Starting phenix.real_space_refine on Wed Mar 4 19:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm2_32598/03_2026/7wm2_32598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm2_32598/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wm2_32598/03_2026/7wm2_32598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm2_32598/03_2026/7wm2_32598.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wm2_32598/03_2026/7wm2_32598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm2_32598/03_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-5986/lib/python3.9/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: 3.30, per 1000 atoms: 0.21 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: 1.17 Conformation dependent library (CDL) restraints added in 670.7 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: 0.50 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: 2.37 Time building geometry restraints manager: 1.49 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: 7999 17.87 - 35.75: 1055 35.75 - 53.62: 291 53.62 - 71.49: 71 71.49 - 89.37: 24 Dihedral angle restraints: 9440 sinusoidal: 3878 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 9437 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 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 : 18.172 89.366 5836 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 covalent geometry : bond 0.01167 (15846) covalent geometry : angle 1.03477 (21476) hydrogen bonds : bond 0.28070 ( 818) hydrogen bonds : angle 9.73045 ( 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 : 0.549 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: 0.5584 time to fit residues: 263.5633 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 : 0.565 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 383 GLN D 477 ASN D 491 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.223628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133599 restraints weight = 16089.333| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.99 r_work: 0.3252 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15846 Z= 0.171 Angle : 0.720 9.614 21476 Z= 0.378 Chirality : 0.045 0.178 2422 Planarity : 0.005 0.036 2688 Dihedral : 12.137 93.227 2384 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.96 % Allowed : 27.12 % Favored : 66.92 % 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: -1.88 (0.18), residues: 1870 helix: -0.97 (0.14), residues: 1146 sheet: -2.26 (0.49), residues: 102 loop : -1.25 (0.25), residues: 622 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 0.015 0.001 PHE B 382 TRP 0.014 0.002 TRP B 135 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00347 (15846) covalent geometry : angle 0.72014 (21476) hydrogen bonds : bond 0.06986 ( 818) hydrogen bonds : angle 5.34936 ( 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 328 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 228 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7785 (t70) cc_final: 0.7511 (t0) REVERT: A 155 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7417 (mp10) REVERT: A 162 MET cc_start: 0.8756 (tpt) cc_final: 0.8201 (mmm) REVERT: A 183 ASN cc_start: 0.7033 (m-40) cc_final: 0.6394 (t160) REVERT: A 194 LEU cc_start: 0.8253 (mt) cc_final: 0.7997 (mt) REVERT: A 232 LEU cc_start: 0.8796 (mt) cc_final: 0.8559 (mm) REVERT: A 249 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8461 (m) REVERT: A 267 MET cc_start: 0.8992 (mtt) cc_final: 0.8690 (mtm) REVERT: A 298 ARG cc_start: 0.8072 (ttp-170) cc_final: 0.7642 (ttm-80) REVERT: A 339 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5730 (mt-10) REVERT: A 510 MET cc_start: 0.0520 (mtt) cc_final: -0.0593 (ptm) REVERT: B 46 ARG cc_start: 0.5614 (ttm-80) cc_final: 0.5230 (ttm-80) REVERT: B 83 ARG cc_start: 0.7788 (ptp-110) cc_final: 0.7381 (mtm110) REVERT: B 86 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6218 (ptt180) REVERT: B 93 ASP cc_start: 0.7743 (t0) cc_final: 0.7024 (m-30) REVERT: B 105 ILE cc_start: 0.8158 (mt) cc_final: 0.7925 (mt) REVERT: B 109 PHE cc_start: 0.7497 (m-10) cc_final: 0.7222 (m-80) REVERT: B 133 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6434 (mtm-85) REVERT: B 307 GLN cc_start: 0.7568 (pp30) cc_final: 0.7316 (tp40) REVERT: B 337 ASP cc_start: 0.7309 (m-30) cc_final: 0.7069 (m-30) REVERT: B 344 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 352 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5218 (tmtt) REVERT: B 397 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: B 401 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4958 (mt) REVERT: B 485 MET cc_start: 0.4550 (tpt) cc_final: 0.3575 (mmt) REVERT: B 495 MET cc_start: 0.5796 (ttm) cc_final: 0.5571 (tpp) REVERT: C 93 ASP cc_start: 0.8224 (t0) cc_final: 0.7954 (m-30) REVERT: C 103 ASP cc_start: 0.7928 (t70) cc_final: 0.7583 (t0) REVERT: C 113 LEU cc_start: 0.7706 (mm) cc_final: 0.7393 (tp) REVERT: C 122 ASP cc_start: 0.6695 (p0) cc_final: 0.6412 (p0) REVERT: C 151 ARG cc_start: 0.7522 (ttm110) cc_final: 0.6954 (ppt170) REVERT: C 155 GLN cc_start: 0.7873 (mm110) cc_final: 0.7409 (mp10) REVERT: C 177 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7161 (ttp-110) REVERT: C 183 ASN cc_start: 0.7194 (m-40) cc_final: 0.6868 (t160) REVERT: C 194 LEU cc_start: 0.8064 (mt) cc_final: 0.7843 (mt) REVERT: C 230 ASN cc_start: 0.6387 (m110) cc_final: 0.6085 (p0) REVERT: C 267 MET cc_start: 0.8988 (mtt) cc_final: 0.8653 (mtm) REVERT: C 288 MET cc_start: 0.8872 (tpt) cc_final: 0.8544 (tpp) REVERT: C 298 ARG cc_start: 0.7464 (mtp-110) cc_final: 0.6819 (ttm-80) REVERT: C 343 GLN cc_start: 0.5198 (OUTLIER) cc_final: 0.4288 (pp30) REVERT: C 388 MET cc_start: 0.5714 (mtt) cc_final: 0.5443 (mtp) REVERT: C 401 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6672 (pp) REVERT: D 56 LYS cc_start: 0.6864 (tmtt) cc_final: 0.6337 (mttp) REVERT: D 58 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7802 (ttm170) REVERT: D 86 ARG cc_start: 0.6791 (mtp180) cc_final: 0.6043 (ptt180) REVERT: D 93 ASP cc_start: 0.7746 (t0) cc_final: 0.7010 (m-30) REVERT: D 105 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8053 (pt) REVERT: D 109 PHE cc_start: 0.7827 (m-10) cc_final: 0.7595 (m-80) REVERT: D 125 LYS cc_start: 0.7579 (mmtt) cc_final: 0.6497 (tttt) REVERT: D 162 MET cc_start: 0.9091 (tpt) cc_final: 0.8569 (mmm) REVERT: D 215 ARG cc_start: 0.7200 (ptt180) cc_final: 0.6768 (mtm110) REVERT: D 294 HIS cc_start: 0.6728 (m-70) cc_final: 0.6458 (m-70) REVERT: D 307 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7148 (mm110) REVERT: D 317 HIS cc_start: 0.5344 (OUTLIER) cc_final: 0.4611 (p-80) REVERT: D 330 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6710 (mm) REVERT: D 333 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5633 (tptp) REVERT: D 348 ASP cc_start: 0.6831 (p0) cc_final: 0.6535 (p0) REVERT: D 384 LEU cc_start: 0.4792 (OUTLIER) cc_final: 0.4464 (mm) REVERT: D 395 PRO cc_start: 0.7460 (Cg_endo) cc_final: 0.7147 (Cg_exo) REVERT: D 432 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.4985 (pm20) REVERT: D 506 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4934 (pp20) outliers start: 100 outliers final: 27 residues processed: 309 average time/residue: 0.5390 time to fit residues: 184.9942 Evaluate side-chains 248 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain A residue 251 LEU 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 412 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 228 VAL Chi-restraints excluded: chain C residue 304 ASP 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: 0.9980 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 383 GLN A 402 GLN A 403 ASN A 472 ASN B 218 ASN B 294 HIS B 343 GLN B 491 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 360 HIS C 472 ASN D 343 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.224928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136100 restraints weight = 16237.338| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.15 r_work: 0.3229 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15846 Z= 0.144 Angle : 0.634 12.325 21476 Z= 0.327 Chirality : 0.044 0.316 2422 Planarity : 0.004 0.035 2688 Dihedral : 10.236 83.096 2265 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.90 % Allowed : 27.12 % 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: -0.82 (0.19), residues: 1870 helix: -0.12 (0.15), residues: 1146 sheet: -1.81 (0.49), residues: 102 loop : -0.86 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.015 0.001 TYR D 245 PHE 0.020 0.001 PHE A 409 TRP 0.014 0.002 TRP A 246 HIS 0.006 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00312 (15846) covalent geometry : angle 0.63373 (21476) hydrogen bonds : bond 0.05785 ( 818) hydrogen bonds : angle 4.76818 ( 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 312 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 213 time to evaluate : 0.586 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: 0.7944 (t70) cc_final: 0.7711 (t0) REVERT: A 119 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7167 (mt) REVERT: A 122 ASP cc_start: 0.6906 (p0) cc_final: 0.6582 (p0) REVERT: A 151 ARG cc_start: 0.6317 (ppt170) cc_final: 0.6108 (ppt170) REVERT: A 155 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7407 (mp10) REVERT: A 159 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 162 MET cc_start: 0.8762 (tpt) cc_final: 0.8397 (tpt) REVERT: A 183 ASN cc_start: 0.7122 (m-40) cc_final: 0.6382 (t160) REVERT: A 267 MET cc_start: 0.9061 (mtt) cc_final: 0.8799 (mtm) REVERT: A 298 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7704 (ttm-80) REVERT: A 339 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5774 (mt-10) REVERT: A 356 SER cc_start: 0.7471 (t) cc_final: 0.7217 (p) REVERT: A 464 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6540 (ttp-110) REVERT: A 510 MET cc_start: 0.0385 (mtt) cc_final: -0.0572 (ptm) REVERT: B 46 ARG cc_start: 0.5628 (ttm-80) cc_final: 0.5270 (ttm-80) REVERT: B 59 ILE cc_start: 0.8075 (tp) cc_final: 0.7642 (pt) REVERT: B 83 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7432 (mtm110) REVERT: B 86 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6053 (ptt180) REVERT: B 93 ASP cc_start: 0.7852 (t0) cc_final: 0.7155 (m-30) REVERT: B 105 ILE cc_start: 0.8178 (mt) cc_final: 0.7951 (mt) REVERT: B 109 PHE cc_start: 0.7620 (m-10) cc_final: 0.7371 (m-80) REVERT: B 162 MET cc_start: 0.9083 (tpt) cc_final: 0.8795 (mmm) REVERT: B 327 LEU cc_start: 0.7118 (mt) cc_final: 0.6902 (mt) REVERT: B 333 LYS cc_start: 0.6122 (tppt) cc_final: 0.5573 (ttpp) REVERT: B 337 ASP cc_start: 0.7219 (m-30) cc_final: 0.6967 (m-30) REVERT: B 352 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6267 (tppt) REVERT: B 401 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4861 (mt) REVERT: B 485 MET cc_start: 0.4513 (tpt) cc_final: 0.3618 (mmt) REVERT: B 500 MET cc_start: 0.3556 (ppp) cc_final: 0.3155 (pp-130) REVERT: C 93 ASP cc_start: 0.8300 (t0) cc_final: 0.8069 (m-30) REVERT: C 103 ASP cc_start: 0.7999 (t70) cc_final: 0.7661 (t0) REVERT: C 113 LEU cc_start: 0.7796 (mm) cc_final: 0.7527 (tp) REVERT: C 122 ASP cc_start: 0.6567 (p0) cc_final: 0.6251 (p0) REVERT: C 151 ARG cc_start: 0.7480 (ttm110) cc_final: 0.6968 (ppt170) REVERT: C 155 GLN cc_start: 0.7905 (mm110) cc_final: 0.7421 (mp10) REVERT: C 177 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7403 (ttp-110) REVERT: C 179 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7189 (mm-30) REVERT: C 183 ASN cc_start: 0.7232 (m-40) cc_final: 0.6959 (t160) REVERT: C 194 LEU cc_start: 0.8155 (mt) cc_final: 0.7946 (mt) REVERT: C 230 ASN cc_start: 0.6403 (m110) cc_final: 0.6087 (p0) REVERT: C 232 LEU cc_start: 0.8732 (mt) cc_final: 0.8446 (mm) REVERT: C 267 MET cc_start: 0.9076 (mtt) cc_final: 0.8821 (mtm) REVERT: C 288 MET cc_start: 0.8934 (tpt) cc_final: 0.8655 (tpp) REVERT: C 298 ARG cc_start: 0.7597 (mtp-110) cc_final: 0.6944 (ttm-80) REVERT: C 381 LEU cc_start: 0.5517 (OUTLIER) cc_final: 0.5293 (mp) REVERT: C 388 MET cc_start: 0.5448 (mtt) cc_final: 0.5186 (mtp) REVERT: C 401 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6597 (pp) REVERT: D 56 LYS cc_start: 0.7014 (tmtt) cc_final: 0.6325 (mtmm) REVERT: D 58 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7807 (ttm170) REVERT: D 59 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7431 (pt) REVERT: D 86 ARG cc_start: 0.6690 (mtp180) cc_final: 0.5863 (ptt180) REVERT: D 93 ASP cc_start: 0.7821 (t0) cc_final: 0.7112 (m-30) REVERT: D 105 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8038 (pp) REVERT: D 108 PHE cc_start: 0.8268 (m-10) cc_final: 0.8017 (m-80) REVERT: D 109 PHE cc_start: 0.7910 (m-10) cc_final: 0.7653 (m-80) REVERT: D 125 LYS cc_start: 0.7474 (mmtt) cc_final: 0.6388 (tttt) REVERT: D 215 ARG cc_start: 0.7356 (ptt180) cc_final: 0.6880 (mtm110) REVERT: D 248 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8325 (mm) REVERT: D 294 HIS cc_start: 0.6710 (m-70) cc_final: 0.6469 (m-70) REVERT: D 337 ASP cc_start: 0.7356 (t70) cc_final: 0.7142 (m-30) REVERT: D 397 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6833 (tp30) REVERT: D 400 ILE cc_start: 0.5392 (OUTLIER) cc_final: 0.4763 (tp) REVERT: D 401 LEU cc_start: 0.4330 (OUTLIER) cc_final: 0.4017 (mt) outliers start: 99 outliers final: 32 residues processed: 292 average time/residue: 0.5492 time to fit residues: 178.4140 Evaluate side-chains 248 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 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 65 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 439 ILE Chi-restraints excluded: chain C residue 444 VAL 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 311 ASN Chi-restraints excluded: chain D residue 347 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4423 r_free = 0.4423 target = 0.225030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134150 restraints weight = 