Starting phenix.real_space_refine on Sat Jun 14 03:45:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm2_32598/06_2025/7wm2_32598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm2_32598/06_2025/7wm2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wm2_32598/06_2025/7wm2_32598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm2_32598/06_2025/7wm2_32598.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm2_32598/06_2025/7wm2_32598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm2_32598/06_2025/7wm2_32598.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.17, per 1000 atoms: 0.59 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.55 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: 4.32 Time building geometry restraints manager: 4.56 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: 0.570 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- 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 : 18.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.059 0.004 TRP D 246 HIS 0.020 0.002 HIS B 294 PHE 0.018 0.002 PHE C 184 TYR 0.032 0.002 TYR C 186 ARG 0.012 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.28070 ( 818) hydrogen bonds : angle 9.73045 ( 2361) covalent geometry : bond 0.01167 (15846) covalent geometry : angle 1.03477 (21476) *********************** 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 : 1.632 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: 0.5032 (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: 0.8327 (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: 0.6416 (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: 1.0922 time to fit residues: 518.6589 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 : 1.652 ------------------------------------------------------------------------------- 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 157 optimal weight: 0.3980 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 343 GLN B 472 ASN B 475 GLN C 323 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN D 126 GLN D 216 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 383 GLN D 477 ASN D 491 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.223885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134108 restraints weight = 16057.123| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.94 r_work: 0.3264 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15846 Z= 0.166 Angle : 0.727 9.690 21476 Z= 0.379 Chirality : 0.046 0.180 2422 Planarity : 0.005 0.042 2688 Dihedral : 12.057 90.535 2384 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.14 % Allowed : 26.64 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 1870 helix: -0.92 (0.14), residues: 1148 sheet: -2.25 (0.49), residues: 102 loop : -1.25 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 246 HIS 0.005 0.001 HIS A 360 PHE 0.017 0.001 PHE B 382 TYR 0.019 0.002 TYR D 364 ARG 0.007 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.06723 ( 818) hydrogen bonds : angle 5.26799 ( 2361) covalent geometry : bond 0.00350 (15846) covalent geometry : angle 0.72729 (21476) *********************** 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 337 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 234 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7714 (t70) cc_final: 0.7429 (t0) REVERT: A 137 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6770 (tt) REVERT: A 155 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7409 (mp10) REVERT: A 162 MET cc_start: 0.8699 (tpt) cc_final: 0.8151 (mmm) REVERT: A 183 ASN cc_start: 0.7087 (m-40) cc_final: 0.6427 (t160) REVERT: A 194 LEU cc_start: 0.8166 (mt) cc_final: 0.7938 (mt) REVERT: A 232 LEU cc_start: 0.8739 (mt) cc_final: 0.8490 (mm) REVERT: A 267 MET cc_start: 0.8968 (mtt) cc_final: 0.8660 (mtm) REVERT: A 298 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7559 (ttm-80) REVERT: A 339 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5720 (mt-10) REVERT: A 356 SER cc_start: 0.7508 (t) cc_final: 0.7295 (p) REVERT: A 510 MET cc_start: 0.0504 (mtt) cc_final: -0.0584 (ptm) REVERT: B 46 ARG cc_start: 0.5600 (ttm-80) cc_final: 0.5223 (ttm-80) REVERT: B 83 ARG cc_start: 0.7742 (ptp-110) cc_final: 0.7308 (mtm110) REVERT: B 86 