 ( 3497) metal coordination : bond 0.00452 / 0.27 ( 28) metal coordination : angle 3.87277 / 1.91 ( 45) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9232 (pp) REVERT: A 276 MET cc_start: 0.8468 (ttt) cc_final: 0.8070 (ttt) REVERT: A 450 MET cc_start: 0.8186 (ptm) cc_final: 0.7580 (ttt) REVERT: B 1 MET cc_start: 0.8414 (ppp) cc_final: 0.7998 (ppp) REVERT: B 25 MET cc_start: 0.9482 (mmm) cc_final: 0.9260 (mmm) REVERT: B 57 MET cc_start: 0.8940 (mmt) cc_final: 0.8649 (mmm) REVERT: B 118 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.6420 (m-70) REVERT: B 724 MET cc_start: 0.8509 (tpp) cc_final: 0.7734 (tpp) REVERT: C 493 MET cc_start: 0.9243 (mmm) cc_final: 0.8790 (mmp) REVERT: C 516 TYR cc_start: 0.9158 (m-80) cc_final: 0.8943 (m-10) REVERT: C 545 MET cc_start: 0.5170 (mtt) cc_final: 0.4621 (ptp) REVERT: D 441 MET cc_start: 0.8594 (ttm) cc_final: 0.8017 (mtt) REVERT: E 252 MET cc_start: 0.9054 (mpp) cc_final: 0.8617 (mpp) REVERT: G 16 MET cc_start: 0.9399 (mmm) cc_final: 0.9156 (mmm) REVERT: G 48 GLU cc_start: 0.9044 (pt0) cc_final: 0.8789 (pp20) REVERT: H 799 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6358 (p90) REVERT: H 823 THR cc_start: 0.9047 (t) cc_final: 0.8714 (p) REVERT: H 827 ASN cc_start: 0.9141 (t0) cc_final: 0.8857 (m-40) REVERT: H 904 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7147 (t-100) REVERT: J 147 ASP cc_start: 0.8700 (t0) cc_final: 0.8402 (m-30) REVERT: K 104 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9215 (tp) REVERT: K 118 MET cc_start: 0.9293 (tpt) cc_final: 0.9085 (mmm) REVERT: K 256 MET cc_start: 0.8383 (tpp) cc_final: 0.7268 (mmm) outliers start: 50 outliers final: 23 residues processed: 159 average time/residue: 0.1716 time to fit residues: 44.4440 Evaluate side-chains 138 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 29 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 402 ASN ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN F 65 GLN F 108 ASN F 248 HIS H 685 HIS H 778 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.046289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.031583 restraints weight = 266783.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.032371 restraints weight = 146690.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032866 restraints weight = 102661.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.033123 restraints weight = 83327.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.033296 restraints weight = 74440.799| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27799 Z= 0.165 Angle : 0.572 11.929 37952 Z= 0.291 Chirality : 0.041 0.299 4213 Planarity : 0.003 0.057 4537 Dihedral : 15.957 170.426 4459 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.56 % Allowed : 8.69 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 3094 helix: 1.94 (0.14), residues: 1491 sheet: 0.12 (0.27), residues: 409 loop : -0.74 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 453 TYR 0.017 0.001 TYR A 534 PHE 0.018 0.001 PHE B 473 TRP 0.014 0.001 TRP A 421 HIS 0.006 0.001 HIS H 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (27769) covalent geometry : angle 0.55342 / 0.29 (37907) hydrogen bonds : bond 0.03655 / 2.48 ( 1245) hydrogen bonds : angle 4.30076 / 2.98 ( 3497) metal coordination : bond 0.00788 / 0.49 ( 28) metal coordination : angle 4.21235 / 2.25 ( 45) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9272 (pp) REVERT: A 276 MET cc_start: 0.8490 (ttt) cc_final: 0.8195 (ttt) REVERT: A 450 MET cc_start: 0.8112 (ptm) cc_final: 0.7753 (ptm) REVERT: B 1 MET cc_start: 0.8269 (ppp) cc_final: 0.7893 (ppp) REVERT: B 25 MET cc_start: 0.9460 (mmm) cc_final: 0.9248 (mmm) REVERT: B 57 MET cc_start: 0.8855 (mmt) cc_final: 0.8630 (mmm) REVERT: B 118 