15962.015| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.17 r_work: 0.3179 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15846 Z= 0.162 Angle : 0.627 9.995 21476 Z= 0.324 Chirality : 0.044 0.322 2422 Planarity : 0.004 0.046 2688 Dihedral : 9.699 87.144 2240 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.78 % Allowed : 27.18 % Favored : 67.04 % 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: -0.52 (0.19), residues: 1870 helix: 0.07 (0.15), residues: 1150 sheet: -1.57 (0.49), residues: 102 loop : -0.67 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 182 TYR 0.021 0.002 TYR D 364 PHE 0.020 0.001 PHE C 409 TRP 0.016 0.002 TRP A 246 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00373 (15846) covalent geometry : angle 0.62689 (21476) hydrogen bonds : bond 0.05756 ( 818) hydrogen bonds : angle 4.64974 ( 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 299 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 202 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7989 (t70) cc_final: 0.7751 (t0) REVERT: A 119 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7083 (mt) REVERT: A 125 LYS cc_start: 0.6442 (tppt) cc_final: 0.5905 (ttmm) REVERT: A 155 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7409 (mp10) REVERT: A 162 MET cc_start: 0.8728 (tpt) cc_final: 0.8295 (mmm) REVERT: A 183 ASN cc_start: 0.7107 (m-40) cc_final: 0.6338 (t160) REVERT: A 267 MET cc_start: 0.9071 (mtt) cc_final: 0.8802 (mtm) REVERT: A 298 ARG cc_start: 0.8072 (ttp-170) cc_final: 0.7630 (ttt90) REVERT: A 356 SER cc_start: 0.7535 (t) cc_final: 0.7281 (p) REVERT: A 464 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6537 (ttp-110) REVERT: A 510 MET cc_start: 0.0143 (mtt) cc_final: -0.0821 (ptm) REVERT: B 46 ARG cc_start: 0.5632 (ttm-80) cc_final: 0.5297 (ttm-80) REVERT: B 59 ILE cc_start: 0.8032 (tp) cc_final: 0.7592 (pt) REVERT: B 83 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7380 (mtm110) REVERT: B 86 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6044 (ptt180) REVERT: B 93 ASP cc_start: 0.7899 (t0) cc_final: 0.7207 (m-30) REVERT: B 109 PHE cc_start: 0.7488 (m-10) cc_final: 0.7251 (m-80) REVERT: B 248 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8685 (mt) REVERT: B 337 ASP cc_start: 0.7204 (m-30) cc_final: 0.6982 (m-30) REVERT: B 397 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6759 (tp30) REVERT: B 401 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4688 (mt) REVERT: B 485 MET cc_start: 0.4467 (tpt) cc_final: 0.3621 (mmt) REVERT: B 500 MET cc_start: 0.3629 (ppp) cc_final: 0.3233 (pp-130) REVERT: C 93 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: C 103 ASP cc_start: 0.7951 (t70) cc_final: 0.7624 (t0) REVERT: C 113 LEU cc_start: 0.7786 (mm) cc_final: 0.7523 (tp) REVERT: C 122 ASP cc_start: 0.6794 (p0) cc_final: 0.6440 (p0) REVERT: C 151 ARG cc_start: 0.7505 (ttm110) cc_final: 0.6949 (ppt170) REVERT: C 155 GLN cc_start: 0.7936 (mm110) cc_final: 0.7453 (mp10) REVERT: C 177 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7347 (ttp-110) REVERT: C 179 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 183 ASN cc_start: 0.7057 (m-40) cc_final: 0.6722 (t160) REVERT: C 194 LEU cc_start: 0.8128 (mt) cc_final: 0.7922 (mt) REVERT: C 230 ASN cc_start: 0.6408 (m110) cc_final: 0.6064 (p0) REVERT: C 232 LEU cc_start: 0.8700 (mt) cc_final: 0.8429 (mm) REVERT: C 267 MET cc_start: 0.9101 (mtt) cc_final: 0.8817 (mtm) REVERT: C 288 MET cc_start: 0.8939 (tpt) cc_final: 0.8676 (tpp) REVERT: C 298 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.6954 (ttm-80) REVERT: C 388 MET cc_start: 0.5247 (mtt) cc_final: 0.4990 (mtp) REVERT: C 389 LYS cc_start: 0.6849 (mttp) cc_final: 0.6170 (mptt) REVERT: C 401 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6549 (pp) REVERT: D 56 LYS cc_start: 0.6887 (tmtt) cc_final: 0.6189 (mtmm) REVERT: D 58 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7731 (ttm170) REVERT: D 59 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7518 (pt) REVERT: D 86 ARG cc_start: 0.6598 (mtp180) cc_final: 0.5789 (ptt180) REVERT: D 93 ASP cc_start: 0.7783 (t0) cc_final: 0.7173 (m-30) REVERT: D 105 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8029 (pp) REVERT: D 108 PHE cc_start: 0.8319 (m-10) cc_final: 0.8112 (m-80) REVERT: D 109 PHE cc_start: 0.7878 (m-10) cc_final: 0.7594 (m-80) REVERT: D 215 ARG cc_start: 0.7291 (ptt180) cc_final: 0.6713 (mtm110) REVERT: D 248 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8357 (mm) REVERT: D 294 HIS cc_start: 0.6750 (m-70) cc_final: 0.6456 (m-70) REVERT: D 337 ASP cc_start: 0.7279 (t70) cc_final: 0.7064 (m-30) REVERT: D 400 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.4740 (tp) REVERT: D 401 LEU cc_start: 0.4347 (OUTLIER) cc_final: 0.4136 (mt) REVERT: D 439 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5663 (pp) outliers start: 97 outliers final: 37 residues processed: 275 average time/residue: 0.5795 time to fit residues: 176.5503 Evaluate side-chains 248 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 VAL 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 150 MET 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 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 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 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 367 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 10.0000 chunk 138 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS B 307 GLN B 472 ASN C 216 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.221615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133029 restraints weight = 15983.575| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.19 r_work: 0.3090 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 15846 Z= 0.337 Angle : 0.766 9.326 21476 Z= 0.395 Chirality : 0.052 0.292 2422 Planarity : 0.005 0.047 2688 Dihedral : 9.803 89.806 2231 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.56 % Allowed : 26.04 % 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: -0.96 (0.19), residues: 1870 helix: -0.35 (0.15), residues: 1148 sheet: -1.50 (0.51), residues: 102 loop : -0.72 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 182 TYR 0.025 0.003 TYR B 364 PHE 0.027 0.002 PHE B 272 TRP 0.026 0.004 TRP A 246 HIS 0.008 0.002 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00829 (15846) covalent geometry : angle 0.76582 (21476) hydrogen bonds : bond 0.07346 ( 818) hydrogen bonds : angle 4.90809 ( 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 311 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 201 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8022 (t70) cc_final: 0.7769 (t0) REVERT: A 119 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7024 (mt) REVERT: A 125 LYS cc_start: 0.6526 (tppt) cc_final: 0.5983 (ttmm) REVERT: A 151 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5399 (ppt170) REVERT: A 162 MET cc_start: 0.8702 (tpt) cc_final: 0.8313 (mmm) REVERT: A 183 ASN cc_start: 0.7302 (m-40) cc_final: 0.6581 (t160) REVERT: A 298 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7805 (tmm-80) REVERT: A 367 MET cc_start: 0.6870 (ttp) cc_final: 0.6594 (ttp) REVERT: A 441 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5745 (tm-30) REVERT: A 497 ASP cc_start: 0.6201 (OUTLIER) cc_final: 0.5947 (p0) REVERT: A 510 MET cc_start: 0.0119 (mtt) cc_final: -0.0854 (ptm) REVERT: B 46 ARG cc_start: 0.5660 (ttm-80) cc_final: 0.5337 (ttm-80) REVERT: B 58 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7845 (tpt-90) REVERT: B 83 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7637 (mtm110) REVERT: B 84 LYS cc_start: 0.8227 (pttm) cc_final: 0.7979 (ptmm) REVERT: B 86 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6093 (ptt180) REVERT: B 93 ASP cc_start: 0.7987 (t0) cc_final: 0.7324 (m-30) REVERT: B 109 PHE cc_start: 0.7603 (m-10) cc_final: 0.7366 (m-80) REVERT: B 115 LYS cc_start: 0.7895 (tppt) cc_final: 0.7692 (tppt) REVERT: B 162 MET cc_start: 0.9153 (tpt) cc_final: 0.8658 (mmm) REVERT: B 190 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8549 (mmm160) REVERT: B 238 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7985 (tmt) REVERT: B 248 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 330 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6522 (mm) REVERT: B 337 ASP cc_start: 0.7382 (m-30) cc_final: 0.7163 (m-30) REVERT: B 397 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: B 400 ILE cc_start: 0.5535 (OUTLIER) cc_final: 0.5039 (tp) REVERT: B 401 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4586 (mt) REVERT: B 485 MET cc_start: 0.4439 (tpt) cc_final: 0.3618 (mmt) REVERT: B 500 MET cc_start: 0.3672 (ppp) cc_final: 0.3296 (pp-130) REVERT: C 103 ASP cc_start: 0.8026 (t70) cc_final: 0.7680 (t0) REVERT: C 122 ASP cc_start: 0.6811 (p0) cc_final: 0.6571 (p0) REVERT: C 155 GLN cc_start: 0.7863 (mm110) cc_final: 0.7444 (mp10) REVERT: C 177 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7352 (ttp-110) REVERT: C 179 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 183 ASN cc_start: 0.7166 (m-40) cc_final: 0.6640 (t160) REVERT: C 230 ASN cc_start: 0.6508 (m110) cc_final: 0.6085 (p0) REVERT: C 288 MET cc_start: 0.9032 (tpt) cc_final: 0.8742 (tpp) REVERT: C 298 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7032 (ttm-80) REVERT: C 388 MET cc_start: 0.5295 (mtt) cc_final: 0.5037 (mtp) REVERT: C 389 LYS cc_start: 0.6825 (mttp) cc_final: 0.6143 (mptt) REVERT: C 432 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6545 (pp20) REVERT: C 472 ASN cc_start: 0.6136 (OUTLIER) cc_final: 0.5880 (p0) REVERT: D 56 LYS cc_start: 0.6955 (tmtt) cc_final: 0.6334 (mtmm) REVERT: D 58 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7815 (ttm170) REVERT: D 86 ARG cc_start: 0.6757 (mtp180) cc_final: 0.5853 (ptt180) REVERT: D 93 ASP cc_start: 0.7878 (t0) cc_final: 0.7210 (m-30) REVERT: D 105 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8277 (pp) REVERT: D 109 PHE cc_start: 0.7894 (m-10) cc_final: 0.7597 (m-80) REVERT: D 215 ARG cc_start: 0.7479 (ptt180) cc_final: 0.6901 (mtm110) REVERT: D 238 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8007 (tmt) REVERT: D 248 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8567 (mt) REVERT: D 330 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6677 (mm) REVERT: D 333 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5693 (tptp) REVERT: D 395 PRO cc_start: 0.7404 (Cg_endo) cc_final: 0.7105 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: D 400 ILE cc_start: 0.5469 (OUTLIER) cc_final: 0.4874 (tp) REVERT: D 401 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.4292 (mt) REVERT: D 439 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5429 (pp) outliers start: 110 outliers final: 47 residues processed: 282 average time/residue: 0.5938 time to fit residues: 184.7778 Evaluate side-chains 267 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 196 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 474 ILE 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 141 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 238 MET 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 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 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 376 VAL 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 472 ASN 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 333 LYS Chi-restraints excluded: chain D residue 356 SER 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 Chi-restraints excluded: chain D residue 439 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** 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 = 0.4426 r_free = 0.4426 target = 0.225514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135247 restraints weight = 15993.973| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.21 r_work: 0.3207 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15846 Z= 0.134 Angle : 0.619 19.114 21476 Z= 0.317 Chirality : 0.043 0.250 2422 Planarity : 0.004 0.053 2688 Dihedral : 9.159 88.925 2229 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 5.01 % Allowed : 27.65 % 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: -0.28 (0.19), residues: 1870 helix: 0.24 (0.15), residues: 1156 sheet: -1.37 (0.51), residues: 100 loop : -0.54 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 182 TYR 0.024 0.002 TYR B 364 PHE 0.021 0.001 PHE A 409 TRP 0.018 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00288 (15846) covalent geometry : angle 0.61916 (21476) hydrogen bonds : bond 0.05248 ( 818) hydrogen bonds : angle 4.53942 ( 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 289 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 205 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7997 (t70) cc_final: 0.7727 (t0) REVERT: A 119 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6917 (mt) REVERT: A 125 LYS cc_start: 0.6468 (tppt) cc_final: 0.5921 (ttmm) REVERT: A 162 MET cc_start: 0.8710 (tpt) cc_final: 0.8360 (mmm) REVERT: A 183 ASN cc_start: 0.7244 (m-40) cc_final: 0.6536 (t160) REVERT: A 267 MET cc_start: 0.9075 (mtt) cc_final: 0.8783 (mtm) REVERT: A 298 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7649 (tmm-80) REVERT: A 441 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5197 (tt0) REVERT: A 464 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6543 (ttp-110) REVERT: A 510 MET cc_start: -0.0172 (mtt) cc_final: -0.1072 (ptm) REVERT: B 46 ARG cc_start: 0.5625 (ttm-80) cc_final: 0.5312 (ttm-80) REVERT: B 58 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7759 (tpt-90) REVERT: B 59 ILE cc_start: 0.7902 (tp) cc_final: 0.7534 (pt) REVERT: B 83 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7416 (mtm110) REVERT: B 86 ARG cc_start: 0.6675 (mtp180) cc_final: 0.5858 (ptt180) REVERT: B 93 ASP cc_start: 0.7795 (t0) cc_final: 0.7177 (m-30) REVERT: B 109 PHE cc_start: 0.7400 (m-10) cc_final: 0.7175 (m-80) REVERT: B 115 LYS cc_start: 