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6172 (ptt180) REVERT: B 93 ASP cc_start: 0.7686 (t0) cc_final: 0.6943 (m-30) REVERT: B 105 ILE cc_start: 0.8110 (mt) cc_final: 0.7873 (mt) REVERT: B 109 PHE cc_start: 0.7402 (m-10) cc_final: 0.7126 (m-80) REVERT: B 133 ARG cc_start: 0.7014 (mtp180) cc_final: 0.6440 (mtm-85) REVERT: B 307 GLN cc_start: 0.7592 (pp30) cc_final: 0.7326 (tp40) REVERT: B 337 ASP cc_start: 0.7199 (m-30) cc_final: 0.6981 (m-30) REVERT: B 344 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: B 352 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5029 (tmtt) REVERT: B 397 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6599 (tp30) REVERT: B 401 LEU cc_start: 0.5152 (OUTLIER) cc_final: 0.4892 (mt) REVERT: B 485 MET cc_start: 0.4521 (tpt) cc_final: 0.3558 (mmt) REVERT: B 495 MET cc_start: 0.5953 (ttm) cc_final: 0.5665 (tpp) REVERT: C 93 ASP cc_start: 0.8162 (t0) cc_final: 0.7870 (m-30) REVERT: C 103 ASP cc_start: 0.7867 (t70) cc_final: 0.7515 (t0) REVERT: C 113 LEU cc_start: 0.7807 (mm) cc_final: 0.7514 (tp) REVERT: C 122 ASP cc_start: 0.6697 (p0) cc_final: 0.6411 (p0) REVERT: C 151 ARG cc_start: 0.7505 (ttm110) cc_final: 0.6947 (ppt170) REVERT: C 155 GLN cc_start: 0.7873 (mm110) cc_final: 0.7388 (mp10) REVERT: C 177 ARG cc_start: 0.7360 (mtm110) cc_final: 0.7065 (ttp-110) REVERT: C 179 GLU cc_start: 0.7434 (mm-30) cc_final: 0.6923 (mm-30) REVERT: C 182 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7269 (ttm-80) REVERT: C 183 ASN cc_start: 0.7171 (m-40) cc_final: 0.6876 (t160) REVERT: C 190 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7675 (mtp180) REVERT: C 194 LEU cc_start: 0.7968 (mt) cc_final: 0.7753 (mt) REVERT: C 230 ASN cc_start: 0.6350 (m110) cc_final: 0.6026 (p0) REVERT: C 288 MET cc_start: 0.8779 (tpt) cc_final: 0.8438 (tpp) REVERT: C 298 ARG cc_start: 0.7399 (mtp-110) cc_final: 0.6746 (ttm-80) REVERT: C 300 ARG cc_start: 0.7587 (ptt90) cc_final: 0.7358 (ptt-90) REVERT: C 343 GLN cc_start: 0.5169 (OUTLIER) cc_final: 0.4311 (pp30) REVERT: C 388 MET cc_start: 0.5555 (mtt) cc_final: 0.5289 (mtp) REVERT: C 401 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6593 (pp) REVERT: C 494 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4531 (mp0) REVERT: D 56 LYS cc_start: 0.6730 (tmtt) cc_final: 0.6200 (mttp) REVERT: D 86 ARG cc_start: 0.6748 (mtp180) cc_final: 0.5949 (ptt180) REVERT: D 93 ASP cc_start: 0.7680 (t0) cc_final: 0.6932 (m-30) REVERT: D 105 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8004 (pt) REVERT: D 109 PHE cc_start: 0.7737 (m-10) cc_final: 0.7505 (m-80) REVERT: D 125 LYS cc_start: 0.7579 (mmtt) cc_final: 0.6512 (tttt) REVERT: D 162 MET cc_start: 0.9033 (tpt) cc_final: 0.8563 (mmm) REVERT: D 215 ARG cc_start: 0.7113 (ptt180) cc_final: 0.6692 (mtm110) REVERT: D 294 HIS cc_start: 0.6664 (m-70) cc_final: 0.6371 (m-70) REVERT: D 307 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7150 (mm110) REVERT: D 317 HIS cc_start: 0.5275 (OUTLIER) cc_final: 0.4544 (p-80) REVERT: D 330 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6626 (mm) REVERT: D 333 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5506 (tptp) REVERT: D 348 ASP cc_start: 0.6757 (p0) cc_final: 0.6489 (p0) REVERT: D 384 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.4595 (mm) REVERT: D 395 PRO cc_start: 0.7421 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: D 432 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4934 (pm20) REVERT: D 506 GLU cc_start: 0.5093 (OUTLIER) cc_final: 0.4864 (pp20) outliers start: 103 outliers final: 27 residues processed: 318 average time/residue: 1.5311 time to fit residues: 543.9098 Evaluate side-chains 252 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 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 66 VAL Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER 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 421 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 504 LEU 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 68 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 163 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 218 ASN B 491 HIS C 343 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.222597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128917 