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6445 (m-70) REVERT: C 493 MET cc_start: 0.9298 (mmm) cc_final: 0.8891 (mmp) REVERT: C 528 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8989 (mpp) REVERT: C 545 MET cc_start: 0.5146 (mtt) cc_final: 0.4377 (ptp) REVERT: D 441 MET cc_start: 0.8539 (ttm) cc_final: 0.7907 (mtt) REVERT: H 766 MET cc_start: -0.0013 (mtt) cc_final: -0.0429 (mmm) REVERT: H 799 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6437 (p90) REVERT: H 823 THR cc_start: 0.9074 (t) cc_final: 0.8757 (p) REVERT: H 827 ASN cc_start: 0.9112 (t0) cc_final: 0.8830 (m-40) REVERT: H 904 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7117 (t-100) REVERT: J 147 ASP cc_start: 0.8721 (t0) cc_final: 0.8422 (m-30) REVERT: K 104 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9201 (tp) REVERT: K 118 MET cc_start: 0.9307 (tpt) cc_final: 0.9099 (mmm) outliers start: 43 outliers final: 25 residues processed: 144 average time/residue: 0.1719 time to fit residues: 40.9090 Evaluate side-chains 134 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 685 HIS Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 145 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 57 optimal weight: 0.0370 chunk 229 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 ASN C 446 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.046564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.032146 restraints weight = 259171.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.032924 restraints weight = 141621.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033384 restraints weight = 99117.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033660 restraints weight = 79838.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.033785 restraints weight = 70492.119| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27799 Z= 0.114 Angle : 0.541 12.296 37952 Z= 0.275 Chirality : 0.040 0.302 4213 Planarity : 0.003 0.063 4537 Dihedral : 15.978 170.195 4459 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 9.02 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.97 (0.16), residues: 3094 helix: 1.89 (0.14), residues: 1493 sheet: 0.12 (0.27), residues: 408 loop : -0.77 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 651 TYR 0.018 0.001 TYR A 534 PHE 0.017 0.001 PHE B 473 TRP 0.031 0.001 TRP C 539 HIS 0.009 0.001 HIS K 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (27769) covalent geometry : angle 0.52323 / 0.27 (37907) hydrogen bonds : bond 0.03207 / 2.18 ( 1245) hydrogen bonds : angle 4.16032 / 2.88 ( 3497) metal coordination : bond 0.00427 / 0.25 ( 28) metal coordination : angle 3.98095 / 2.04 ( 45) Misc. bond : bond 0.00043 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8086 (ptp) cc_final: 0.7865 (ptp) REVERT: A 140 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9273 (pp) REVERT: A 276 MET cc_start: 0.8580 (ttt) cc_final: 0.8169 (ttp) REVERT: B 1 MET cc_start: 0.8372 (ppp) cc_final: 0.8005 (ppp) REVERT: B 25 MET cc_start: 0.9472 (mmm) cc_final: 0.9244 (mmm) REVERT: B 57 MET cc_start: 0.8928 (mmt) cc_final: 0.8665 (mmm) REVERT: B 118 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6494 (m-70) REVERT: C 493 MET cc_start: 0.9345 (mmm) cc_final: 0.8942 (mmp) REVERT: C 516 TYR cc_start: 0.9061 (m-10) cc_final: 0.8476 (p90) REVERT: C 545 MET cc_start: 0.5277 (mtt) cc_final: 0.4671 (ptt) REVERT: E 252 MET cc_start: 0.8883 (mpp) cc_final: 0.8648 (mpp) REVERT: H 766 MET cc_start: 0.0008 (mtt) cc_final: -0.0454 (mmm) REVERT: H 799 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6132 (p90) REVERT: H 823 THR cc_start: 0.9087 (t) cc_final: 0.8770 (p) REVERT: H 827 ASN cc_start: 0.9101 (t0) cc_final: 0.8816 (m-40) REVERT: H 904 