Starting phenix.real_space_refine on Fri Jul 3 19:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm2_32598/07_2026/7wm2_32598.map" } resolution = 2.69 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= 0.011 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 92 5.16 5 C 10072 2.51 5 N 2596 2.21 5 O 2718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15485 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3837 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain: "B" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3826 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain: "C" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3837 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain: "D" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3826 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' K': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 4.08, per 1000 atoms: 0.26 Number of scatterers: 15485 At special positions: 0 Unit cell: (117.426, 115.271, 131.431, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 92 16.00 P 4 15.00 O 2718 8.00 N 2596 7.00 C 10072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 683.7 milliseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 11 sheets defined 67.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 54 through 82 removed outlier: 3.605A pdb=" N ARG A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.803A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.505A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 removed outlier: 3.534A pdb=" N ASP A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.674A pdb=" N ALA A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.983A pdb=" N ARG A 164 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.711A pdb=" N LYS A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 191 through 216 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.549A pdb=" N LYS A 221 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 222 " --> pdb=" O PRO A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.645A pdb=" N GLU A 234 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 263 through 316 removed outlier: 3.548A pdb=" N PHE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 298 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 338 removed outlier: 3.502A pdb=" N ASP A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 351 through 368 removed outlier: 4.029A pdb=" N SER A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.591A pdb=" N LEU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.611A pdb=" N VAL A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 removed outlier: 3.823A pdb=" N ILE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.587A pdb=" N GLY A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 495 " --> pdb=" O HIS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 508 removed outlier: 4.493A pdb=" N LEU A 504 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.696A pdb=" N ALA A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 82 removed outlier: 3.827A pdb=" N TRP B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 86 through 95 removed outlier: 4.972A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 removed outlier: 3.811A pdb=" N ALA B 101 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 4.136A pdb=" N PHE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.822A pdb=" N ALA B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.962A pdb=" N ARG B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.537A pdb=" N GLY B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 215 removed outlier: 3.510A pdb=" N HIS B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.686A pdb=" N LYS B 221 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.790A pdb=" N GLU B 233 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 253 Processing helix chain 'B' and resid 263 through 294 Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.845A pdb=" N ASN B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 346 removed outlier: 3.542A pdb=" N ASP B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.737A pdb=" N SER B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.902A pdb=" N ASP B 368 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 369 " --> pdb=" O LEU B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.512A pdb=" N LEU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 467 through 475 removed outlier: 3.628A pdb=" N ILE B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.576A pdb=" N ILE B 484 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.932A pdb=" N LEU B 504 " --> pdb=" O MET B 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 82 removed outlier: 3.560A pdb=" N ILE C 59 " --> pdb=" O HIS C 55 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 63 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 106 removed outlier: 5.033A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.571A pdb=" N PHE C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 removed outlier: 3.516A pdb=" N ASP C 139 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.629A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 removed outlier: 4.176A pdb=" N ARG C 164 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.354A pdb=" N LYS C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 216 removed outlier: 3.851A pdb=" N LEU C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.529A pdb=" N LYS C 221 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.770A pdb=" N GLU C 234 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 252 removed outlier: 3.602A pdb=" N ILE C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 296 removed outlier: 3.574A pdb=" N PHE C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.799A pdb=" N ASP C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 removed outlier: 3.722A pdb=" N GLN C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 327 " --> pdb=" O GLN C 323 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 4.051A pdb=" N LEU C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 368 removed outlier: 4.161A pdb=" N SER C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 358 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 removed outlier: 3.919A pdb=" N LEU C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 467 through 475 removed outlier: 4.011A pdb=" N ILE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 495 removed outlier: 3.741A pdb=" N THR C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.789A pdb=" N LEU C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 82 removed outlier: 3.603A pdb=" N ALA D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE D 63 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 86 through 95 removed outlier: 4.816A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.797A pdb=" N ALA D 101 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 removed outlier: 4.177A pdb=" N PHE D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.762A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.930A pdb=" N ARG D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 168 through 179 Processing helix chain 'D' and resid 185 through 215 removed outlier: 3.807A pdb=" N ALA D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.779A pdb=" N LYS D 221 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 263 through 294 Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.589A pdb=" N ASP D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 306 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 349 removed outlier: 3.525A pdb=" N GLN D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 4.869A pdb=" N SER D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.745A pdb=" N ARG D 374 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.590A pdb=" N PHE D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 447 removed outlier: 4.004A pdb=" N VAL D 444 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 475 removed outlier: 3.556A pdb=" N ILE D 474 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 495 removed outlier: 3.503A pdb=" N ASN D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 512 removed outlier: 4.022A pdb=" N VAL D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.790A pdb=" N GLN A 461 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 426 through 433 removed outlier: 4.864A pdb=" N LEU A 419 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU A 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA A 417 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 393 removed outlier: 7.121A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 439 " --> pdb=" O