0.7929 (tppt) cc_final: 0.7719 (tppt) REVERT: B 162 MET cc_start: 0.9074 (tpt) cc_final: 0.8825 (mmm) REVERT: B 248 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8662 (mt) REVERT: B 315 ARG cc_start: 0.7056 (mmm160) cc_final: 0.5892 (tpt170) REVERT: B 337 ASP cc_start: 0.7173 (m-30) cc_final: 0.6909 (m-30) REVERT: B 397 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: B 400 ILE cc_start: 0.5433 (OUTLIER) cc_final: 0.4939 (tp) REVERT: B 401 LEU cc_start: 0.4674 (OUTLIER) cc_final: 0.4450 (mt) REVERT: B 485 MET cc_start: 0.4517 (tpt) cc_final: 0.3674 (mmt) REVERT: B 500 MET cc_start: 0.3656 (ppp) cc_final: 0.3352 (pp-130) REVERT: C 103 ASP cc_start: 0.7867 (t70) cc_final: 0.7570 (t0) REVERT: C 113 LEU cc_start: 0.7897 (mm) cc_final: 0.7628 (tp) REVERT: C 122 ASP cc_start: 0.6729 (p0) cc_final: 0.6458 (p0) REVERT: C 155 GLN cc_start: 0.7822 (mm110) cc_final: 0.7423 (mp10) REVERT: C 177 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7270 (ttp-110) REVERT: C 179 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 183 ASN cc_start: 0.7217 (m-40) cc_final: 0.6697 (t160) REVERT: C 185 ASN cc_start: 0.7124 (m-40) cc_final: 0.6407 (t0) REVERT: C 230 ASN cc_start: 0.6355 (m110) cc_final: 0.6015 (p0) REVERT: C 232 LEU cc_start: 0.8750 (mt) cc_final: 0.8415 (mm) REVERT: C 267 MET cc_start: 0.9101 (mtt) cc_final: 0.8793 (mtm) REVERT: C 288 MET cc_start: 0.8957 (tpt) cc_final: 0.8710 (tpp) REVERT: C 298 ARG cc_start: 0.7565 (mtp-110) cc_final: 0.6884 (ttm-80) REVERT: C 389 LYS cc_start: 0.6702 (mttp) cc_final: 0.6022 (mptt) REVERT: C 511 LEU cc_start: 0.2889 (OUTLIER) cc_final: 0.2661 (mt) REVERT: C 513 ARG cc_start: -0.1074 (OUTLIER) cc_final: -0.1488 (ppt-90) REVERT: D 56 LYS cc_start: 0.6860 (tmtt) cc_final: 0.6069 (mtmm) REVERT: D 58 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7758 (ttm170) REVERT: D 59 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7534 (pt) REVERT: D 86 ARG cc_start: 0.6681 (mtp180) cc_final: 0.5840 (ptt180) REVERT: D 93 ASP cc_start: 0.7758 (t0) cc_final: 0.7233 (m-30) REVERT: D 105 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8134 (pp) REVERT: D 109 PHE cc_start: 0.7729 (m-10) cc_final: 0.7467 (m-80) REVERT: D 215 ARG cc_start: 0.7254 (ptt180) cc_final: 0.6676 (mtm110) REVERT: D 248 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 294 HIS cc_start: 0.6807 (m-70) cc_final: 0.6493 (m-70) REVERT: D 317 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4350 (p-80) REVERT: D 333 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5597 (tptp) REVERT: D 395 PRO cc_start: 0.7438 (Cg_endo) cc_final: 0.7167 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: D 400 ILE cc_start: 0.5322 (OUTLIER) cc_final: 0.4673 (tp) REVERT: D 401 LEU cc_start: 0.4376 (OUTLIER) cc_final: 0.4176 (mt) REVERT: D 439 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5326 (pp) outliers start: 84 outliers final: 39 residues processed: 271 average time/residue: 0.6088 time to fit residues: 181.8075 Evaluate side-chains 254 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 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 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 372 LEU 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 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 439 ILE Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 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 Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 439 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 HIS B 307 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN D 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.225480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132388 restraints weight = 15902.963| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.77 r_work: 0.3197 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15846 Z= 0.176 Angle : 0.635 9.433 21476 Z= 0.328 Chirality : 0.045 0.213 2422 Planarity : 0.004 0.043 2688 Dihedral : 9.136 88.935 2229 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.30 % Allowed : 26.94 % 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: -0.22 (0.19), residues: 1870 helix: 0.28 (0.15), residues: 1152 sheet: -1.30 (0.51), residues: 100 loop : -0.50 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 182 TYR 0.025 0.002 TYR B 364 PHE 0.016 0.001 PHE C 409 TRP 0.016 0.003 TRP A 246 HIS 0.006 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00417 (15846) covalent geometry : angle 0.63535 (21476) hydrogen bonds : bond 0.05706 ( 818) hydrogen bonds : angle 4.54814 ( 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 284 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 195 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7857 (t70) cc_final: 0.7566 (t0) REVERT: A 106 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6557 (tmm) REVERT: A 119 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6941 (mt) REVERT: A 125 LYS cc_start: 0.6270 (tppt) cc_final: 0.5807 (ttmm) REVERT: A 162 MET cc_start: 0.8588 (tpt) cc_final: 0.8161 (mmm) REVERT: A 183 ASN cc_start: 0.7207 (m-40) cc_final: 0.6461 (t160) REVERT: A 267 MET cc_start: 0.8998 (mtt) cc_final: 0.8674 (mtm) REVERT: A 298 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7477 (tmm-80) REVERT: A 432 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: A 441 GLU cc_start: 0.5446 (OUTLIER) cc_final: 0.5009 (tt0) REVERT: A 510 MET cc_start: -0.0332 (mtt) cc_final: -0.1175 (ptm) REVERT: B 46 ARG cc_start: 0.5530 (ttm-80) cc_final: 0.5233 (ttm-80) REVERT: B 58 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7612 (tpt-90) REVERT: B 59 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7298 (pt) REVERT: B 83 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7240 (mtm110) REVERT: B 86 ARG cc_start: 0.6655 (mtp180) cc_final: 0.5818 (ptt180) REVERT: B 93 ASP cc_start: 0.7685 (t0) cc_final: 0.7002 (m-30) REVERT: B 109 PHE cc_start: 0.7131 (m-10) cc_final: 0.6910 (m-80) REVERT: B 115 LYS cc_start: 0.7918 (tppt) cc_final: 0.7641 (tppt) REVERT: B 248 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8589 (mt) REVERT: B 337 ASP cc_start: 0.7062 (m-30) cc_final: 0.6797 (m-30) REVERT: B 397 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: B 400 ILE cc_start: 0.5319 (OUTLIER) cc_final: 0.4887 (tp) REVERT: B 401 LEU cc_start: 0.4560 (OUTLIER) cc_final: 0.4351 (mt) REVERT: B 485 MET cc_start: 0.4485 (tpt) cc_final: 0.3690 (mmp) REVERT: B 500 MET cc_start: 0.3684 (ppp) cc_final: 0.3433 (pp-130) REVERT: C 103 ASP cc_start: 0.7690 (t70) cc_final: 0.7383 (t0) REVERT: C 122 ASP cc_start: 0.6658 (p0) cc_final: 0.6433 (p0) REVERT: C 155 GLN cc_start: 0.7784 (mm110) cc_final: 0.7384 (mp10) REVERT: C 177 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6961 (ttp-110) REVERT: C 179 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7346 (mm-30) REVERT: C 183 ASN cc_start: 0.7084 (m-40) cc_final: 0.6503 (t160) REVERT: C 185 ASN cc_start: 0.6997 (m-40) cc_final: 