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7181 (t-100) REVERT: J 147 ASP cc_start: 0.8721 (t0) cc_final: 0.8433 (m-30) REVERT: K 104 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9201 (tp) REVERT: K 118 MET cc_start: 0.9280 (tpt) cc_final: 0.9059 (mmm) REVERT: K 256 MET cc_start: 0.8604 (tpp) cc_final: 0.7454 (mmm) outliers start: 44 outliers final: 27 residues processed: 147 average time/residue: 0.1515 time to fit residues: 37.2214 Evaluate side-chains 137 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain H residue 651 ARG Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 227 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 293 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 265 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 310 optimal weight: 20.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN H 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.045731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.031395 restraints weight = 267790.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.032452 restraints weight = 164057.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.032251 restraints weight = 98178.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.032461 restraints weight = 90175.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.032520 restraints weight = 80193.932| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27799 Z= 0.190 Angle : 0.584 12.477 37952 Z= 0.294 Chirality : 0.040 0.300 4213 Planarity : 0.003 0.064 4537 Dihedral : 16.095 172.386 4459 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.85 % Allowed : 8.87 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.96 (0.16), residues: 3094 helix: 1.88 (0.14), residues: 1489 sheet: 0.02 (0.27), residues: 418 loop : -0.72 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 641 TYR 0.017 0.001 TYR E 358 PHE 0.015 0.001 PHE B 473 TRP 0.013 0.001 TRP K 175 HIS 0.010 0.001 HIS H 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (27769) covalent geometry : angle 0.56385 / 0.29 (37907) hydrogen bonds : bond 0.03623 / 2.45 ( 1245) hydrogen bonds : angle 4.24950 / 2.95 ( 3497) metal coordination : bond 0.00903 / 0.56 ( 28) metal coordination : angle 4.41077 / 2.42 ( 45) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 140 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9299 (pp) REVERT: A 276 MET cc_start: 0.8652 (ttt) cc_final: 0.8222 (ttp) REVERT: B 1 MET cc_start: 0.8360 (ppp) cc_final: 0.8009 (ppp) REVERT: B 25 MET cc_start: 0.9495 (mmm) cc_final: 0.9247 (mmm) REVERT: B 57 MET cc_start: 0.8913 (mmt) cc_final: 0.8659 (mmm) REVERT: B 118 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: C 493 MET cc_start: 0.9365 (mmm) cc_final: 0.8988 (mmp) REVERT: C 516 TYR cc_start: 0.9166 (m-10) cc_final: 0.8582 (p90) REVERT: C 545 MET cc_start: 0.5304 (mtt) cc_final: 0.4672 (ptp) REVERT: D 163 MET cc_start: 0.9113 (ttm) cc_final: 0.8860 (ttp) REVERT: D 185 MET cc_start: 0.8893 (mpp) cc_final: 0.8119 (mpt) REVERT: G 16 MET cc_start: 0.9439 (mmt) cc_final: 0.9075 (mmm) REVERT: H 799 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6074 (p90) REVERT: H 823 THR cc_start: 0.9064 (t) cc_final: 0.8762 (p) REVERT: H 827 ASN cc_start: 0.9070 (t0) cc_final: 0.8790 (m-40) REVERT: H 904 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.7193 (t-100) REVERT: J 147 ASP cc_start: 0.8744 (t0) cc_final: 0.8454 (m-30) REVERT: K 118 MET cc_start: 0.9272 (tpt) cc_final: 0.9061 (mmm) REVERT: K 256 MET cc_start: 0.8722 (tpp) cc_final: 0.7790 (mmm) outliers start: 51 outliers final: 29 residues processed: 148 average time/residue: 0.1467 time to fit residues: 35.6262 Evaluate side-chains 136 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain H residue 651 ARG Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 161 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 352 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN H 792 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.046149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031285 restraints weight = 261949.