restraints weight = 15915.426| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.21 r_work: 0.3130 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15846 Z= 0.256 Angle : 0.730 11.068 21476 Z= 0.377 Chirality : 0.049 0.315 2422 Planarity : 0.005 0.044 2688 Dihedral : 10.964 94.929 2271 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.85 % Allowed : 26.28 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1870 helix: -0.59 (0.14), residues: 1146 sheet: -1.92 (0.50), residues: 102 loop : -0.99 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 246 HIS 0.006 0.002 HIS D 329 PHE 0.020 0.002 PHE D 272 TYR 0.022 0.002 TYR B 364 ARG 0.009 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.07134 ( 818) hydrogen bonds : angle 5.04888 ( 2361) covalent geometry : bond 0.00624 (15846) covalent geometry : angle 0.73026 (21476) *********************** 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 321 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 206 time to evaluate : 1.588 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: 0.7937 (t70) cc_final: 0.7688 (t0) REVERT: A 119 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7005 (mt) REVERT: A 120 ILE cc_start: 0.7948 (mt) cc_final: 0.7675 (pp) REVERT: A 125 LYS cc_start: 0.6534 (tppt) cc_final: 0.6036 (ttmm) REVERT: A 155 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7427 (mp10) REVERT: A 162 MET cc_start: 0.8732 (tpt) cc_final: 0.8358 (mmm) REVERT: A 183 ASN cc_start: 0.7181 (m-40) cc_final: 0.6421 (t160) REVERT: A 267 MET cc_start: 0.9113 (mtt) cc_final: 0.8806 (mtm) REVERT: A 298 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7707 (ttt90) REVERT: A 339 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5713 (mt-10) REVERT: A 356 SER cc_start: 0.7503 (t) cc_final: 0.7244 (p) REVERT: A 464 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6787 (ttp-110) REVERT: A 485 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.4730 (tpt) REVERT: A 510 MET cc_start: 0.0151 (mtt) cc_final: -0.0723 (ptm) REVERT: B 46 ARG cc_start: 0.5694 (ttm-80) cc_final: 0.5342 (ttm-80) REVERT: B 83 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7542 (mtm110) REVERT: B 84 LYS cc_start: 0.8217 (pttm) cc_final: 0.7969 (ptmm) REVERT: B 86 ARG cc_start: 0.6992 (mtp180) cc_final: 0.6149 (ptt180) REVERT: B 93 ASP cc_start: 0.7933 (t0) cc_final: 0.7212 (m-30) REVERT: B 109 PHE cc_start: 0.7652 (m-10) cc_final: 0.7384 (m-80) REVERT: B 162 MET cc_start: 0.9150 (tpt) cc_final: 0.8669 (mmm) REVERT: B 248 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8684 (mt) REVERT: B 294 HIS cc_start: 0.6358 (m90) cc_final: 0.6131 (m90) REVERT: B 317 HIS cc_start: 0.5631 (OUTLIER) cc_final: 0.4788 (p-80) REVERT: B 337 ASP cc_start: 0.7382 (m-30) cc_final: 0.7161 (m-30) REVERT: B 401 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4665 (mt) REVERT: B 485 MET cc_start: 0.4523 (tpt) cc_final: 0.3579 (mmt) REVERT: B 500 MET cc_start: 0.3722 (ppp) cc_final: 0.3287 (pp-130) REVERT: C 93 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: C 103 ASP cc_start: 0.8045 (t70) cc_final: 0.7690 (t0) REVERT: C 113 LEU cc_start: 0.7725 (mm) cc_final: 0.7472 (tp) REVERT: C 151 ARG cc_start: 0.7509 (ttm110) cc_final: 0.6877 (ppt170) REVERT: C 155 GLN cc_start: 0.7899 (mm110) cc_final: 0.7443 (mp10) REVERT: C 177 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7404 (ttp-110) REVERT: C 179 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7186 (mm-30) REVERT: C 182 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7240 (ttm-80) REVERT: C 183 ASN cc_start: 0.7158 (m-40) cc_final: 0.6729 (t160) REVERT: C 190 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7967 (mtp180) REVERT: C 230 ASN cc_start: 0.6460 (m110) cc_final: 0.6085 (p0) REVERT: C 288 MET cc_start: 0.9009 (tpt) cc_final: 0.8683 (tpp) REVERT: C 298 ARG cc_start: 0.7604 (mtp-110) cc_final: 0.6902 (ttm-80) REVERT: C 358 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.6005 (pp) REVERT: C 381 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5415 (mp) REVERT: C 388 MET cc_start: 0.5472 (mtt) cc_final: 0.5192 (mtp) REVERT: C 401 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6603 (pp) REVERT: C 494 