TYR B 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 393 removed outlier: 7.121A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 398 through 400 removed outlier: 6.907A pdb=" N ASP B 398 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR B 456 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 400 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 431 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.869A pdb=" N GLN C 461 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 410 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 426 through 433 removed outlier: 3.501A pdb=" N ASP C 423 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 428 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 421 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU C 419 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU C 432 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA C 417 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 393 removed outlier: 7.054A pdb=" N GLN D 461 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 439 " --> pdb=" O TYR D 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 398 through 400 removed outlier: 7.026A pdb=" N ASP D 398 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR D 456 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 400 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 431 " --> pdb=" O LEU D 419 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2394 1.27 - 1.40: 4238 1.40 - 1.54: 8969 1.54 - 1.67: 89 1.67 - 1.81: 156 Bond restraints: 15846 Sorted by residual: bond pdb=" C PRO C 76 " pdb=" O PRO C 76 " ideal model delta sigma weight residual 1.237 1.131 0.106 1.26e-02 6.30e+03 7.09e+01 bond pdb=" C PRO A 76 " pdb=" O PRO A 76 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.26e-02 6.30e+03 6.87e+01 bond pdb=" C PRO D 76 " pdb=" O PRO D 76 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.26e-02 6.30e+03 6.82e+01 bond pdb=" C PRO B 76 " pdb=" O PRO B 76 " ideal model delta sigma weight residual 1.237 1.134 0.103 1.26e-02 6.30e+03 6.69e+01 bond pdb=" C THR A 250 " pdb=" O THR A 250 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.19e-02 7.06e+03 6.46e+01 ... (remaining 15841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 20879 2.81 - 5.62: 498 5.62 - 8.44: 84 8.44 - 11.25: 12 11.25 - 14.06: 3 Bond angle restraints: 21476 Sorted by residual: angle pdb=" N GLN A 344 " pdb=" CA GLN A 344 " pdb=" C GLN A 344 " ideal model delta sigma weight residual 114.56 104.96 9.60 1.27e+00 6.20e-01 5.71e+01 angle pdb=" CA THR B 250 " pdb=" CB THR B 250 " pdb=" OG1 THR B 250 " ideal model delta sigma weight residual 109.60 99.30 10.30 1.50e+00 4.44e-01 4.72e+01 angle pdb=" CA ARG B 300 " pdb=" C ARG B 300 " pdb=" N ASN B 301 " ideal model delta sigma weight residual 116.92 124.70 -7.78 1.16e+00 7.43e-01 4.50e+01 angle pdb=" N PHE C 187 " pdb=" CA PHE C 187 " pdb=" C PHE C 187 " ideal model delta sigma weight residual 111.36 104.38 6.98 1.09e+00 8.42e-01 4.10e+01 angle pdb=" C GLU B 339 " pdb=" CA GLU B 339 " pdb=" CB GLU B 339 " ideal model delta sigma weight residual 110.79 100.50 10.29 1.66e+00 3.63e-01 3.84e+01 ... (remaining 21471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7990 17.87 - 35.75: 1047 35.75 - 53.62: 290 53.62 - 71.49: 66 71.49 - 89.37: 23 Dihedral angle restraints: 9416 sinusoidal: 3854 harmonic: 5562 Sorted by residual: dihedral pdb=" C SER B 297 " pdb=" N SER B 297 " pdb=" CA SER B 297 " pdb=" CB SER B 297 " ideal model delta harmonic sigma weight residual -122.60 -138.08 15.48 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" C GLN B 342 " pdb=" N GLN B 342 " pdb=" CA GLN B 342 " pdb=" CB GLN B 342 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" N SER B 297 " pdb=" C SER B 297 " pdb=" CA SER B 297 " pdb=" CB SER B 297 " ideal model delta harmonic sigma weight residual 122.80 136.02 -13.22 0 2.50e+00 1.60e-01 2.80e+01 ... (remaining 9413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2310 0.118 - 0.236: 84 0.236 - 0.354: 19 0.354 - 0.472: 7 0.472 - 0.590: 2 Chirality restraints: 2422 Sorted by residual: chirality pdb=" CA SER B 297 " pdb=" N SER B 297 " pdb=" C SER B 297 " pdb=" CB SER B 297 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" CA GLN B 342 " pdb=" N GLN B 342 " pdb=" C GLN B 342 " pdb=" CB GLN B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CA GLN C 343 " pdb=" N GLN C 343 " pdb=" C GLN C 343 " pdb=" CB GLN C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 2419 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 901 " -0.185 2.00e-02 2.50e+03 1.87e-01 3.49e+02 pdb=" C29 POV B 901 " 0.178 2.00e-02 2.50e+03 pdb="C210 POV B 901 " 0.195 2.00e-02 2.50e+03 pdb="C211 POV B 901 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 901 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C29 POV A 901 " 0.159 2.00e-02 2.50e+03 pdb="C210 POV A 901 " 0.158 2.00e-02 2.50e+03 pdb="C211 POV A 901 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 901 " 0.134 2.00e-02 2.50e+03 1.34e-01 1.81e+02 pdb=" C29 POV C 901 " -0.132 2.00e-02 2.50e+03 pdb="C210 POV C 901 " -0.136 2.00e-02 2.50e+03 pdb="C211 POV C 901 " 0.135 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.72: 1429 2.72 - 3.32: 19247 3.32 - 3.93: 28876 3.93 - 4.53: 40721 4.53 - 5.14: 60142 Nonbonded interactions: 150415 Sorted by model distance: nonbonded pdb=" N ASP B 304 " pdb=" OD1 ASP B 304 " model vdw 2.110 3.120 nonbonded pdb=" O ASN B 301 " pdb=" ND2 ASN B 301 " model vdw 2.171 3.120 nonbonded pdb=" O SER B 356 " pdb=" OG SER B 356 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASP A 139 " pdb=" NE1 TRP A 166 " model vdw 2.209 3.120 nonbonded pdb=" O THR C 252 " pdb=" OG1 THR C 253 " model vdw 2.212 3.040 ... (remaining 150410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 512) selection = (chain 'B' and resid 44 through 512) selection = (chain 'C' and resid 44 through 512) selection = (chain 'D' and resid 44 through 512) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 : 0.012 0.106 15846 Z= 0.641 Angle : 1.035 14.061 21476 Z= 0.640 Chirality : 0.065 0.590 2422 Planarity : 0.008 0.187 2688 Dihedral : 18.064 89.366 5812 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.88 % Favored : 93.96 % Rotamer: Outliers : 12.04 % Allowed : 22.88 % Favored : 65.08 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.16), residues: 1870 helix: -3.02 (0.12), residues: 1096 sheet: -2.76 (0.48), residues: 100 loop : -2.06 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 190 TYR 0.032 0.002 TYR C 186 PHE 0.018 0.002 PHE C 184 TRP 0.059 0.004 TRP D 246 HIS 0.020 0.002 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.01167 / 0.64 (15846) covalent geometry : angle 1.03477 / 0.64 (21476) hydrogen bonds : bond 0.28070 / 18.11 ( 818) hydrogen bonds : angle 9.73045 / 6.96 ( 2361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 265 time to evaluate : 0.639 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 103 ASP cc_start: 0.7361 (t70) cc_final: 0.7159 (t0) REVERT: A 124 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6087 (mtt180) REVERT: A 151 ARG cc_start: 0.6571 (ttm170) cc_final: 0.6188 (mtp-110) REVERT: A 159 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8340 (mt) REVERT: A 162 MET cc_start: 0.8159 (tpt) cc_final: 0.7761 (tpt) REVERT: A 183 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.5947 (t160) REVERT: A 188 TRP cc_start: 0.6941 (m100) cc_final: 0.6739 (m100) REVERT: A 232 LEU cc_start: 0.8423 (mt) cc_final: 0.8064 (mm) REVERT: A 249 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 267 MET cc_start: 0.8339 (mtt) cc_final: 0.7880 (mtm) REVERT: A 294 HIS cc_start: 0.7319 (m-70) cc_final: 0.7090 (m90) REVERT: A 298 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.7036 (ttm-80) REVERT: A 339 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5502 (mt-10) REVERT: A 343 GLN cc_start: 0.5299 (OUTLIER) cc_final: 0.5020 (mm110) REVERT: A 466 ASN cc_start: 0.5077 (p0) cc_final: 0.4760 (p0) REVERT: A 510 MET cc_start: 0.0472 (mtt) cc_final: -0.0590 (ptm) REVERT: B 46 ARG cc_start: 0.5632 (ttm-80) cc_final: 0.5315 (mtp85) REVERT: B 83 ARG cc_start: 0.7438 (ptp-110) cc_final: 0.7079 (mtm110) REVERT: B 86 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6464 (ptt180) REVERT: B 105 ILE cc_start: 0.7944 (mt) cc_final: 0.7734 (mt) REVERT: B 109 PHE cc_start: 0.7072 (m-10) cc_final: 0.6798 (m-80) REVERT: B 133 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6510 (mtm-85) REVERT: B 162 MET cc_start: 0.8568 (mmt) cc_final: 0.8285 (mmm) REVERT: B 294 HIS cc_start: 0.6670 (m-70) cc_final: 0.6399 (m-70) REVERT: B 301 ASN cc_start: 0.5398 (OUTLIER) cc_final: 0.4709 (p0) REVERT: B 333 LYS cc_start: 0.5701 (tppt) cc_final: 