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.032077 restraints weight = 143450.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032564 restraints weight = 100514.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032763 restraints weight = 81555.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.033000 restraints weight = 73738.166| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27799 Z= 0.110 Angle : 0.545 12.780 37952 Z= 0.273 Chirality : 0.040 0.302 4213 Planarity : 0.003 0.064 4537 Dihedral : 16.060 172.189 4457 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.41 % Allowed : 9.45 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.94 (0.16), residues: 3094 helix: 1.88 (0.14), residues: 1491 sheet: 0.03 (0.27), residues: 417 loop : -0.78 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 641 TYR 0.019 0.001 TYR A 534 PHE 0.013 0.001 PHE C 142 TRP 0.011 0.001 TRP C 539 HIS 0.006 0.001 HIS H 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (27769) covalent geometry : angle 0.52630 / 0.27 (37907) hydrogen bonds : bond 0.03126 / 2.12 ( 1245) hydrogen bonds : angle 4.10772 / 2.84 ( 3497) metal coordination : bond 0.00440 / 0.26 ( 28) metal coordination : angle 4.18737 / 2.19 ( 45) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8153 (ptp) cc_final: 0.7801 (ptp) REVERT: A 76 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 140 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9285 (pp) REVERT: A 276 MET cc_start: 0.8674 (ttt) cc_final: 0.8205 (ttp) REVERT: B 1 MET cc_start: 0.8303 (ppp) cc_final: 0.7956 (ppp) REVERT: B 25 MET cc_start: 0.9473 (mmm) cc_final: 0.9229 (mmm) REVERT: B 57 MET cc_start: 0.8911 (mmt) cc_final: 0.8642 (mmm) REVERT: B 118 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6730 (m-70) REVERT: C 442 GLN cc_start: 0.5326 (OUTLIER) cc_final: 0.4506 (pp30) REVERT: C 516 TYR cc_start: 0.9110 (m-10) cc_final: 0.8584 (p90) REVERT: C 545 MET cc_start: 0.5221 (mtt) cc_final: 0.4540 (ptp) REVERT: D 163 MET cc_start: 0.9099 (ttm) cc_final: 0.8890 (ttp) REVERT: D 185 MET cc_start: 0.8842 (mpp) cc_final: 0.8115 (mpt) REVERT: E 252 MET cc_start: 0.8891 (mpp) cc_final: 0.8684 (mpp) REVERT: F 229 TRP cc_start: 0.9146 (OUTLIER) cc_final: 0.7518 (t60) REVERT: H 766 MET cc_start: 0.0314 (mtt) cc_final: -0.0108 (mmm) REVERT: H 767 MET cc_start: 0.1384 (tpt) cc_final: 0.1182 (tpt) REVERT: H 799 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6430 (p90) REVERT: H 823 THR cc_start: 0.9038 (t) cc_final: 0.8742 (p) REVERT: H 827 ASN cc_start: 0.9119 (t0) cc_final: 0.8856 (m-40) REVERT: H 904 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7239 (t-100) REVERT: J 147 ASP cc_start: 0.8734 (t0) cc_final: 0.8453 (m-30) REVERT: K 118 MET cc_start: 0.9286 (tpt) cc_final: 0.9056 (mmm) REVERT: K 256 MET cc_start: 0.8600 (tpp) cc_final: 0.7622 (mmm) REVERT: K 273 MET cc_start: 0.6094 (mtm) cc_final: 0.5362 (ptp) outliers start: 39 outliers final: 24 residues processed: 138 average time/residue: 0.1545 time to fit residues: 35.5240 Evaluate side-chains 133 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 310 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 309 optimal weight: 30.0000 chunk 132 optimal weight: 0.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 37 HIS ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.046264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.031478 restraints weight = 264275.