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.4121 (mp0) REVERT: D 56 LYS cc_start: 0.7005 (tmtt) cc_final: 0.6377 (mtmm) REVERT: D 58 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7512 (tpm170) REVERT: D 86 ARG cc_start: 0.6709 (mtp180) cc_final: 0.5880 (ptt180) REVERT: D 93 ASP cc_start: 0.7849 (t0) cc_final: 0.7148 (m-30) REVERT: D 109 PHE cc_start: 0.7891 (m-10) cc_final: 0.7616 (m-80) REVERT: D 125 LYS cc_start: 0.7569 (mmtt) cc_final: 0.6363 (tttt) REVERT: D 215 ARG cc_start: 0.7433 (ptt180) cc_final: 0.6803 (mtm110) REVERT: D 248 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8394 (mt) REVERT: D 294 HIS cc_start: 0.6974 (m-70) cc_final: 0.6697 (m-70) REVERT: D 307 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7176 (mm110) REVERT: D 330 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6584 (mm) REVERT: D 348 ASP cc_start: 0.7043 (p0) cc_final: 0.6802 (p0) REVERT: D 395 PRO cc_start: 0.7410 (Cg_endo) cc_final: 0.7121 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6790 (tp30) REVERT: D 400 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.4864 (tp) REVERT: D 439 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5624 (pp) outliers start: 115 outliers final: 51 residues processed: 296 average time/residue: 1.1113 time to fit residues: 366.7956 Evaluate side-chains 271 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR 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 459 LEU Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 485 MET 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 141 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 THR 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 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 358 ILE 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 472 ASN Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 347 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 131 optimal weight: 0.0000 chunk 41 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 180 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 100 optimal weight: 0.0060 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 403 ASN A 472 ASN B 218 ASN B 307 GLN C 216 ASN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 472 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.226525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140048 restraints weight = 15910.765| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.44 r_work: 0.3222 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15846 Z= 0.126 Angle : 0.603 10.898 21476 Z= 0.313 Chirality : 0.043 0.222 2422 Planarity : 0.004 0.043 2688 Dihedral : 9.798 98.742 2245 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.42 % Allowed : 27.47 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1870 helix: 0.09 (0.15), residues: 1148 sheet: -1.62 (0.50), residues: 100 loop : -0.70 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 135 HIS 0.004 0.001 HIS D 329 PHE 0.013 0.001 PHE A 187 TYR 0.021 0.001 TYR B 364 ARG 0.008 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.05187 ( 818) hydrogen bonds : angle 4.63310 ( 2361) covalent geometry : bond 0.00254 (15846) covalent geometry : angle 0.60287 (21476) *********************** 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 300 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 209 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7992 (t70) cc_final: 0.7731 (t0) REVERT: A 119 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7084 (mt) REVERT: A 122 ASP cc_start: 0.6923 (p0) cc_final: 0.6613 (p0) REVERT: A 125 LYS cc_start: 0.6526 (tppt) cc_final: 0.5971 (ttmm) REVERT: A 155 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7413 (mp10) REVERT: A 162 MET cc_start: 0.8707 (tpt) cc_final: 0.8302 (mmm) REVERT: A 183 ASN cc_start: 0.7165 (m-40) cc_final: 0.6381 (t160) REVERT: A 267 MET cc_start: 0.9077 (mtt) cc_final: 0.8806 (mtm) REVERT: A 298 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7626 (ttm-80) REVERT: A 356 SER cc_start: 0.7548 (t) cc_final: 0.7288 (p) REVERT: A 464 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6436 (ttp-110) REVERT: A 510 MET cc_start: 0.0288 (mtt) cc_final: -0.0682 (ptm) REVERT: B 46 ARG cc_start: 0.5631 (ttm-80) cc_final: 