0.5268 (ttpp) REVERT: B 344 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.6204 (tm-30) REVERT: B 352 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.4870 (tmtt) REVERT: B 389 LYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4480 (mtmt) REVERT: B 401 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4980 (mt) REVERT: B 485 MET cc_start: 0.4557 (tpt) cc_final: 0.3511 (tpt) REVERT: B 500 MET cc_start: 0.3298 (tmm) cc_final: 0.3051 (ptm) REVERT: C 58 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7318 (mpt-90) REVERT: C 103 ASP cc_start: 0.7696 (t70) cc_final: 0.7352 (t0) REVERT: C 155 GLN cc_start: 0.7742 (mm110) cc_final: 0.7371 (mp10) REVERT: C 177 ARG cc_start: 0.6829 (mtm110) cc_final: 0.6507 (mtp-110) REVERT: C 180 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6055 (pptt) REVERT: C 183 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6059 (t160) REVERT: C 190 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7969 (tpt90) REVERT: C 194 LEU cc_start: 0.7487 (mt) cc_final: 0.7156 (mt) REVERT: C 230 ASN cc_start: 0.6079 (m110) cc_final: 0.5868 (p0) REVERT: C 258 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.6903 (p0) REVERT: C 267 MET cc_start: 0.8326 (mtt) cc_final: 0.7840 (mtm) REVERT: C 288 MET cc_start: 0.7938 (tpt) cc_final: 0.7473 (tpp) REVERT: C 298 ARG cc_start: 0.6746 (mtp-110) cc_final: 0.6131 (ttm-80) REVERT: C 314 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.5505 (m-70) REVERT: C 316 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7697 (m110) REVERT: C 343 GLN cc_start: 0.4889 (OUTLIER) cc_final: 0.3898 (pp30) REVERT: C 352 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5971 (tppt) REVERT: C 388 MET cc_start: 0.5247 (mtt) cc_final: 0.4929 (mtm) REVERT: C 401 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6275 (pt) REVERT: C 464 ARG cc_start: 0.6100 (ttm170) cc_final: 0.5723 (ttp-110) REVERT: C 504 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6086 (tt) REVERT: D 56 LYS cc_start: 0.6738 (tmtt) cc_final: 0.6196 (mttt) REVERT: D 86 ARG cc_start: 0.6619 (mtp180) cc_final: 0.5942 (ptt180) REVERT: D 93 ASP cc_start: 0.7391 (t0) cc_final: 0.6611 (m-30) REVERT: D 105 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7624 (pp) REVERT: D 109 PHE cc_start: 0.7496 (m-10) cc_final: 0.7258 (m-80) REVERT: D 125 LYS cc_start: 0.7494 (mmtt) cc_final: 0.6669 (pttt) REVERT: D 215 ARG cc_start: 0.6417 (ptt180) cc_final: 0.6210 (mtm110) REVERT: D 294 HIS cc_start: 0.6855 (m-70) cc_final: 0.6523 (m-70) REVERT: D 333 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5398 (tptp) REVERT: D 367 MET cc_start: 0.6166 (tpp) cc_final: 0.5900 (tpt) REVERT: D 398 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5002 (p0) REVERT: D 432 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.5205 (pm20) REVERT: D 506 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4362 (pp20) outliers start: 202 outliers final: 65 residues processed: 427 average time/residue: 0.4817 time to fit residues: 228.2446 Evaluate side-chains 307 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 506 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 HIS A 323 GLN A 325 GLN A 343 GLN A 383 GLN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 472 ASN A 502 ASN B 216 ASN B 218 ASN B 290 ASN B 294 HIS B 343 GLN B 472 ASN B 475 GLN C 323 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN D 126 GLN D 216 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 383 GLN D 477 ASN D 491 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.223693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139975 restraints weight = 16080.292| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.33 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15846 Z= 0.172 Angle : 0.722 9.236 21476 Z= 0.379 Chirality : 0.046 0.189 2422 Planarity : 0.005 0.035 2688 Dihedral : 11.646 91.915 2360 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.02 % Allowed : 27.00 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.18), residues: 1870 helix: -0.97 (0.14), residues: 1152 sheet: -2.25 (0.48), residues: 102 loop : -1.30 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 182 TYR 0.018 0.002 TYR D 364 PHE 0.016 0.001 PHE B 382 TRP 0.015 0.002 TRP C 188 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (15846) covalent geometry : angle 0.72189 / 0.38 (21476) hydrogen bonds : bond 0.06828 / 4.47 ( 818) hydrogen bonds : angle 5.32417 / 3.81 ( 2361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 232 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7891 (t70) cc_final: 0.7624 (t0) REVERT: A 155 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7454 (mp10) REVERT: A 162 MET cc_start: 0.8815 (tpt) cc_final: 0.8279 (mmm) REVERT: A 183 ASN cc_start: 0.7154 (m-40) cc_final: 0.6512 (t160) REVERT: A 194 LEU cc_start: 0.8323 (mt) cc_final: 0.8089 (mt) REVERT: A 232 LEU cc_start: 0.8854 (mt) cc_final: 0.8619 (mm) REVERT: A 267 MET cc_start: 0.9035 (mtt) cc_final: 0.8775 (mtm) REVERT: A 298 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7767 (ttm-80) REVERT: A 339 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5739 (mt-10) REVERT: A 510 MET cc_start: 0.0579 (mtt) cc_final: -0.0537 (ptm) REVERT: B 46 ARG cc_start: 0.5667 (ttm-80) cc_final: 0.5275 (ttm-80) REVERT: B 83 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7464 (mtm110) REVERT: B 86 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6261 (ptt180) REVERT: B 93 ASP cc_start: 0.7858 (t0) cc_final: 0.7143 (m-30) REVERT: B 105 ILE cc_start: 0.8268 (mt) cc_final: 0.8039 (mt) REVERT: B 109 PHE cc_start: 0.7668 (m-10) cc_final: 0.7390 (m-80) REVERT: B 133 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6579 (mtm-85) REVERT: B 307 GLN cc_start: 0.7567 (pp30) cc_final: 0.7306 (tp40) REVERT: B 337 ASP cc_start: 0.7399 (m-30) cc_final: 0.7157 (m-30) REVERT: B 344 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: B 352 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.5325 (tmtt) REVERT: B 397 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6673 (tp30) REVERT: B 401 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.5016 (mt) REVERT: B 485 MET cc_start: 0.4593 (tpt) cc_final: 0.3603 (mmt) REVERT: C 93 ASP cc_start: 0.8297 (t0) cc_final: 0.8049 (m-30) REVERT: C 103 ASP cc_start: 0.8035 (t70) cc_final: 0.7696 (t0) REVERT: C 113 LEU cc_start: 0.7755 (mm) cc_final: 0.7443 (tp) REVERT: C 122 ASP cc_start: 0.6737 (p0) cc_final: 0.6461 (p0) REVERT: C 151 ARG cc_start: 0.7527 (ttm110) cc_final: 0.6975 (ppt170) REVERT: C 155 GLN cc_start: 0.7906 (mm110) cc_final: 0.7441 (mp10) REVERT: C 177 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7270 (ttp-110) REVERT: C 179 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7097 (mm-30) REVERT: C 183 ASN cc_start: 0.7250 (m-40) cc_final: 0.6947 (t160) REVERT: C 190 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7868 (mtp180) REVERT: C 194 LEU cc_start: 0.8163 (mt) cc_final: 0.7944 (mt) REVERT: C 230 ASN cc_start: 0.6462 (m110) cc_final: 0.6124 (p0) REVERT: C 267 MET cc_start: 0.9027 (mtt) cc_final: 0.8714 (mtm) REVERT: C 288 MET cc_start: 0.8955 (tpt) cc_final: 0.8660 (tpp) REVERT: C 298 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.6994 (ttm-80) REVERT: C 300 ARG cc_start: 0.7782 (ptt90) cc_final: 0.7580 (ptt-90) REVERT: C 343 GLN cc_start: 0.5203 (OUTLIER) cc_final: 0.4258 (pp30) REVERT: C 388 MET cc_start: 0.5836 (mtt) cc_final: 0.5563 (mtp) REVERT: C 401 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6633 (pt) REVERT: D 56 LYS cc_start: 0.6913 (tmtt) cc_final: 0.6382 (mttp) REVERT: D 86 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6031 (ptt180) REVERT: D 93 ASP cc_start: 0.7857 (t0) cc_final: 0.7145 (m-30) REVERT: D 105 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8171 (pt) REVERT: D 109 PHE cc_start: 0.7951 (m-10) cc_final: 0.7725 (m-80) REVERT: D 125 LYS cc_start: 0.7650 (mmtt) cc_final: 0.6577 (tttt) REVERT: D 162 MET cc_start: 0.9108 (tpt) cc_final: 0.8598 (mmm) REVERT: D 215 ARG cc_start: 0.7304 (ptt180) cc_final: 0.6918 (mtm110) REVERT: D 294 HIS cc_start: 0.6787 (m-70) cc_final: 0.6517 (m-70) REVERT: D 307 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7148 (mm110) REVERT: D 317 HIS cc_start: 0.5245 (OUTLIER) cc_final: 0.4499 (p-80) REVERT: D 330 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6793 (mm) REVERT: D 333 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5729 (tptp) REVERT: D 348 ASP cc_start: 0.6928 (p0) cc_final: 0.6587 (p0) REVERT: D 384 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4761 (mm) REVERT: D 395 PRO cc_start: 0.7528 (Cg_endo) cc_final: 0.7222 (Cg_exo) REVERT: D 432 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.4943 (pm20) REVERT: D 506 