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.032230 restraints weight = 143275.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.032721 restraints weight = 99666.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.033024 restraints weight = 80662.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.033175 restraints weight = 71853.957| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27799 Z= 0.109 Angle : 0.543 12.514 37952 Z= 0.270 Chirality : 0.040 0.299 4213 Planarity : 0.003 0.057 4537 Dihedral : 16.025 171.186 4457 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.38 % Allowed : 9.71 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.91 (0.16), residues: 3094 helix: 1.87 (0.14), residues: 1492 sheet: -0.02 (0.27), residues: 419 loop : -0.78 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 641 TYR 0.018 0.001 TYR A 534 PHE 0.015 0.001 PHE B 720 TRP 0.012 0.001 TRP A 421 HIS 0.005 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (27769) covalent geometry : angle 0.52491 / 0.27 (37907) hydrogen bonds : bond 0.03077 / 2.07 ( 1245) hydrogen bonds : angle 4.05659 / 2.79 ( 3497) metal coordination : bond 0.00412 / 0.24 ( 28) metal coordination : angle 4.07757 / 2.14 ( 45) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8236 (ptp) cc_final: 0.7941 (ptp) REVERT: A 76 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8650 (mp) REVERT: A 140 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9281 (pp) REVERT: A 276 MET cc_start: 0.8700 (ttt) cc_final: 0.8291 (ttt) REVERT: B 1 MET cc_start: 0.8316 (ppp) cc_final: 0.7981 (ppp) REVERT: B 25 MET cc_start: 0.9465 (mmm) cc_final: 0.9240 (mmm) REVERT: B 57 MET cc_start: 0.8918 (mmt) cc_final: 0.8646 (mmm) REVERT: B 118 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6722 (m-70) REVERT: C 442 GLN cc_start: 0.5498 (OUTLIER) cc_final: 0.4611 (pp30) REVERT: C 516 TYR cc_start: 0.9123 (m-10) cc_final: 0.8588 (p90) REVERT: C 545 MET cc_start: 0.5214 (mtt) cc_final: 0.4535 (ptp) REVERT: D 185 MET cc_start: 0.8802 (mpp) cc_final: 0.8115 (mpt) REVERT: D 441 MET cc_start: 0.8377 (mmt) cc_final: 0.8139 (mmm) REVERT: E 252 MET cc_start: 0.8900 (mpp) cc_final: 0.8661 (mpp) REVERT: F 229 TRP cc_start: 0.9148 (OUTLIER) cc_final: 0.7502 (t60) REVERT: G 16 MET cc_start: 0.9433 (mmt) cc_final: 0.9057 (mmm) REVERT: H 766 MET cc_start: 0.0098 (mtt) cc_final: -0.0745 (mmm) REVERT: H 799 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6404 (p90) REVERT: H 823 THR cc_start: 0.9040 (t) cc_final: 0.8740 (p) REVERT: H 827 ASN cc_start: 0.9121 (t0) cc_final: 0.8854 (m-40) REVERT: H 904 TRP cc_start: 0.8322 (OUTLIER) cc_final: 0.7225 (t-100) REVERT: J 147 ASP cc_start: 0.8741 (t0) cc_final: 0.8491 (m-30) REVERT: K 118 MET cc_start: 0.9279 (tpt) cc_final: 0.9049 (mmm) REVERT: K 256 MET cc_start: 0.8677 (tpp) cc_final: 0.7767 (mmm) REVERT: K 273 MET cc_start: 0.6037 (mtm) cc_final: 0.5369 (ptp) outliers start: 38 outliers final: 26 residues processed: 136 average time/residue: 0.1607 time to fit residues: 35.9228 Evaluate side-chains 133 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 186 optimal weight: 8.9990 chunk 198 optimal weight: 0.0470 chunk 152 optimal weight: 7.9990 chunk 136 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.046425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.031625 restraints weight = 263614.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.032447 restraints weight = 142412.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032947 restraints weight = 99189.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.033165 restraints weight = 80171.