0.5286 (ttm-80) REVERT: B 59 ILE cc_start: 0.7947 (tp) cc_final: 0.7573 (pt) REVERT: B 83 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7387 (mtm110) REVERT: B 84 LYS cc_start: 0.8152 (pttm) cc_final: 0.7949 (ptmm) REVERT: B 86 ARG cc_start: 0.6750 (mtp180) cc_final: 0.5902 (ptt180) REVERT: B 93 ASP cc_start: 0.7935 (t0) cc_final: 0.7275 (m-30) REVERT: B 109 PHE cc_start: 0.7677 (m-10) cc_final: 0.7425 (m-80) REVERT: B 248 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8581 (mm) REVERT: B 337 ASP cc_start: 0.7260 (m-30) cc_final: 0.7052 (m-30) REVERT: B 397 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: B 401 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4785 (mt) REVERT: B 485 MET cc_start: 0.4513 (tpt) cc_final: 0.3725 (mmt) REVERT: B 500 MET cc_start: 0.3608 (ppp) cc_final: 0.3237 (pp-130) REVERT: C 93 ASP cc_start: 0.8216 (t0) cc_final: 0.7986 (m-30) REVERT: C 103 ASP cc_start: 0.8011 (t70) cc_final: 0.7686 (t0) REVERT: C 113 LEU cc_start: 0.7797 (mm) cc_final: 0.7522 (tp) REVERT: C 151 ARG cc_start: 0.7406 (ttm110) cc_final: 0.6882 (ppt170) REVERT: C 155 GLN cc_start: 0.7956 (mm110) cc_final: 0.7472 (mp10) REVERT: C 177 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7299 (ttp-110) REVERT: C 179 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6966 (mm-30) REVERT: C 182 ARG cc_start: 0.7378 (ttm110) cc_final: 0.7100 (ttm-80) REVERT: C 183 ASN cc_start: 0.7160 (m-40) cc_final: 0.6717 (t160) REVERT: C 230 ASN cc_start: 0.6396 (m110) cc_final: 0.6017 (p0) REVERT: C 232 LEU cc_start: 0.8704 (mt) cc_final: 0.8454 (mm) REVERT: C 288 MET cc_start: 0.8994 (tpt) cc_final: 0.8786 (tpp) REVERT: C 298 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.6991 (ttm-80) REVERT: C 388 MET cc_start: 0.5370 (mtt) cc_final: 0.5130 (mtp) REVERT: C 401 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6668 (pp) REVERT: C 494 GLU cc_start: 0.4633 (OUTLIER) cc_final: 0.4412 (mp0) REVERT: D 56 LYS cc_start: 0.6879 (tmtt) cc_final: 0.6183 (mtmm) REVERT: D 58 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7431 (tpm170) REVERT: D 59 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7524 (pt) REVERT: D 86 ARG cc_start: 0.6637 (mtp180) cc_final: 0.5812 (ptt180) REVERT: D 93 ASP cc_start: 0.7846 (t0) cc_final: 0.7258 (m-30) REVERT: D 105 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8031 (pt) REVERT: D 109 PHE cc_start: 0.7884 (m-10) cc_final: 0.7629 (m-80) REVERT: D 115 LYS cc_start: 0.8512 (tppt) cc_final: 0.7572 (tppt) REVERT: D 152 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7414 (pp) REVERT: D 215 ARG cc_start: 0.7342 (ptt180) cc_final: 0.6743 (mtm110) REVERT: D 248 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8224 (mm) REVERT: D 252 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7234 (t) REVERT: D 294 HIS cc_start: 0.6788 (m-70) cc_final: 0.6497 (m-70) REVERT: D 317 HIS cc_start: 0.5102 (OUTLIER) cc_final: 0.4297 (p-80) REVERT: D 395 PRO cc_start: 0.7526 (Cg_endo) cc_final: 0.7224 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5376 (OUTLIER) cc_final: 0.5035 (tp) outliers start: 91 outliers final: 29 residues processed: 281 average time/residue: 1.1748 time to fit residues: 366.6772 Evaluate side-chains 240 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 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 464 ARG Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG 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 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 C residue 66 VAL Chi-restraints excluded: chain C residue 121 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 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN B 307 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.224834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133272 restraints weight = 16159.511| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.21 r_work: 0.3189 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15846 Z= 0.172 Angle : 0.637 9.812 21476 Z= 0.329 Chirality : 0.045 0.216 2422 Planarity : 0.004 0.046 2688 Dihedral : 9.081 86.002 2229 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.36 % Allowed : 27.41 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1870 helix: 0.17 (0.15), residues: 1152 sheet: -1.43 (0.50), residues: 100 loop : -0.58 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 PHE 0.021 0.001 PHE C 409 TYR 0.022 0.002 TYR D 364 ARG 0.011 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.05755 ( 818) hydrogen bonds : angle 4.62094 ( 2361) covalent geometry : bond 0.00406 (15846) covalent geometry : angle 0.63737 (21476) *********************** 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 292 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 202 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7960 (t70) cc_final: 0.7699 (t0) REVERT: A 119 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7058 (mt) REVERT: A 125 LYS cc_start: 0.6457 (tppt) cc_final: 0.5881 (ttmm) REVERT: A 155 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7402 (mp10) REVERT: A 162 MET cc_start: 0.8667 (tpt) cc_final: 0.8319 (mmm) REVERT: A 183 ASN cc_start: 0.7161 (m-40) cc_final: 0.6290 (t160) REVERT: A 267 MET cc_start: 0.9067 (mtt) cc_final: 0.8751 (mtm) REVERT: A 298 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.7566 (ttm-80) REVERT: A 356 SER cc_start: 0.7507 (t) cc_final: 0.7248 (p) REVERT: A 441 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5486 (tm-30) REVERT: A 464 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6582 (ttp-110) REVERT: A 510 MET cc_start: 0.0164 (mtt) cc_final: -0.0805 (ptm) REVERT: B 46 ARG cc_start: 0.5562 (ttm-80) cc_final: 0.5258 (ttm-80) REVERT: B 58 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7776 (tpt-90) REVERT: B 59 ILE cc_start: 0.7960 (tp) cc_final: 0.7529 (pt) REVERT: B 83 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7383 (mtm110) REVERT: B 86 ARG cc_start: 0.6749 (mtp180) cc_final: 0.5906 (ptt180) REVERT: B 93 ASP cc_start: 0.7859 (t0) cc_final: 0.7176 (m-30) REVERT: B 109 PHE cc_start: 0.7360 (m-10) cc_final: 0.7115 (m-80) REVERT: B 115 LYS cc_start: 0.7885 (tppt) cc_final: 0.7661 (tppt) REVERT: B 190 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8288 (mmm160) REVERT: B 248 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8677 (mt) REVERT: B 337 ASP cc_start: 0.7128 (m-30) cc_final: 0.6902 (m-30) REVERT: B 397 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6826 (tp30) REVERT: B 400 ILE cc_start: 0.5445 (OUTLIER) cc_final: 0.4949 (tp) REVERT: B 485 MET cc_start: 0.4572 (tpt) cc_final: 0.3738 (mmt) REVERT: B 500 MET cc_start: 0.3490 (ppp) cc_final: 0.3158 (pp-130) REVERT: C 93 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: C 103 ASP cc_start: 0.7884 (t70) cc_final: 0.7568 (t0) REVERT: C 113 LEU cc_start: 0.7760 (mm) cc_final: 0.7496 (tp) REVERT: C 155 GLN cc_start: 0.7893 (mm110) cc_final: 0.7444 (mp10) REVERT: C 177 ARG cc_start: 0.7426 (mtm110) cc_final: 0.7154 (ttp-110) REVERT: C 179 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7035 (mm-30) REVERT: C 183 ASN cc_start: 0.7100 (m-40) cc_final: 0.6641 (t160) REVERT: C 230 ASN cc_start: 0.6344 (m110) cc_final: 0.5969 (p0) REVERT: C 232 LEU cc_start: 0.8659 (mt) cc_final: 0.8354 (mm) REVERT: C 288 MET cc_start: 0.8922 (tpt) cc_final: 0.8613 (tpp) REVERT: C 298 ARG cc_start: 0.7513 (mtp-110) cc_final: 0.6810 (ttm-80) REVERT: C 388 MET cc_start: 0.5157 (mtt) cc_final: 0.4922 (mtp) REVERT: C 389 LYS cc_start: 0.6722 (mttp) cc_final: 0.6034 (mptt) REVERT: C 392 TYR cc_start: 0.7810 (m-80) cc_final: 0.7577 (m-80) REVERT: C 494 GLU cc_start: 0.4425 (OUTLIER) cc_final: 0.4145 (mp0) REVERT: D 56 LYS cc_start: 0.6770 (tmtt) cc_final: 0.6085 (mtmm) REVERT: D 58 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7426 (tpm170) REVERT: D 59 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7370 (pt) REVERT: D 86 ARG cc_start: 0.6571 (mtp180) cc_final: 0.5707 (ptt180) REVERT: D 93 ASP cc_start: 0.7750 (t0) cc_final: 0.7126 (m-30) REVERT: D 105 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8013 (pp) REVERT: D 109 PHE cc_start: 0.7676 (m-10) cc_final: 0.7412 (m-80) REVERT: D 115 LYS cc_start: 0.8547 (tppt) cc_final: 0.7539 (tppt) REVERT: D 152 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7400 (pp) REVERT: D 215 ARG cc_start: 0.7193 (ptt180) cc_final: 0.6580 (mtm110) REVERT: D 248 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8411 (mt) REVERT: D 294 HIS cc_start: 