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4881 (pp20) outliers start: 101 outliers final: 25 residues processed: 313 average time/residue: 0.4878 time to fit residues: 170.3596 Evaluate side-chains 247 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 506 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 135 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 0.0010 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN A 383 GLN A 402 GLN A 403 ASN A 472 ASN B 218 ASN B 294 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 360 HIS C 472 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.226116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139462 restraints weight = 16251.184| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.20 r_work: 0.3251 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15846 Z= 0.135 Angle : 0.623 12.414 21476 Z= 0.319 Chirality : 0.044 0.353 2422 Planarity : 0.004 0.036 2688 Dihedral : 9.673 83.783 2241 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.48 % Allowed : 27.41 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1870 helix: -0.04 (0.15), residues: 1146 sheet: -1.80 (0.49), residues: 102 loop : -0.87 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.021 0.001 TYR B 364 PHE 0.020 0.001 PHE A 409 TRP 0.012 0.002 TRP B 135 HIS 0.005 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (15846) covalent geometry : angle 0.62272 / 0.32 (21476) hydrogen bonds : bond 0.05537 / 3.64 ( 818) hydrogen bonds : angle 4.71835 / 3.37 ( 2361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 218 time to evaluate : 0.543 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 103 ASP cc_start: 0.7941 (t70) cc_final: 0.7717 (t0) REVERT: A 119 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7162 (mt) REVERT: A 122 ASP cc_start: 0.6871 (p0) cc_final: 0.6549 (p0) REVERT: A 155 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7406 (mp10) REVERT: A 159 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 162 MET cc_start: 0.8792 (tpt) cc_final: 0.8417 (tpt) REVERT: A 183 ASN cc_start: 0.7102 (m-40) cc_final: 0.6401 (t160) REVERT: A 232 LEU cc_start: 0.8900 (mt) cc_final: 0.8665 (mm) REVERT: A 267 MET cc_start: 0.9062 (mtt) cc_final: 0.8828 (mtm) REVERT: A 298 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7663 (ttm-80) REVERT: A 339 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5752 (mt-10) REVERT: A 356 SER cc_start: 0.7481 (t) cc_final: 0.7216 (p) REVERT: A 464 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6567 (ttp-110) REVERT: A 510 MET cc_start: 0.0018 (mtt) cc_final: -0.0860 (ptm) REVERT: B 46 ARG cc_start: 0.5614 (ttm-80) cc_final: 0.5252 (ttm-80) REVERT: B 59 ILE cc_start: 0.8078 (tp) cc_final: 0.7659 (pt) REVERT: B 83 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7427 (mtm110) REVERT: B 86 ARG cc_start: 0.6907 (mtp180) cc_final: 0.6047 (ptt180) REVERT: B 93 ASP cc_start: 0.7880 (t0) cc_final: 0.7166 (m-30) REVERT: B 105 ILE cc_start: 0.8192 (mt) cc_final: 0.7967 (mt) REVERT: B 109 PHE cc_start: 0.7667 (m-10) cc_final: 0.7417 (m-80) REVERT: B 133 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6949 (mtm110) REVERT: B 327 LEU cc_start: 0.7143 (mt) cc_final: 0.6932 (mt) REVERT: B 333 LYS cc_start: 0.6182 (tppt) cc_final: 0.5634 (ttpp) REVERT: B 337 ASP cc_start: 0.7263 (m-30) cc_final: 0.7026 (m-30) REVERT: B 352 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.5317 (tmtt) REVERT: B 401 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4882 (mt) REVERT: B 485 MET cc_start: 0.4511 (tpt) cc_final: 0.3616 (mmt) REVERT: B 497 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5402 (p0) REVERT: B 500 MET cc_start: 0.3985 (ppp) cc_final: 0.3154 (ppp) REVERT: C 93 ASP cc_start: 0.8271 (t0) cc_final: 0.8060 (m-30) REVERT: C 103 ASP cc_start: 0.8016 (t70) cc_final: 0.7685 (t0) REVERT: C 113 LEU cc_start: 0.7803 (mm) cc_final: 0.7529 (tp) REVERT: C 122 ASP cc_start: 0.6546 (p0) cc_final: 0.6228 (p0) REVERT: C 151 ARG cc_start: 0.7420 (ttm110) cc_final: 0.6973 (ppt170) REVERT: C 155 GLN cc_start: 0.7904 (mm110) cc_final: 0.7420 (mp10) REVERT: C 177 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7289 (ttp-110) REVERT: C 179 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7068 (mm-30) REVERT: C 183 ASN cc_start: 0.7236 (m-40) cc_final: 0.6961 (t160) REVERT: C 194 LEU cc_start: 0.8168 (mt) cc_final: 0.7958 (mt) REVERT: C 230 ASN cc_start: 0.6408 (m110) cc_final: 0.6082 (p0) REVERT: C 288 MET cc_start: 0.8965 (tpt) cc_final: 0.8690 (tpp) REVERT: C 298 ARG cc_start: 0.7604 (mtp-110) cc_final: 0.6956 (ttm-80) REVERT: C 381 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5304 (mp) REVERT: C 388 MET cc_start: 0.5482 (mtt) cc_final: 0.5219 (mtp) REVERT: C 401 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6613 (pp) REVERT: D 56 LYS cc_start: 0.7003 (tmtt) cc_final: 0.6327 (mtmm) REVERT: D 58 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7507 (tpm170) REVERT: D 59 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7483 (pt) REVERT: D 86 ARG cc_start: 0.6681 (mtp180) cc_final: 0.5860 (ptt180) REVERT: D 93 ASP cc_start: 0.7822 (t0) cc_final: 0.7123 (m-30) REVERT: D 105 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8041 (pp) REVERT: D 108 PHE cc_start: 0.8306 (m-10) cc_final: 0.8061 (m-80) REVERT: D 109 PHE cc_start: 0.7908 (m-10) cc_final: 0.7692 (m-80) REVERT: D 125 LYS cc_start: 0.7487 (mmtt) cc_final: 0.6421 (tttt) REVERT: D 215 ARG cc_start: 0.7314 (ptt180) cc_final: 0.6877 (mtm110) REVERT: D 248 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8306 (mm) REVERT: D 294 HIS cc_start: 0.6758 (m-70) cc_final: 0.6468 (m-70) REVERT: D 400 ILE cc_start: 0.5542 (OUTLIER) cc_final: 0.4931 (tp) REVERT: D 401 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4105 (mt) REVERT: D 439 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5862 (pp) outliers start: 92 outliers final: 28 residues processed: 291 average time/residue: 0.4683 time to fit residues: 152.3183 Evaluate side-chains 246 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 439 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN B 294 HIS B 307 GLN C 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.224690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132104 restraints weight = 15962.854| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.93 r_work: 0.3188 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15846 Z= 0.184 Angle : 0.643 9.913 21476 Z= 0.333 Chirality : 0.045 0.328 2422 Planarity : 0.004 0.046 2688 Dihedral : 9.227 85.898 2217 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.96 % Allowed : 26.58 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1870 helix: 0.03 (0.15), residues: 1152 sheet: -1.56 (0.50), residues: 100 loop : -0.69 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 182 TYR 0.024 0.002 TYR B 364 PHE 0.020 0.001 PHE C 409 TRP 0.017 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (15846) covalent geometry : angle 0.64350 / 0.33 (21476) hydrogen bonds : bond 0.05992 / 3.97 ( 818) hydrogen bonds : angle 4.67414 / 3.33 ( 2361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 206 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7988 (t70) cc_final: 0.7762 (t0) REVERT: A 119 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7019 (mt) REVERT: A 122 ASP cc_start: 0.6970 (p0) cc_final: 0.6769 (p0) REVERT: A 125 LYS cc_start: 0.6479 (tppt) cc_final: 0.5982 (ttmm) REVERT: A 155 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7398 (mp10) REVERT: A 162 MET cc_start: 0.8728 (tpt) cc_final: 0.8299 (mmm) REVERT: A 183 ASN cc_start: 0.7083 (m-40) cc_final: 0.6321 (t160) REVERT: A 267 MET cc_start: 0.9072 (mtt) cc_final: 0.8800 (mtm) REVERT: A 298 ARG cc_start: 0.8072 (ttp-170) cc_final: 0.7669 (ttm-80) REVERT: A 356 SER cc_start: 0.7560 (t) cc_final: 0.7301 (p) REVERT: A 464 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6672 (ttp-110) REVERT: A 510 MET cc_start: 0.0178 (mtt) cc_final: -0.0783 (ptm) REVERT: B 46 ARG cc_start: 0.5656 (ttm-80) cc_final: 0.5322 (ttm-80) REVERT: B 83 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (mtm110) REVERT: B 86 ARG cc_start: 0.6840 (mtp180) cc_final: 0.6030 (ptt180) REVERT: B 93 ASP cc_start: 0.7867 (t0) cc_final: 0.7178 (m-30) REVERT: B 109 PHE cc_start: 0.7463 (m-10) cc_final: 0.7213 (m-80) REVERT: B 133 ARG cc_start: 0.7079 (mtp180) cc_final: 0.6857 (mtm110) REVERT: B 162 MET cc_start: 0.9061 (tpt) cc_final: 0.8713 (mmm) REVERT: B 248 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 337 ASP cc_start: 0.7218 (m-30) cc_final: 0.6990 (m-30) REVERT: B 397 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: B 401 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4797 (mt) REVERT: B 485 MET cc_start: 0.4498 (tpt) cc_final: 0.3661 (mmt) REVERT: B 497 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5425 (p0) REVERT: B 500 MET cc_start: 0.3972 (ppp) cc_final: 0.3041 (ppp) REVERT: C 93 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: C 103 ASP cc_start: 0.7933 (t70) cc_final: 0.7604 (t0) REVERT: C 113 LEU cc_start: 0.7798 (mm) cc_final: 0.7510 (tp) REVERT: C 122 ASP cc_start: 0.6846 (p0) cc_final: 0.6502 (p0) REVERT: C 151 ARG cc_start: 0.7421 (ttm110) cc_final: 0.6910 (ppt170) REVERT: C 155 GLN cc_start: 0.7920 (mm110) cc_final: 0.7433 (mp10) REVERT: C 177 ARG cc_start: 0.7545 (mtm110) cc_final: 0.7312 (ttp-110) REVERT: C 179 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7000 (mm-30) REVERT: C 183 ASN cc_start: 0.7082 (m-40) cc_final: 0.6687 (t160) REVERT: C 194 LEU cc_start: 0.8126 (mt) cc_final: 0.7899 (mt) REVERT: C 230 ASN cc_start: 0.6406 (m110) cc_final: 0.6075 (p0) REVERT: C 232 LEU cc_start: 0.8672 (mt) cc_final: 0.8447 (mm) REVERT: C 288 MET cc_start: 0.8935 (tpt) cc_final: 0.8667 (tpp) REVERT: C 298 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.6947 (ttm-80) REVERT: C 388 MET cc_start: 0.5282 (mtt) cc_final: 0.5022 (mtp) REVERT: C 389 LYS cc_start: 0.6898 (mttp) cc_final: 0.6221 (mptt) REVERT: C 401 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6601 (pp) REVERT: D 56 LYS cc_start: 0.6877 (tmtt) cc_final: 0.6181 (mtmm) REVERT: D 58 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7412 (tpm170) REVERT: D 59 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7365 (pt) REVERT: D 86 ARG cc_start: 0.6596 (mtp180) cc_final: 0.5779 (ptt180) REVERT: D 93 ASP cc_start: 0.7744 (t0) cc_final: 0.7141 (m-30) REVERT: D 105 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8037 (pp) REVERT: D 109 PHE cc_start: 0.7855 (m-10) cc_final: 0.7573 (m-80) REVERT: D 162 MET cc_start: 0.9105 (tpt) cc_final: 0.8650 (mmm) REVERT: D 215 ARG cc_start: 0.7361 (ptt180) cc_final: 0.6851 (mtm110) REVERT: D 248 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8389 (mm) REVERT: D 294 HIS cc_start: 0.6733 (m-70) cc_final: 0.6475 (m-70) REVERT: D 330 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6782 (mm) REVERT: D 397 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: D 400 ILE cc_start: 0.5469 (OUTLIER) cc_final: 0.4852 (tp) REVERT: D 401 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.4251 (mt) outliers start: 100 outliers final: 35 residues processed: 281 average time/residue: 0.5225 time to fit residues: 163.6651 Evaluate side-chains 250 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 0.1980 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 133 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN B 294 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN C 216 ASN C 472 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.222734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132312 restraints weight = 15990.750| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.20 r_work: 0.3113 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15846 Z= 0.270 Angle : 0.704 9.302 21476 Z= 0.365 Chirality : 0.049 0.284 2422 Planarity : 0.005 0.048 2688 Dihedral : 9.145 89.251 2208 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 6.02 % Allowed : 26.46 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1870 helix: -0.17 (0.15), residues: 1150 sheet: -1.43 (0.51), residues: 100 loop : -0.62 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 182 TYR 0.023 0.002 TYR B 364 PHE 0.023 0.002 PHE B 272 TRP 0.021 0.003 TRP A 246 HIS 0.007 0.002 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.27 (15846) covalent geometry : angle 0.70360 / 0.36 (21476) hydrogen bonds : bond 0.06752 / 4.48 ( 818) hydrogen bonds : angle 4.77272 / 3.41 ( 2361) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 200 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8026 (t70) cc_final: 0.7779 (t0) REVERT: A 119 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7107 (mt) REVERT: A 125 LYS cc_start: 0.6557 (tppt) cc_final: 0.5968 (ttmm) REVERT: A 151 ARG cc_start: 0.6051 (OUTLIER) cc_final: 0.5357 (ppt170) REVERT: A 155 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7423 (mp10) REVERT: A 162 MET cc_start: 0.8708 (tpt) cc_final: 0.8317 (mmm) REVERT: A 183 ASN cc_start: 0.7259 (m-40) cc_final: 0.6386 (t160) REVERT: A 267 MET cc_start: 0.9110 (mtt) cc_final: 0.8807 (mtm) REVERT: A 298 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7779 (tmm-80) REVERT: A 356 SER cc_start: 0.7579 (t) cc_final: 0.7311 (p) REVERT: A 441 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5669 (tm-30) REVERT: A 510 MET cc_start: 0.0271 (mtt) cc_final: -0.0757 (ptm) REVERT: B 46 ARG cc_start: 0.5699 (ttm-80) cc_final: 0.5383 (ttm-80) REVERT: B 58 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7861 (tpt-90) REVERT: B 83 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7478 (mtm110) REVERT: B 86 ARG cc_start: 0.6837 (mtp180) cc_final: 0.6022 (ptt180) REVERT: B 93 ASP cc_start: 0.7974 (t0) cc_final: 0.7287 (m-30) REVERT: B 109 PHE cc_start: 0.7550 (m-10) cc_final: 0.7310 (m-80) REVERT: B 162 MET cc_start: 0.9124 (tpt) cc_final: 0.8661 (mmm) REVERT: B 238 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7963 (tmt) REVERT: B 248 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 330 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6544 (mm) REVERT: B 337 ASP cc_start: 0.7288 (m-30) cc_final: 0.7067 (m-30) REVERT: B 397 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: B 400 ILE cc_start: 0.5511 (OUTLIER) cc_final: 0.5057 (tp) REVERT: B 401 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4716 (mt) REVERT: B 485 MET cc_start: 0.4527 (tpt) cc_final: 0.3680 (mmt) REVERT: C 103 ASP cc_start: 0.8008 (t70) cc_final: 0.7671 (t0) REVERT: C 122 ASP cc_start: 0.6876 (p0) cc_final: 0.6548 (p0) REVERT: C 155 GLN cc_start: 0.7911 (mm110) cc_final: 0.7457 (mp10) REVERT: C 177 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7334 (ttp-110) REVERT: C 179 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7421 (mm-30) REVERT: C 183 ASN cc_start: 0.7148 (m-40) cc_final: 0.6649 (t160) REVERT: C 230 ASN cc_start: 0.6449 (m110) cc_final: 0.6051 (p0) REVERT: C 232 LEU cc_start: 0.8692 (mt) cc_final: 0.8416 (mm) REVERT: C 288 MET cc_start: 0.8993 (tpt) cc_final: 0.8707 (tpp) REVERT: C 298 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.6959 (ttm-80) REVERT: C 388 MET cc_start: 0.5297 (mtt) cc_final: 0.5041 (mtp) REVERT: C 389 LYS cc_start: 0.6875 (mttp) cc_final: 0.6183 (mptt) REVERT: C 432 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: D 56 LYS cc_start: 0.6892 (tmtt) cc_final: 0.6307 (mtmm) REVERT: D 58 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7564 (tpm170) REVERT: D 86 ARG cc_start: 0.6670 (mtp180) cc_final: 0.5789 (ptt180) REVERT: D 93 ASP cc_start: 0.7869 (t0) cc_final: 0.7284 (m-30) REVERT: D 105 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8225 (pp) REVERT: D 109 PHE cc_start: 0.7874 (m-10) cc_final: 0.7575 (m-80) REVERT: D 162 MET cc_start: 0.9160 (tpt) cc_final: 0.8596 (mmm) REVERT: D 215 ARG cc_start: 0.7448 (ptt180) cc_final: 0.6876 (mtm110) REVERT: D 238 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7955 (tmt) REVERT: D 248 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8505 (mt) REVERT: D 294 HIS cc_start: 0.6863 (m-70) cc_final: 0.6568 (m-70) REVERT: D 330 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6605 (mm) REVERT: D 333 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.6049 (ttpp) REVERT: D 395 PRO cc_start: 0.7429 (Cg_endo) cc_final: 0.7137 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6825 (tp30) REVERT: D 400 ILE cc_start: 0.5453 (OUTLIER) cc_final: 0.4813 (tp) REVERT: D 401 LEU cc_start: 0.4479 (OUTLIER) cc_final: 0.4258 (mt) outliers start: 101 outliers final: 47 residues processed: 272 average time/residue: 0.5702 time to fit residues: 172.6948 Evaluate side-chains 265 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN B 472 ASN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.225896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139087 restraints weight = 15962.440| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.12 r_work: 0.3217 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15846 Z= 0.128 Angle : 0.597 9.537 21476 Z= 0.309 Chirality : 0.042 0.183 2422 Planarity : 0.004 0.051 2688 Dihedral : 8.665 86.053 2206 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.71 % Allowed : 27.89 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1870 helix: 0.32 (0.15), residues: 1154 sheet: -1.34 (0.50), residues: 100 loop : -0.50 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 182 TYR 0.024 0.001 TYR B 364 PHE 0.019 0.001 PHE C 