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033342 restraints weight = 71823.899| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27799 Z= 0.103 Angle : 0.550 12.386 37952 Z= 0.274 Chirality : 0.040 0.319 4213 Planarity : 0.003 0.064 4537 Dihedral : 16.003 170.664 4457 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.34 % Allowed : 10.00 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.83 (0.16), residues: 3094 helix: 1.79 (0.14), residues: 1491 sheet: -0.02 (0.26), residues: 422 loop : -0.81 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 151 TYR 0.018 0.001 TYR A 534 PHE 0.031 0.001 PHE B 720 TRP 0.013 0.001 TRP A 421 HIS 0.004 0.001 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (27769) covalent geometry : angle 0.53336 / 0.27 (37907) hydrogen bonds : bond 0.03052 / 2.07 ( 1245) hydrogen bonds : angle 3.99725 / 2.75 ( 3497) metal coordination : bond 0.00303 / 0.18 ( 28) metal coordination : angle 3.95170 / 2.05 ( 45) Misc. bond : bond 0.00019 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8187 (ptp) cc_final: 0.7932 (ptp) REVERT: A 76 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 140 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9287 (pp) REVERT: A 276 MET cc_start: 0.8672 (ttt) cc_final: 0.8260 (ttt) REVERT: B 1 MET cc_start: 0.8331 (ppp) cc_final: 0.8004 (ppp) REVERT: B 25 MET cc_start: 0.9441 (mmm) cc_final: 0.9231 (mmm) REVERT: B 57 MET cc_start: 0.8923 (mmt) cc_final: 0.8645 (mmm) REVERT: B 118 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6727 (m-70) REVERT: C 442 GLN cc_start: 0.5428 (OUTLIER) cc_final: 0.4558 (pp30) REVERT: C 493 MET cc_start: 0.9234 (mmm) cc_final: 0.8770 (mmm) REVERT: C 516 TYR cc_start: 0.9125 (m-80) cc_final: 0.8594 (p90) REVERT: D 441 MET cc_start: 0.8323 (mmt) cc_final: 0.8112 (mmm) REVERT: E 252 MET cc_start: 0.8894 (mpp) cc_final: 0.8643 (mpp) REVERT: F 229 TRP cc_start: 0.9134 (OUTLIER) cc_final: 0.7463 (t60) REVERT: G 16 MET cc_start: 0.9431 (mmt) cc_final: 0.9022 (mmm) REVERT: H 766 MET cc_start: 0.0293 (mtt) cc_final: -0.0150 (mmm) REVERT: H 799 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6302 (p90) REVERT: H 823 THR cc_start: 0.9035 (t) cc_final: 0.8727 (p) REVERT: H 827 ASN cc_start: 0.9129 (t0) cc_final: 0.8864 (m-40) REVERT: H 904 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7201 (t-100) REVERT: J 147 ASP cc_start: 0.8688 (t0) cc_final: 0.8394 (m-30) REVERT: K 118 MET cc_start: 0.9275 (tpt) cc_final: 0.9056 (mmm) REVERT: K 256 MET cc_start: 0.8660 (tpp) cc_final: 0.7795 (mmm) REVERT: K 273 MET cc_start: 0.5990 (mtm) cc_final: 0.5300 (ptp) outliers start: 37 outliers final: 28 residues processed: 134 average time/residue: 0.1507 time to fit residues: 33.5585 Evaluate side-chains 136 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 169 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 297 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.046393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.031572 restraints weight = 262184.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.032384 restraints weight = 142058.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.032872 restraints weight = 99144.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.033138 restraints weight = 80675.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.033321 restraints weight = 71710.925| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27799 Z= 0.105 Angle : 0.555 13.323 37952 Z= 0.274 Chirality : 0.041 0.462 4213 Planarity : 0.003 0.056 4537 Dihedral : 15.997 170.308 4457 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.45 % Allowed : 10.00 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.84 (0.16), residues: 3094 helix: 1.80 (0.14), residues: 1491 sheet: -0.07 (0.26), residues: 426 loop : -0.80 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 151 TYR 0.017 0.001 