0.6191 (t0) REVERT: C 230 ASN cc_start: 0.6257 (m110) cc_final: 0.5877 (p0) REVERT: C 232 LEU cc_start: 0.8567 (mt) cc_final: 0.8179 (mm) REVERT: C 267 MET cc_start: 0.9006 (mtt) cc_final: 0.8665 (mtm) REVERT: C 288 MET cc_start: 0.8781 (tpt) cc_final: 0.8415 (tpp) REVERT: C 298 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.6726 (ttm-80) REVERT: C 389 LYS cc_start: 0.6485 (mttp) cc_final: 0.5818 (mptt) REVERT: C 392 TYR cc_start: 0.7833 (m-80) cc_final: 0.7584 (m-80) REVERT: C 511 LEU cc_start: 0.2893 (OUTLIER) cc_final: 0.2691 (mt) REVERT: C 513 ARG cc_start: -0.1250 (OUTLIER) cc_final: -0.1649 (ppt-90) REVERT: D 58 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7543 (ttm170) REVERT: D 59 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7266 (pt) REVERT: D 86 ARG cc_start: 0.6556 (mtp180) cc_final: 0.5684 (ptt180) REVERT: D 93 ASP cc_start: 0.7644 (t0) cc_final: 0.7006 (m-30) REVERT: D 105 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8004 (pp) REVERT: D 109 PHE cc_start: 0.7483 (m-10) cc_final: 0.7219 (m-80) REVERT: D 215 ARG cc_start: 0.6970 (ptt180) cc_final: 0.6372 (mtm110) REVERT: D 248 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8324 (mm) REVERT: D 294 HIS cc_start: 0.6684 (m-70) cc_final: 0.6370 (m-70) REVERT: D 317 HIS cc_start: 0.5063 (OUTLIER) cc_final: 0.4337 (p-80) REVERT: D 333 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5462 (tptp) REVERT: D 387 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7476 (pt0) REVERT: D 395 PRO cc_start: 0.7337 (Cg_endo) cc_final: 0.7063 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: D 400 ILE cc_start: 0.5163 (OUTLIER) cc_final: 0.4532 (tp) REVERT: D 439 ILE cc_start: 0.5304 (OUTLIER) cc_final: 0.5099 (pp) REVERT: D 495 MET cc_start: 0.5063 (pp-130) cc_final: 0.4732 (tmm) REVERT: D 500 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.5166 (tmm) outliers start: 89 outliers final: 43 residues processed: 264 average time/residue: 0.5952 time to fit residues: 173.5287 Evaluate side-chains 254 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET 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 299 THR Chi-restraints excluded: chain A residue 358 ILE 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 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 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 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 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 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 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 THR 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 366 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 499 VAL 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: 4.9990 chunk 132 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 307 GLN B 307 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.226291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135058 restraints weight = 16047.216| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.11 r_work: 0.3233 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15846 Z= 0.130 Angle : 0.599 10.086 21476 Z= 0.308 Chirality : 0.043 0.199 2422 Planarity : 0.004 0.052 2688 Dihedral : 8.782 87.750 2229 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.71 % Allowed : 27.77 % 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: 0.07 (0.19), residues: 1870 helix: 0.53 (0.15), residues: 1154 sheet: -1.19 (0.51), residues: 100 loop : -0.45 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 182 TYR 0.026 0.001 TYR B 364 PHE 0.023 0.001 PHE A 409 TRP 0.016 0.002 TRP D 135 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00286 (15846) covalent geometry : angle 0.59884 (21476) hydrogen bonds : bond 0.04970 ( 818) hydrogen bonds : angle 4.40388 ( 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 274 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 195 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6980 (mt) REVERT: A 125 LYS cc_start: 0.6409 (tppt) cc_final: 0.5937 (ttmm) REVERT: A 162 MET cc_start: 0.8723 (tpt) cc_final: 0.8322 (mmm) REVERT: A 183 ASN cc_start: 0.7213 (m-40) cc_final: 0.6538 (t160) REVERT: A 267 MET cc_start: 0.9080 (mtt) cc_final: 0.8795 (mtm) REVERT: A 298 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7502 (ttt90) REVERT: A 432 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: A 441 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5201 (tt0) REVERT: A 510 MET cc_start: -0.0350 (mtt) cc_final: -0.1216 (ptm) REVERT: B 46 ARG cc_start: 0.5677 (ttm-80) cc_final: 0.5292 (ttm-80) REVERT: B 58 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7805 (tpt-90) REVERT: B 59 ILE cc_start: 0.7874 (tp) cc_final: 0.7532 (pt) REVERT: B 83 ARG cc_start: 0.7776 (ptp-110) cc_final: 0.7424 (mtm110) REVERT: B 86 ARG cc_start: 0.6617 (mtp180) cc_final: 0.5764 (ptt180) REVERT: B 93 ASP cc_start: 0.7756 (t0) cc_final: 0.7183 (m-30) REVERT: B 109 PHE cc_start: 0.7326 (m-10) cc_final: 0.7112 (m-80) REVERT: B 115 LYS cc_start: 0.7906 (tppt) cc_final: 0.7697 (tppt) REVERT: B 248 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 315 ARG cc_start: 0.7081 (mmm160) cc_final: 0.5993 (tpt170) REVERT: B 337 ASP cc_start: 0.7254 (m-30) cc_final: 0.6985 (m-30) REVERT: B 397 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6723 (tp30) REVERT: B 400 ILE cc_start: 0.5456 (OUTLIER) cc_final: 0.5044 (tp) REVERT: B 401 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4621 (mt) REVERT: B 485 MET cc_start: 0.4538 (tpt) cc_final: 0.3741 (mmp) REVERT: B 500 MET cc_start: 0.3548 (ppp) cc_final: 0.3319 (pp-130) REVERT: C 103 ASP cc_start: 0.7866 (t70) cc_final: 0.7604 (t0) REVERT: C 122 ASP cc_start: 0.6741 (p0) cc_final: 0.6496 (p0) REVERT: C 179 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7350 (mm-30) REVERT: C 183 ASN cc_start: 0.7233 (m-40) cc_final: 0.6636 (t160) REVERT: C 185 ASN cc_start: 0.6893 (m-40) cc_final: 0.6198 (t0) REVERT: C 230 ASN cc_start: 0.6310 (m110) cc_final: 0.5957 (p0) REVERT: C 232 LEU cc_start: 0.8723 (mt) cc_final: 0.8331 (mm) REVERT: C 234 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7829 (mt-10) REVERT: C 267 MET cc_start: 0.9104 (mtt) cc_final: 0.8818 (mtt) REVERT: C 288 MET cc_start: 0.9010 (tpt) cc_final: 0.8705 (tpp) REVERT: C 298 ARG cc_start: 0.7541 (mtp-110) cc_final: 0.6960 (ttm-80) REVERT: C 511 LEU cc_start: 0.2973 (OUTLIER) cc_final: 0.2711 (mt) REVERT: C 513 ARG cc_start: -0.1235 (OUTLIER) cc_final: -0.1725 (ppt-90) REVERT: D 58 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7714 (mmt90) REVERT: D 59 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7474 (pt) REVERT: D 86 ARG cc_start: 0.6642 (mtp180) cc_final: 0.5772 (ptt180) REVERT: D 93 ASP cc_start: 0.7772 (t0) cc_final: 0.7208 (m-30) REVERT: D 105 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8152 (pp) REVERT: D 109 PHE cc_start: 0.7693 (m-10) cc_final: 0.7438 (m-80) REVERT: D 215 ARG cc_start: 0.7108 (ptt180) cc_final: 0.6603 (mmm160) REVERT: D 248 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8403 (mm) REVERT: D 294 HIS cc_start: 0.6763 (m-70) cc_final: 0.6442 (m-70) REVERT: D 317 HIS cc_start: 0.4959 (OUTLIER) cc_final: 0.4231 (p-80) REVERT: D 333 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.5775 (tptp) REVERT: D 387 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7638 (pt0) REVERT: D 395 PRO cc_start: 0.7525 (Cg_endo) cc_final: 0.7257 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.4964 (tp) REVERT: D 439 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5361 (pp) REVERT: D 495 MET cc_start: 0.5115 (pp-130) cc_final: 0.4730 (tmm) REVERT: D 500 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5200 (tmm) outliers start: 79 outliers final: 41 residues processed: 257 average time/residue: 0.5717 time to fit residues: 162.2298 Evaluate side-chains 249 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 408 ASP 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 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 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 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 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 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 333 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 119 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 21 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.226025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134700 restraints weight = 16016.037| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.08 r_work: 0.3222 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15846 Z= 0.139 Angle : 0.611 11.441 21476 Z= 0.313 Chirality : 0.043 0.205 2422 Planarity : 0.004 0.054 2688 Dihedral : 8.701 86.922 2229 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.23 % Allowed : 28.37 % 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: 0.14 (0.19), residues: 1870 helix: 0.58 (0.15), residues: 1154 sheet: -1.14 (0.51), residues: 100 loop : -0.40 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 182 TYR 0.025 0.002 TYR B 364 PHE 0.011 0.001 PHE A 187 TRP 0.014 0.002 TRP A 73 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00313 (15846) covalent geometry : angle 0.61128 (21476) hydrogen bonds : bond 0.05042 ( 818) hydrogen bonds : angle 4.38291 ( 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 257 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7061 (tmm) cc_final: 0.6719 (tmm) REVERT: A 119 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6950 (mt) REVERT: A 125 LYS cc_start: 0.6409 (tppt) cc_final: 0.5937 (ttmm) REVERT: A 162 MET cc_start: 0.8736 (tpt) cc_final: 0.8358 (mmm) REVERT: A 183 ASN cc_start: 0.7219 (m-40) cc_final: 0.6552 (t160) REVERT: A 267 MET cc_start: 0.9076 (mtt) cc_final: 0.8817 (mtm) REVERT: A 298 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7580 (ttt90) REVERT: A 408 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6440 (t0) REVERT: A 432 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6597 (tt0) REVERT: A 441 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5230 (tt0) REVERT: A 510 MET cc_start: -0.0322 (mtt) cc_final: -0.1208 (ptm) REVERT: B 46 ARG cc_start: 0.5663 (ttm-80) cc_final: 0.5289 (ttm-80) REVERT: B 58 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7816 (tpt-90) REVERT: B 59 ILE cc_start: 0.7982 (tp) cc_final: 0.7678 (pt) REVERT: B 83 ARG cc_start: 0.7734 (ptp-110) cc_final: 0.7376 (mtm110) REVERT: B 86 ARG cc_start: 0.6620 (mtp180) cc_final: 0.5791 (ptt180) REVERT: B 93 ASP cc_start: 0.7731 (t0) cc_final: 0.7157 (m-30) REVERT: B 109 PHE cc_start: 0.7335 (m-10) cc_final: 0.7129 (m-80) REVERT: B 115 LYS cc_start: 0.7886 (tppt) cc_final: 0.7683 (tppt) REVERT: B 248 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 315 ARG cc_start: 0.7047 (mmm160) cc_final: 0.5978 (tpt170) REVERT: B 337 ASP cc_start: 0.7266 (m-30) cc_final: 0.7018 (m-30) REVERT: B 397 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: B 400 ILE cc_start: 0.5473 (OUTLIER) cc_final: 0.5058 (tp) REVERT: B 401 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4669 (mt) REVERT: B 485 MET cc_start: 0.4542 (tpt) cc_final: 0.3743 (mmt) REVERT: B 500 MET cc_start: 0.3561 (ppp) cc_final: 0.3301 (pp-130) REVERT: C 103 ASP cc_start: 0.7867 (t70) cc_final: 0.7618 (t0) REVERT: C 179 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 182 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7043 (ttm-80) REVERT: C 183 ASN cc_start: 0.7256 (m-40) cc_final: 0.6648 (t160) REVERT: C 185 ASN cc_start: 0.7058 (m-40) cc_final: 0.6373 (t0) REVERT: C 230 ASN cc_start: 0.6317 (m110) cc_final: 0.5943 (p0) REVERT: C 267 MET cc_start: 0.9108 (mtt) cc_final: 0.8823 (mtm) REVERT: C 288 MET cc_start: 0.9021 (tpt) cc_final: 0.8725 (tpp) REVERT: C 298 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.6953 (ttm-80) REVERT: C 392 TYR cc_start: 0.7937 (m-80) cc_final: 0.7656 (m-80) REVERT: C 511 LEU cc_start: 0.2990 (OUTLIER) cc_final: 0.2719 (mt) REVERT: C 513 ARG cc_start: -0.1202 (OUTLIER) cc_final: -0.1575 (pmt-80) REVERT: D 59 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7480 (pt) REVERT: D 86 ARG cc_start: 0.6661 (mtp180) cc_final: 0.5804 (ptt180) REVERT: D 93 ASP cc_start: 0.7690 (t0) cc_final: 0.7144 (m-30) REVERT: D 105 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8152 (pp) REVERT: D 109 PHE cc_start: 0.7707 (m-10) cc_final: 0.7461 (m-80) REVERT: D 215 ARG cc_start: 0.7132 (ptt180) cc_final: 0.6629 (mmm160) REVERT: D 248 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8414 (mm) REVERT: D 294 HIS cc_start: 0.6765 (m-70) cc_final: 0.6453 (m-70) REVERT: D 317 HIS cc_start: 0.4921 (OUTLIER) cc_final: 0.4189 (p-80) REVERT: D 330 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6534 (mm) REVERT: D 333 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.5732 (tptp) REVERT: D 387 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7622 (pt0) REVERT: D 395 PRO cc_start: 0.7546 (Cg_endo) cc_final: 0.7282 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5001 (tp) REVERT: D 439 ILE cc_start: 0.5569 (OUTLIER) cc_final: 0.5362 (pp) REVERT: D 495 MET cc_start: 0.5096 (pp-130) cc_final: 0.4699 (tmm) REVERT: D 500 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.5160 (tmm) outliers start: 71 outliers final: 41 residues processed: 242 average time/residue: 0.5800 time to fit residues: 155.4164 Evaluate side-chains 245 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 299 THR 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 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 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 327 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 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 159 LEU Chi-restraints excluded: chain C residue 182 ARG 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 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 