409 TRP 0.017 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (15846) covalent geometry : angle 0.59727 / 0.31 (21476) hydrogen bonds : bond 0.05165 / 3.41 ( 818) hydrogen bonds : angle 4.49417 / 3.20 ( 2361) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8026 (t70) cc_final: 0.7772 (t0) REVERT: A 119 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7073 (mt) REVERT: A 125 LYS cc_start: 0.6567 (tppt) cc_final: 0.6026 (ttmm) REVERT: A 162 MET cc_start: 0.8754 (tpt) cc_final: 0.8354 (mmm) REVERT: A 183 ASN cc_start: 0.7283 (m-40) cc_final: 0.6400 (t160) REVERT: A 267 MET cc_start: 0.9100 (mtt) cc_final: 0.8815 (mtm) REVERT: A 298 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7618 (ttm-80) REVERT: A 356 SER cc_start: 0.7582 (t) cc_final: 0.7314 (p) REVERT: A 432 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: A 441 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5240 (tt0) REVERT: A 464 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6659 (ttp-110) REVERT: A 497 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5840 (p0) REVERT: A 510 MET cc_start: -0.0075 (mtt) cc_final: -0.1103 (ptm) REVERT: B 46 ARG cc_start: 0.5578 (ttm-80) cc_final: 0.5268 (ttm-80) REVERT: B 58 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7847 (tpt-90) REVERT: B 59 ILE cc_start: 0.7945 (tp) cc_final: 0.7577 (pt) REVERT: B 83 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7419 (mtm110) REVERT: B 86 ARG cc_start: 0.6741 (mtp180) cc_final: 0.5866 (ptt180) REVERT: B 93 ASP cc_start: 0.7872 (t0) cc_final: 0.7251 (m-30) REVERT: B 109 PHE cc_start: 0.7490 (m-10) cc_final: 0.7262 (m-80) REVERT: B 115 LYS cc_start: 0.7930 (tppt) cc_final: 0.7712 (tppt) REVERT: B 162 MET cc_start: 0.9081 (tpt) cc_final: 0.8718 (mmm) REVERT: B 248 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 315 ARG cc_start: 0.7076 (mmm160) cc_final: 0.5920 (tpt170) REVERT: B 337 ASP cc_start: 0.7289 (m-30) cc_final: 0.7052 (m-30) REVERT: B 397 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6731 (tp30) REVERT: B 400 ILE cc_start: 0.5522 (OUTLIER) cc_final: 0.5022 (tp) REVERT: B 401 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4664 (mt) REVERT: B 485 MET cc_start: 0.4648 (tpt) cc_final: 0.3757 (mmt) REVERT: B 497 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5157 (p0) REVERT: B 500 MET cc_start: 0.4116 (pp-130) cc_final: 0.2429 (tmm) REVERT: C 103 ASP cc_start: 0.7920 (t70) cc_final: 0.7626 (t0) REVERT: C 122 ASP cc_start: 0.6860 (p0) cc_final: 0.6590 (p0) REVERT: C 125 LYS cc_start: 0.8153 (tptp) cc_final: 0.7428 (mmtm) REVERT: C 177 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7279 (ttp-110) REVERT: C 179 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 183 ASN cc_start: 0.7169 (m-40) cc_final: 0.6661 (t160) REVERT: C 230 ASN cc_start: 0.6361 (m110) cc_final: 0.6003 (p0) REVERT: C 232 LEU cc_start: 0.8725 (mt) cc_final: 0.8521 (mm) REVERT: C 288 MET cc_start: 0.9050 (tpt) cc_final: 0.8755 (tpp) REVERT: C 298 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7014 (ttm-80) REVERT: C 388 MET cc_start: 0.5312 (mtt) cc_final: 0.5074 (mtp) REVERT: C 389 LYS cc_start: 0.6933 (mttp) cc_final: 0.6233 (mptt) REVERT: C 511 LEU cc_start: 0.2922 (OUTLIER) cc_final: 0.2682 (mt) REVERT: C 513 ARG cc_start: -0.0894 (OUTLIER) cc_final: -0.1341 (ppt-90) REVERT: D 56 LYS cc_start: 0.6936 (tmtt) cc_final: 0.6128 (mtmm) REVERT: D 58 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7630 (tpm170) REVERT: D 59 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7518 (pt) REVERT: D 86 ARG cc_start: 0.6721 (mtp180) cc_final: 0.5841 (ptt180) REVERT: D 93 ASP cc_start: 0.7845 (t0) cc_final: 0.7275 (m-30) REVERT: D 105 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8145 (pp) REVERT: D 109 PHE cc_start: 0.7848 (m-10) cc_final: 0.7585 (m-80) REVERT: D 215 ARG cc_start: 0.7333 (ptt180) cc_final: 0.6699 (mtm110) REVERT: D 248 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8441 (mm) REVERT: D 274 MET cc_start: 0.9468 (mtt) cc_final: 0.9246 (mtm) REVERT: D 294 HIS cc_start: 0.6799 (m-70) cc_final: 0.6497 (m-70) REVERT: D 317 HIS cc_start: 0.5122 (OUTLIER) cc_final: 0.4319 (p-80) REVERT: D 333 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.6014 (ttpp) REVERT: D 395 PRO cc_start: 0.7473 (Cg_endo) cc_final: 0.7222 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6869 (tp30) REVERT: D 400 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.4730 (tp) outliers start: 79 outliers final: 32 residues processed: 263 average time/residue: 0.5983 time to fit residues: 174.3412 Evaluate side-chains 248 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 150 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN B 218 ASN B 294 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.225180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132059 restraints weight = 15920.766| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.77 r_work: 0.3240 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15846 Z= 0.155 Angle : 0.620 10.213 21476 Z= 0.320 Chirality : 0.044 0.198 2422 Planarity : 0.004 0.049 2688 Dihedral : 8.565 84.623 2206 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.95 % Allowed : 27.35 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1870 helix: 0.41 (0.15), residues: 1150 sheet: -1.28 (0.50), residues: 100 loop : -0.37 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 182 TYR 0.026 0.002 TYR B 364 PHE 0.021 0.001 PHE A 409 TRP 0.015 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (15846) covalent geometry : angle 0.62004 / 0.32 (21476) hydrogen bonds : bond 0.05425 / 3.60 ( 818) hydrogen bonds : angle 4.48142 / 3.19 ( 2361) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 199 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7824 (t70) cc_final: 0.7541 (t0) REVERT: A 106 MET cc_start: 0.7339 (tmm) cc_final: 0.6960 (tmm) REVERT: A 119 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7079 (mt) REVERT: A 122 ASP cc_start: 0.6867 (p0) cc_final: 0.6539 (p0) REVERT: A 125 LYS cc_start: 0.6422 (tppt) cc_final: 0.5894 (ttmm) REVERT: A 151 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.5226 (ppt170) REVERT: A 162 MET cc_start: 0.8573 (tpt) cc_final: 0.8154 (mmm) REVERT: A 183 ASN cc_start: 0.7191 (m-40) cc_final: 0.6448 (t160) REVERT: A 267 MET cc_start: 0.9008 (mtt) cc_final: 0.8697 (mtm) REVERT: A 298 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7383 (ttm-80) REVERT: A 356 SER cc_start: 0.7476 (t) cc_final: 0.7210 (p) REVERT: A 381 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5642 (pp) REVERT: A 432 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: A 441 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.5021 (tt0) REVERT: A 464 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6409 (ttp-110) REVERT: A 497 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.5903 (p0) REVERT: A 510 MET cc_start: -0.0327 (mtt) cc_final: -0.1175 (ptm) REVERT: B 46 ARG cc_start: 0.5522 (ttm-80) cc_final: 0.5231 (ttm-80) REVERT: B 58 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7680 (tpt-90) REVERT: B 59 ILE cc_start: 0.7785 (tp) cc_final: 0.7386 (pt) REVERT: B 83 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7177 (mtm110) REVERT: B 86 ARG cc_start: 0.6589 (mtp180) cc_final: 0.5727 (ptt180) REVERT: B 93 ASP cc_start: 0.7691 (t0) cc_final: 0.7024 (m-30) REVERT: B 109 PHE cc_start: 0.7104 (m-10) cc_final: 0.6886 (m-80) REVERT: B 115 LYS cc_start: 0.7908 (tppt) cc_final: 0.7679 (tppt) REVERT: B 248 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8615 (mt) REVERT: B 315 ARG cc_start: 0.7091 (mmm160) cc_final: 0.5930 (tpt170) REVERT: B 337 ASP cc_start: 0.7083 (m-30) cc_final: 0.6843 (m-30) REVERT: B 397 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6694 (tp30) REVERT: B 400 ILE cc_start: 0.5302 (OUTLIER) cc_final: 0.4900 (tp) REVERT: B 485 MET cc_start: 0.4502 (tpt) cc_final: 0.3705 (mmt) REVERT: B 500 MET cc_start: 0.4377 (pp-130) cc_final: 0.3089 (tmm) REVERT: C 103 ASP cc_start: 0.7675 (t70) cc_final: 0.7386 (t0) REVERT: C 125 LYS cc_start: 0.8085 (tptp) cc_final: 0.7343 (mmtm) REVERT: C 155 GLN cc_start: 0.7844 (mm110) cc_final: 0.7405 (mp10) REVERT: C 177 ARG cc_start: 0.7251 (mtm110) cc_final: 0.7008 (ttp-110) REVERT: C 179 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7190 (mm-30) REVERT: C 183 ASN cc_start: 0.7049 (m-40) cc_final: 0.6516 (t160) REVERT: C 185 ASN cc_start: 0.6962 (m-40) cc_final: 0.6134 (t0) REVERT: C 230 ASN cc_start: 0.6243 (m110) cc_final: 0.5882 (p0) REVERT: C 232 LEU cc_start: 0.8565 (mt) cc_final: 0.8312 (mm) REVERT: C 288 MET cc_start: 0.8820 (tpt) cc_final: 0.8494 (tpp) REVERT: C 298 ARG cc_start: 0.7405 (mtp-110) cc_final: 0.6723 (ttm-80) REVERT: C 368 ASP cc_start: 0.6160 (p0) cc_final: 0.5944 (p0) REVERT: C 388 MET cc_start: 0.5061 (mtt) cc_final: 0.4749 (mtp) REVERT: C 392 TYR cc_start: 0.7833 (m-80) cc_final: 0.7587 (m-80) REVERT: C 472 ASN cc_start: 0.5660 (OUTLIER) cc_final: 0.5452 (p0) REVERT: C 511 LEU cc_start: 0.2902 (OUTLIER) cc_final: 0.2697 (mt) REVERT: C 513 ARG cc_start: -0.1393 (OUTLIER) cc_final: -0.1735 (ppt-90) REVERT: D 58 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7398 (tpm170) REVERT: D 59 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7250 (pt) REVERT: D 86 ARG cc_start: 0.6577 (mtp180) cc_final: 0.5696 (ptt180) REVERT: D 93 ASP cc_start: 0.7641 (t0) cc_final: 0.6995 (m-30) REVERT: D 105 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8004 (pp) REVERT: D 109 PHE cc_start: 0.7513 (m-10) cc_final: 0.7250 (m-80) REVERT: D 215 ARG cc_start: 0.7084 (ptt180) cc_final: 0.6448 (mtm110) REVERT: D 248 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8330 (mm) REVERT: D 294 HIS cc_start: 0.6654 (m-70) cc_final: 0.6356 (m-70) REVERT: D 317 HIS cc_start: 0.5012 (OUTLIER) cc_final: 0.4238 (p-80) REVERT: D 333 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5863 (ttpp) REVERT: D 387 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7360 (pt0) REVERT: D 395 PRO cc_start: 0.7437 (Cg_endo) cc_final: 0.7169 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5237 (OUTLIER) cc_final: 0.4876 (tp) REVERT: D 500 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.5213 (tmm) outliers start: 83 outliers final: 39 residues processed: 265 average time/residue: 0.5614 time to fit residues: 165.7243 Evaluate side-chains 253 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.224201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132864 restraints weight = 15964.413| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.36 r_work: 0.3139 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15846 Z= 0.209 Angle : 0.657 10.438 21476 Z= 0.339 Chirality : 0.046 0.210 2422 Planarity : 0.004 0.045 2688 Dihedral : 8.663 84.155 2204 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.01 % Allowed : 27.23 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1870 helix: 0.31 (0.15), residues: 1146 sheet: -1.28 (0.51), residues: 100 loop : -0.38 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 182 TYR 0.026 0.002 TYR B 364 PHE 0.020 0.002 PHE A 409 TRP 0.019 0.003 TRP A 246 HIS 0.007 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (15846) covalent geometry : angle 0.65731 / 0.34 (21476) hydrogen bonds : bond 0.05985 / 3.98 ( 818) hydrogen bonds : angle 4.57194 / 3.26 ( 2361) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8002 (t70) cc_final: 0.7767 (t0) REVERT: A 119 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7146 (mt) REVERT: A 122 ASP cc_start: 0.7037 (p0) cc_final: 0.6700 (p0) REVERT: A 151 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.5314 (ppt170) REVERT: A 162 MET cc_start: 0.8721 (tpt) cc_final: 0.8303 (mmm) REVERT: A 183 ASN cc_start: 0.7315 (m-40) cc_final: 0.6610 (t160) REVERT: A 267 MET cc_start: 0.9093 (mtt) cc_final: 0.8806 (mtm) REVERT: A 298 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7558 (ttm-80) REVERT: A 356 SER cc_start: 0.7544 (t) cc_final: 0.7280 (p) REVERT: A 432 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: A 441 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5164 (tt0) REVERT: A 497 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.5925 (p0) REVERT: A 510 MET cc_start: -0.0281 (mtt) cc_final: -0.1181 (ptm) REVERT: B 46 ARG cc_start: 0.5698 (ttm-80) cc_final: 0.5319 (ttm-80) REVERT: B 58 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7786 (tpt-90) REVERT: B 59 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7479 (pt) REVERT: B 83 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7417 (mtm110) REVERT: B 86 ARG cc_start: 0.6780 (mtp180) cc_final: 0.5934 (ptt180) REVERT: B 93 ASP cc_start: 0.7861 (t0) cc_final: 0.7237 (m-30) REVERT: B 109 PHE cc_start: 0.7385 (m-10) cc_final: 0.7162 (m-80) REVERT: B 115 LYS cc_start: 0.7925 (tppt) cc_final: 0.7695 (tppt) REVERT: B 248 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8727 (mt) REVERT: B 330 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6606 (mm) REVERT: B 337 ASP cc_start: 0.7283 (m-30) cc_final: 0.7047 (m-30) REVERT: B 400 ILE cc_start: 0.5242 (OUTLIER) cc_final: 0.5003 (tp) REVERT: B 485 MET cc_start: 0.4506 (tpt) cc_final: 0.3696 (mmp) REVERT: B 500 MET cc_start: 0.4295 (pp-130) cc_final: 0.3044 (tmm) REVERT: C 58 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6110 (mpt-90) REVERT: C 155 GLN cc_start: 0.7879 (mm110) cc_final: 0.7451 (mp10) REVERT: C 177 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7202 (ttp-110) REVERT: C 179 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7463 (mm-30) REVERT: C 183 ASN cc_start: 0.7184 (m-40) cc_final: 0.6599 (t160) REVERT: C 185 ASN cc_start: 0.7118 (m-40) cc_final: 0.6301 (t0) REVERT: C 230 ASN cc_start: 0.6389 (m110) cc_final: 0.6001 (p0) REVERT: C 232 LEU cc_start: 0.8652 (mt) cc_final: 0.8387 (mm) REVERT: C 288 MET cc_start: 0.8971 (tpt) cc_final: 0.8659 (tpp) REVERT: C 298 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.6939 (ttm-80) REVERT: C 388 MET cc_start: 0.5269 (mtt) cc_final: 0.5069 (mtp) REVERT: C 432 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6273 (pp20) REVERT: C 511 LEU cc_start: 0.2926 (OUTLIER) cc_final: 0.2678 (mt) REVERT: C 513 ARG cc_start: -0.1363 (OUTLIER) cc_final: -0.1780 (ppt-90) REVERT: D 58 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7539 (tpm170) REVERT: D 86 ARG cc_start: 0.6718 (mtp180) cc_final: 0.5817 (ptt180) REVERT: D 93 ASP cc_start: 0.7815 (t0) cc_final: 0.7262 (m-30) REVERT: D 105 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8138 (pp) REVERT: D 109 PHE cc_start: 0.7753 (m-10) cc_final: 0.7491 (m-80) REVERT: D 215 ARG cc_start: 0.7224 (ptt180) cc_final: 0.6644 (mtm110) REVERT: D 248 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8475 (mt) REVERT: D 294 HIS cc_start: 0.6813 (m-70) cc_final: 0.6510 (m-70) REVERT: D 317 HIS cc_start: 0.5055 (OUTLIER) cc_final: 0.4296 (p-80) REVERT: D 333 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5980 (ttpp) REVERT: D 395 PRO cc_start: 0.7489 (Cg_endo) cc_final: 0.7216 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4770 (tp) REVERT: D 495 MET cc_start: 0.5077 (pp-130) cc_final: 0.4867 (tmm) outliers start: 84 outliers final: 48 residues processed: 251 average time/residue: 0.5946 time to fit residues: 164.9875 Evaluate side-chains 253 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 119 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.226635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134623 restraints weight = 16013.625| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.93 r_work: 0.3253 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15846 Z= 0.127 Angle : 0.598 11.090 21476 Z= 0.309 Chirality : 0.042 0.205 2422 Planarity : 0.004 0.055 2688 Dihedral : 8.306 82.769 2204 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.11 % Allowed : 28.43 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1870 helix: 0.56 (0.15), residues: 1160 sheet: -1.22 (0.50), residues: 100 loop : -0.41 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 182 TYR 0.026 0.001 TYR B 364 PHE 0.021 0.001 PHE A 409 TRP 0.019 0.002 TRP B 135 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (15846) covalent geometry : angle 0.59800 / 0.31 (21476) hydrogen bonds : bond 0.04923 / 3.25 ( 818) hydrogen bonds : angle 4.36123 / 3.10 ( 2361) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7271 (tmm) cc_final: 0.6913 (tmm) REVERT: A 119 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6932 (mt) REVERT: A 122 ASP cc_start: 0.6919 (p0) cc_final: 0.6604 (p0) REVERT: A 151 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5276 (ppt170) REVERT: A 162 MET cc_start: 0.8641 (tpt) cc_final: 0.8233 (mmm) REVERT: A 183 ASN cc_start: 0.7202 (m-40) cc_final: 0.6489 (t160) REVERT: A 267 MET cc_start: 0.9008 (mtt) cc_final: 0.8694 (mtm) REVERT: A 298 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7327 (ttt180) REVERT: A 356 SER cc_start: 0.7459 (t) cc_final: 0.7155 (p) REVERT: A 441 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5078 (tt0) REVERT: A 497 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.6017 (p0) REVERT: A 510 MET cc_start: 0.0170 (mtt) cc_final: -0.0761 (ptm) REVERT: B 46 ARG cc_start: 0.5608 (ttm-80) cc_final: 0.5240 (ttm-80) REVERT: B 58 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7721 (tpt-90) REVERT: B 59 ILE cc_start: 0.7738 (tp) cc_final: 0.7386 (pt) REVERT: B 83 ARG cc_start: 0.7649 (ptp-110) cc_final: 0.7249 (mtm110) REVERT: B 86 ARG cc_start: 0.6467 (mtp180) cc_final: 