TYR A 534 PHE 0.045 0.001 PHE B 720 TRP 0.013 0.001 TRP A 421 HIS 0.004 0.001 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (27769) covalent geometry : angle 0.53879 / 0.27 (37907) hydrogen bonds : bond 0.02998 / 2.02 ( 1245) hydrogen bonds : angle 3.95247 / 2.72 ( 3497) metal coordination : bond 0.00339 / 0.20 ( 28) metal coordination : angle 3.92522 / 2.05 ( 45) Misc. bond : bond 0.00018 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8215 (ptp) cc_final: 0.7928 (ptp) REVERT: A 140 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9280 (pp) REVERT: A 276 MET cc_start: 0.8684 (ttt) cc_final: 0.8144 (ttt) REVERT: B 1 MET cc_start: 0.8311 (ppp) cc_final: 0.7987 (ppp) REVERT: B 57 MET cc_start: 0.8928 (mmt) cc_final: 0.8655 (mmm) REVERT: B 118 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6698 (m-70) REVERT: C 442 GLN cc_start: 0.5389 (OUTLIER) cc_final: 0.4518 (pp30) REVERT: C 516 TYR cc_start: 0.9132 (m-80) cc_final: 0.8612 (p90) REVERT: E 252 MET cc_start: 0.8879 (mpp) cc_final: 0.8635 (mpp) REVERT: F 229 TRP cc_start: 0.9140 (OUTLIER) cc_final: 0.7469 (t60) REVERT: G 16 MET cc_start: 0.9444 (mmt) cc_final: 0.9034 (mmm) REVERT: H 766 MET cc_start: 0.0440 (mtt) cc_final: -0.0372 (mmm) REVERT: H 799 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6365 (p90) REVERT: H 823 THR cc_start: 0.9043 (t) cc_final: 0.8742 (p) REVERT: H 827 ASN cc_start: 0.9102 (t0) cc_final: 0.8836 (m-40) REVERT: H 904 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7161 (t-100) REVERT: J 147 ASP cc_start: 0.8821 (t0) cc_final: 0.8577 (m-30) REVERT: K 118 MET cc_start: 0.9268 (tpt) cc_final: 0.9006 (tpt) REVERT: K 256 MET cc_start: 0.8629 (tpp) cc_final: 0.7782 (mmm) REVERT: K 273 MET cc_start: 0.5944 (mtm) cc_final: 0.5230 (ptp) outliers start: 40 outliers final: 28 residues processed: 131 average time/residue: 0.1614 time to fit residues: 35.4785 Evaluate side-chains 133 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 711 SER Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 84 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 308 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 chunk 105 optimal weight: 0.0070 chunk 146 optimal weight: 10.0000 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.045690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.030974 restraints weight = 255427.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.031710 restraints weight = 140921.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.032173 restraints weight = 98794.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.032471 restraints weight = 80171.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032608 restraints weight = 71226.075| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27799 Z= 0.148 Angle : 0.595 16.999 37952 Z= 0.291 Chirality : 0.041 0.384 4213 Planarity : 0.003 0.062 4537 Dihedral : 16.067 172.317 4457 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.23 % Allowed : 10.18 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.88 (0.16), residues: 3094 helix: 1.84 (0.14), residues: 1493 sheet: -0.14 (0.26), residues: 429 loop : -0.76 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 641 TYR 0.017 0.001 TYR A 534 PHE 0.033 0.001 PHE B 720 TRP 0.023 0.001 TRP A 77 HIS 0.005 0.001 HIS B 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (27769) covalent geometry : angle 0.57729 / 0.29 (37907) hydrogen bonds : bond 0.03248 / 2.18 ( 1245) hydrogen bonds : angle 4.03274 / 2.77 ( 3497) metal coordination : bond 0.00686 / 0.42 ( 28) metal coordination : angle 4.22778 / 2.29 ( 45) Misc. bond : bond 0.00013 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5836.52 seconds wall clock time: 101 minutes 3.10 seconds (6063.10 seconds total)