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 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 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 499 VAL 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: 0.9980 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.224233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131849 restraints weight = 16003.624| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.08 r_work: 0.3160 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15846 Z= 0.202 Angle : 0.662 11.383 21476 Z= 0.339 Chirality : 0.046 0.219 2422 Planarity : 0.004 0.050 2688 Dihedral : 8.700 82.589 2226 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.99 % Allowed : 28.43 % Favored : 67.58 % 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: -0.06 (0.19), residues: 1870 helix: 0.38 (0.15), residues: 1150 sheet: -1.18 (0.51), residues: 100 loop : -0.41 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 182 TYR 0.026 0.002 TYR B 364 PHE 0.023 0.002 PHE A 409 TRP 0.018 0.003 TRP A 246 HIS 0.007 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00489 (15846) covalent geometry : angle 0.66187 (21476) hydrogen bonds : bond 0.05879 ( 818) hydrogen bonds : angle 4.52162 ( 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 252 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6949 (mt) REVERT: A 125 LYS cc_start: 0.6386 (tppt) cc_final: 0.5922 (ttmm) REVERT: A 162 MET cc_start: 0.8712 (tpt) cc_final: 0.8318 (mmm) REVERT: A 183 ASN cc_start: 0.7195 (m-40) cc_final: 0.6442 (t160) REVERT: A 267 MET cc_start: 0.9094 (mtt) cc_final: 0.8806 (mtm) REVERT: A 298 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7578 (ttt90) REVERT: A 432 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6279 (tt0) REVERT: A 510 MET cc_start: 0.0399 (mtt) cc_final: -0.0721 (ptm) REVERT: B 46 ARG cc_start: 0.5642 (ttm-80) cc_final: 0.5317 (ttm-80) REVERT: B 58 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7811 (mmt90) REVERT: B 59 ILE cc_start: 0.7969 (tp) cc_final: 0.7611 (pt) REVERT: B 83 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mtm110) REVERT: B 86 ARG cc_start: 0.6716 (mtp180) cc_final: 0.5927 (ptt180) REVERT: B 93 ASP cc_start: 0.7722 (t0) cc_final: 0.7171 (m-30) REVERT: B 109 PHE cc_start: 0.7342 (m-10) cc_final: 0.7128 (m-80) REVERT: B 115 LYS cc_start: 0.7911 (tppt) cc_final: 0.7651 (tppt) REVERT: B 248 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 317 HIS cc_start: 0.5436 (OUTLIER) cc_final: 0.4676 (p-80) REVERT: B 337 ASP cc_start: 0.7333 (m-30) cc_final: 0.7089 (m-30) REVERT: B 397 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: B 400 ILE cc_start: 0.5507 (OUTLIER) cc_final: 0.5052 (tp) REVERT: B 401 LEU cc_start: 0.4806 (OUTLIER) cc_final: 0.4555 (mt) REVERT: B 485 MET cc_start: 0.4349 (tpt) cc_final: 0.3637 (mmp) REVERT: C 179 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7313 (mm-30) REVERT: C 182 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7014 (ttm-80) REVERT: C 183 ASN cc_start: 0.7233 (m-40) cc_final: 0.6572 (t160) REVERT: C 185 ASN cc_start: 0.7043 (m-40) cc_final: 0.6322 (t0) REVERT: C 230 ASN cc_start: 0.6358 (m110) cc_final: 0.6050 (p0) REVERT: C 232 LEU cc_start: 0.8726 (mt) cc_final: 0.8501 (mm) REVERT: C 234 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7827 (mt-10) REVERT: C 267 MET cc_start: 0.9112 (mtt) cc_final: 0.8820 (mtm) REVERT: C 288 MET cc_start: 0.8971 (tpt) cc_final: 0.8668 (tpp) REVERT: C 298 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6850 (ttm-80) REVERT: C 511 LEU cc_start: 0.2970 (OUTLIER) cc_final: 0.2709 (mt) REVERT: C 513 ARG cc_start: -0.1204 (OUTLIER) cc_final: -0.1546 (pmt-80) REVERT: D 86 ARG cc_start: 0.6696 (mtp180) cc_final: 0.5795 (ptt180) REVERT: D 93 ASP cc_start: 0.7800 (t0) cc_final: 0.7244 (m-30) REVERT: D 105 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8127 (pp) REVERT: D 109 PHE cc_start: 0.7683 (m-10) cc_final: 0.7421 (m-80) REVERT: D 215 ARG cc_start: 0.6985 (ptt180) cc_final: 0.6540 (mmm160) REVERT: D 248 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8452 (mt) REVERT: D 317 HIS cc_start: 0.4989 (OUTLIER) cc_final: 0.4257 (p-80) REVERT: D 330 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6569 (mm) REVERT: D 333 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.5837 (tptp) REVERT: D 387 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7583 (pt0) REVERT: D 395 PRO cc_start: 0.7500 (Cg_endo) cc_final: 0.7226 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5161 (OUTLIER) cc_final: 0.4822 (tp) REVERT: D 495 MET cc_start: 0.5122 (pp-130) cc_final: 0.4739 (tmm) REVERT: D 500 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.5132 (tmm) outliers start: 67 outliers final: 40 residues processed: 234 average time/residue: 0.5848 time to fit residues: 151.2687 Evaluate side-chains 240 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 408 ASP 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 452 PHE Chi-restraints excluded: chain A residue 453 THR 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 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 327 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 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 182 ARG 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 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 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 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 330 LEU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 338 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 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 150 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 144 optimal weight: 0.0020 chunk 142 optimal weight: 0.5980 chunk 92 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN 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 = 0.226655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135104 restraints weight = 15929.402| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.05 r_work: 0.3230 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3824 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= 0.124 Angle : 0.609 11.252 21476 Z= 0.312 Chirality : 0.042 0.208 2422 Planarity : 0.004 0.060 2688 Dihedral : 8.358 83.256 2226 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.99 % Allowed : 28.55 % 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: 0.23 (0.20), residues: 1870 helix: 0.63 (0.15), residues: 1154 sheet: -1.10 (0.51), residues: 100 loop : -0.33 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 182 TYR 0.026 0.001 TYR B 364 PHE 0.024 0.001 PHE A 409 TRP 0.017 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00261 (15846) covalent geometry : angle 0.60884 (21476) hydrogen bonds : bond 0.04888 ( 818) hydrogen bonds : angle 4.36121 ( 2361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7886.13 seconds wall clock time: 134 minutes 25.59 seconds (8065.59 seconds total)