0.5632 (ptt180) REVERT: B 93 ASP cc_start: 0.7662 (t0) cc_final: 0.7038 (m-30) REVERT: B 109 PHE cc_start: 0.7122 (m-10) cc_final: 0.6912 (m-80) REVERT: B 115 LYS cc_start: 0.7908 (tppt) cc_final: 0.7680 (tppt) REVERT: B 315 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6019 (tpt170) REVERT: B 317 HIS cc_start: 0.5463 (OUTLIER) cc_final: 0.4697 (p-80) REVERT: B 337 ASP cc_start: 0.7100 (m-30) cc_final: 0.6854 (m-30) REVERT: B 485 MET cc_start: 0.4290 (tpt) cc_final: 0.3561 (mmp) REVERT: B 500 MET cc_start: 0.4288 (pp-130) cc_final: 0.2221 (tmm) REVERT: C 103 ASP cc_start: 0.7744 (t70) cc_final: 0.7490 (t0) REVERT: C 179 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7178 (mm-30) REVERT: C 183 ASN cc_start: 0.7186 (m-40) cc_final: 0.6537 (t160) REVERT: C 185 ASN cc_start: 0.6841 (m-40) cc_final: 0.6096 (t0) REVERT: C 230 ASN cc_start: 0.6183 (m110) cc_final: 0.5826 (p0) REVERT: C 232 LEU cc_start: 0.8597 (mt) cc_final: 0.8359 (mm) REVERT: C 288 MET cc_start: 0.8889 (tpt) cc_final: 0.8534 (tpp) REVERT: C 298 ARG cc_start: 0.7432 (mtp-110) cc_final: 0.6834 (ttm-80) REVERT: C 388 MET cc_start: 0.5103 (mtt) cc_final: 0.4873 (mtp) REVERT: C 392 TYR cc_start: 0.7859 (m-80) cc_final: 0.7567 (m-80) REVERT: C 513 ARG cc_start: -0.1279 (OUTLIER) cc_final: -0.1742 (ppt-90) REVERT: D 58 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7592 (mmt90) REVERT: D 59 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7390 (pt) REVERT: D 86 ARG cc_start: 0.6543 (mtp180) cc_final: 0.5675 (ptt180) REVERT: D 93 ASP cc_start: 0.7648 (t0) cc_final: 0.7036 (m-30) REVERT: D 105 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8029 (pp) REVERT: D 109 PHE cc_start: 0.7543 (m-10) cc_final: 0.7284 (m-80) REVERT: D 215 ARG cc_start: 0.6989 (ptt180) cc_final: 0.6434 (mmm160) REVERT: D 248 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8300 (mm) REVERT: D 274 MET cc_start: 0.9358 (mtt) cc_final: 0.9158 (mtm) REVERT: D 294 HIS cc_start: 0.6629 (m-70) cc_final: 0.6330 (m-70) REVERT: D 317 HIS cc_start: 0.5008 (OUTLIER) cc_final: 0.4260 (p-80) REVERT: D 330 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6416 (mm) REVERT: D 387 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7420 (pt0) REVERT: D 395 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.7143 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5029 (OUTLIER) cc_final: 0.4688 (tp) REVERT: D 495 MET cc_start: 0.5153 (pp-130) cc_final: 0.4744 (tmm) REVERT: D 500 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.5185 (tmm) outliers start: 69 outliers final: 37 residues processed: 250 average time/residue: 0.5554 time to fit residues: 154.2267 Evaluate side-chains 240 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 102 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.226015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132707 restraints weight = 15967.472| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.77 r_work: 0.3231 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15846 Z= 0.151 Angle : 0.635 11.361 21476 Z= 0.324 Chirality : 0.044 0.213 2422 Planarity : 0.004 0.054 2688 Dihedral : 8.114 82.563 2201 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.58 % Allowed : 29.08 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1870 helix: 0.59 (0.15), residues: 1156 sheet: -1.12 (0.50), residues: 100 loop : -0.37 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 182 TYR 0.025 0.002 TYR B 364 PHE 0.012 0.001 PHE D 272 TRP 0.015 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (15846) covalent geometry : angle 0.63463 / 0.32 (21476) hydrogen bonds : bond 0.05246 / 3.48 ( 818) hydrogen bonds : angle 4.38577 / 3.12 ( 2361) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7238 (tmm) cc_final: 0.6866 (tmm) REVERT: A 119 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6928 (mt) REVERT: A 151 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5260 (ppt170) REVERT: A 162 MET cc_start: 0.8604 (tpt) cc_final: 0.8207 (mmm) REVERT: A 183 ASN cc_start: 0.7189 (m-40) cc_final: 0.6466 (t160) REVERT: A 233 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7794 (mm-30) REVERT: A 267 MET cc_start: 0.9000 (mtt) cc_final: 0.8681 (mtm) REVERT: A 298 ARG cc_start: 0.7802 (ttp-170) cc_final: 0.7392 (ttt90) REVERT: A 356 SER cc_start: 0.7446 (t) cc_final: 0.7143 (p) REVERT: A 441 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.4953 (tt0) REVERT: A 497 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5924 (p0) REVERT: A 510 MET cc_start: 0.0146 (mtt) cc_final: -0.0783 (ptm) REVERT: B 46 ARG cc_start: 0.5563 (ttm-80) cc_final: 0.5219 (ttm-80) REVERT: B 58 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7678 (tpt-90) REVERT: B 59 ILE cc_start: 0.7829 (tp) cc_final: 0.7506 (pt) REVERT: B 83 ARG cc_start: 0.7641 (ptp-110) cc_final: 0.7233 (mtm110) REVERT: B 86 ARG cc_start: 0.6377 (mtp180) cc_final: 0.5563 (ptt180) REVERT: B 93 ASP cc_start: 0.7563 (t0) cc_final: 0.6959 (m-30) REVERT: B 109 PHE cc_start: 0.7055 (m-10) cc_final: 0.6847 (m-80) REVERT: B 115 LYS cc_start: 0.7926 (tppt) cc_final: 0.7704 (tppt) REVERT: B 162 MET cc_start: 0.9001 (tpt) cc_final: 0.8645 (mmm) REVERT: B 248 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8605 (mt) REVERT: B 315 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6017 (tpt170) REVERT: B 317 HIS cc_start: 0.5461 (OUTLIER) cc_final: 0.4732 (p-80) REVERT: B 337 ASP cc_start: 0.6971 (m-30) cc_final: 0.6730 (m-30) REVERT: B 397 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6897 (tp30) REVERT: B 485 MET cc_start: 0.4332 (tpt) cc_final: 0.3613 (mmp) REVERT: B 500 MET cc_start: 0.4027 (pp-130) cc_final: 0.3050 (tmm) REVERT: C 103 ASP cc_start: 0.7701 (t70) cc_final: 0.7458 (t0) REVERT: C 179 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 181 ASP cc_start: 0.7818 (t0) cc_final: 0.7234 (t0) REVERT: C 183 ASN cc_start: 0.7158 (m-40) cc_final: 0.6488 (t160) REVERT: C 185 ASN cc_start: 0.7000 (m-40) cc_final: 0.6233 (t0) REVERT: C 230 ASN cc_start: 0.6175 (m110) cc_final: 0.5819 (p0) REVERT: C 232 LEU cc_start: 0.8551 (mt) cc_final: 0.8267 (mm) REVERT: C 288 MET cc_start: 0.8875 (tpt) cc_final: 0.8479 (tpp) REVERT: C 298 ARG cc_start: 0.7360 (mtp-110) cc_final: 0.6765 (ttm-80) REVERT: C 388 MET cc_start: 0.4990 (mtt) cc_final: 0.4731 (mtp) REVERT: C 392 TYR cc_start: 0.7828 (m-80) cc_final: 0.7545 (m-80) REVERT: C 432 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6261 (pp20) REVERT: C 513 ARG cc_start: -0.1448 (OUTLIER) cc_final: -0.1942 (ppt90) REVERT: D 58 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7390 (tpm170) REVERT: D 59 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7240 (pt) REVERT: D 86 ARG cc_start: 0.6483 (mtp180) cc_final: 0.5609 (ptt180) REVERT: D 93 ASP cc_start: 0.7545 (t0) cc_final: 0.6895 (m-30) REVERT: D 105 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8011 (pp) REVERT: D 109 PHE cc_start: 0.7474 (m-10) cc_final: 0.7221 (m-80) REVERT: D 215 ARG cc_start: 0.6962 (ptt180) cc_final: 0.6380 (mmm160) REVERT: D 294 HIS cc_start: 0.6621 (m-70) cc_final: 0.6309 (m-70) REVERT: D 317 HIS cc_start: 0.5047 (OUTLIER) cc_final: 0.4325 (p-80) REVERT: D 330 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6345 (mm) REVERT: D 387 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7482 (pt0) REVERT: D 395 PRO cc_start: 0.7375 (Cg_endo) cc_final: 0.7100 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5056 (OUTLIER) cc_final: 0.4729 (tp) outliers start: 60 outliers final: 38 residues processed: 236 average time/residue: 0.5338 time to fit residues: 140.0546 Evaluate side-chains 241 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 150 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.225406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133401 restraints weight = 15870.253| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.00 r_work: 0.3197 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15846 Z= 0.174 Angle : 0.651 11.291 21476 Z= 0.332 Chirality : 0.045 0.217 2422 Planarity : 0.004 0.052 2688 Dihedral : 8.180 82.597 2201 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.75 % Allowed : 28.96 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1870 helix: 0.52 (0.15), residues: 1156 sheet: -1.07 (0.51), residues: 100 loop : -0.35 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 182 TYR 0.026 0.002 TYR D 364 PHE 0.015 0.001 PHE B 272 TRP 0.016 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (15846) covalent geometry : angle 0.65080 / 0.33 (21476) hydrogen bonds : bond 0.05489 / 3.64 ( 818) hydrogen bonds : angle 4.42550 / 3.15 ( 2361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7542.78 seconds wall clock time: 128 minutes 51.09 seconds (7731.09 seconds total)