0.6859 (m-70) cc_final: 0.6511 (m-70) REVERT: D 317 HIS cc_start: 0.5232 (OUTLIER) cc_final: 0.4448 (p-80) REVERT: D 395 PRO cc_start: 0.7384 (Cg_endo) cc_final: 0.7091 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5262 (OUTLIER) cc_final: 0.4906 (tp) outliers start: 90 outliers final: 42 residues processed: 271 average time/residue: 1.1468 time to fit residues: 345.4956 Evaluate side-chains 255 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 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 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 A residue 500 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP 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 350 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 472 ASN Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 243 SER 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 367 MET Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 157 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.226573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136258 restraints weight = 16027.417| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.15 r_work: 0.3216 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3474 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= 0.124 Angle : 0.590 9.775 21476 Z= 0.304 Chirality : 0.042 0.189 2422 Planarity : 0.004 0.049 2688 Dihedral : 8.669 84.301 2225 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.18 % Allowed : 27.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1870 helix: 0.44 (0.15), residues: 1158 sheet: -1.27 (0.50), residues: 100 loop : -0.56 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 PHE 0.019 0.001 PHE C 409 TYR 0.024 0.001 TYR B 364 ARG 0.011 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 818) hydrogen bonds : angle 4.47442 ( 2361) covalent geometry : bond 0.00265 (15846) covalent geometry : angle 0.58979 (21476) *********************** 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 288 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 201 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.6335 (tppt) cc_final: 0.5776 (ttmm) REVERT: A 162 MET cc_start: 0.8595 (tpt) cc_final: 0.8167 (mmm) REVERT: A 183 ASN cc_start: 0.7126 (m-40) cc_final: 0.6233 (t160) REVERT: A 267 MET cc_start: 0.8983 (mtt) cc_final: 0.8645 (mtm) REVERT: A 298 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7311 (ttm-80) REVERT: A 356 SER cc_start: 0.7433 (t) cc_final: 0.7162 (p) REVERT: A 432 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: A 441 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.5089 (tt0) REVERT: A 464 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6321 (ttp-110) REVERT: A 497 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5851 (p0) REVERT: A 510 MET cc_start: -0.0119 (mtt) cc_final: -0.1011 (ptm) REVERT: B 46 ARG cc_start: 0.5489 (ttm-80) cc_final: 0.5200 (ttm-80) REVERT: B 58 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7603 (tpt-90) REVERT: B 59 ILE cc_start: 0.7749 (tp) cc_final: 0.7362 (pt) REVERT: B 83 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7225 (mtm110) REVERT: B 86 ARG cc_start: 0.6476 (mtp180) cc_final: 0.5636 (ptt180) REVERT: B 93 ASP cc_start: 0.7694 (t0) cc_final: 0.6963 (m-30) REVERT: B 109 PHE cc_start: 0.7133 (m-10) cc_final: 0.6897 (m-80) REVERT: B 115 LYS cc_start: 0.7906 (tppt) cc_final: 0.7659 (tppt) REVERT: B 190 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8147 (mmm160) REVERT: B 248 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 274 MET cc_start: 0.9261 (mtm) cc_final: 0.8959 (mtm) REVERT: B 315 ARG cc_start: 0.7016 (mmm160) cc_final: 0.5893 (tpt170) REVERT: B 400 ILE cc_start: 0.5106 (OUTLIER) cc_final: 0.4871 (tp) REVERT: B 485 MET cc_start: 0.4575 (tpt) cc_final: 0.3779 (mmt) REVERT: B 500 MET cc_start: 0.3510 (ppp) cc_final: 0.3159 (pp-130) REVERT: C 93 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: C 103 ASP cc_start: 0.7706 (t70) cc_final: 0.7417 (t0) REVERT: C 120 ILE cc_start: 0.7859 (tt) cc_final: 0.7449 (mp) REVERT: C 155 GLN cc_start: 0.7851 (mm110) cc_final: 0.7398 (mp10) REVERT: C 177 ARG cc_start: 0.7243 (mtm110) cc_final: 0.7004 (ttp-110) REVERT: C 179 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6842 (mm-30) REVERT: C 183 ASN cc_start: 0.7042 (m-40) cc_final: 0.6560 (t160) REVERT: C 185 ASN cc_start: 0.6959 (m-40) cc_final: 0.6139 (t0) REVERT: C 230 ASN cc_start: 0.6209 (m110) cc_final: 0.5821 (p0) REVERT: C 232 LEU cc_start: 0.8536 (mt) cc_final: 0.8181 (mm) REVERT: C 288 MET cc_start: 0.8867 (tpt) cc_final: 0.8496 (tpp) REVERT: C 298 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.6722 (ttm-80) REVERT: C 389 LYS cc_start: 0.6649 (mttp) cc_final: 0.5950 (mptt) REVERT: C 494 GLU cc_start: 0.4438 (OUTLIER) cc_final: 0.4153 (mp0) REVERT: C 513 ARG cc_start: -0.1127 (OUTLIER) cc_final: -0.1591 (ppt-90) REVERT: D 56 LYS cc_start: 0.6706 (tmtt) cc_final: 0.5892 (mtmm) REVERT: D 58 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7413 (tpt-90) REVERT: D 59 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7324 (pt) REVERT: D 86 ARG cc_start: 0.6520 (mtp180) cc_final: 0.5650 (ptt180) REVERT: D 93 ASP cc_start: 0.7644 (t0) cc_final: 0.6950 (m-30) REVERT: D 105 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7920 (pp) REVERT: D 109 PHE cc_start: 0.7541 (m-10) cc_final: 0.7278 (m-80) REVERT: D 115 LYS cc_start: 0.8535 (tppt) cc_final: 0.8097 (mptp) REVERT: D 152 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7324 (pp) REVERT: D 215 ARG cc_start: 0.7081 (ptt180) cc_final: 0.6382 (mtm110) REVERT: D 274 MET cc_start: 0.9423 (mtm) cc_final: 0.9211 (mtm) REVERT: D 294 HIS cc_start: 0.6632 (m-70) cc_final: 0.6267 (m-70) REVERT: D 317 HIS cc_start: 0.5122 (OUTLIER) cc_final: 0.4374 (p-80) REVERT: D 395 PRO cc_start: 0.7336 (Cg_endo) cc_final: 0.7059 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5218 (OUTLIER) cc_final: 0.4857 (tp) REVERT: D 500 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.5290 (tmm) outliers start: 87 outliers final: 36 residues processed: 267 average time/residue: 1.1832 time to fit residues: 350.4250 Evaluate side-chains 250 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 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 431 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP 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 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 472 ASN Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 106 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 0.0970 chunk 79 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 218 ASN B 307 GLN C 472 ASN D 414 ASN D 461 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.227297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138237 restraints weight = 16129.056| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.52 r_work: 0.3218 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15846 Z= 0.120 Angle : 0.587 9.985 21476 Z= 0.302 Chirality : 0.042 0.192 2422 Planarity : 0.004 0.051 2688 Dihedral : 8.438 84.008 2225 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.35 % Allowed : 27.83 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1870 helix: 0.60 (0.15), residues: 1158 sheet: -1.16 (0.51), residues: 100 loop : -0.41 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 PHE 0.022 0.001 PHE A 409 TYR 0.023 0.001 TYR B 364 ARG 0.013 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 818) hydrogen bonds : angle 4.38414 ( 2361) covalent geometry : bond 0.00253 (15846) covalent geometry : angle 0.58710 (21476) *********************** 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 271 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7173 (tmm) cc_final: 0.6804 (tmm) REVERT: A 125 LYS cc_start: 0.6463 (tppt) cc_final: 0.5853 (ttmm) REVERT: A 162 MET cc_start: 0.8725 (tpt) cc_final: 0.8111 (mmm) REVERT: A 183 ASN cc_start: 0.7185 (m-40) cc_final: 0.6339 (t160) REVERT: A 267 MET cc_start: 0.9078 (mtt) cc_final: 0.8754 (mtm) REVERT: A 298 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7483 (ttm-80) REVERT: A 300 ARG cc_start: 0.7572 (ptt90) cc_final: 0.7335 (ptt-90) REVERT: A 356 SER cc_start: 0.7505 (t) cc_final: 0.7182 (p) REVERT: A 441 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.5074 (tt0) REVERT: A 464 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6451 (ttp-110) REVERT: A 497 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5807 (p0) REVERT: A 510 MET cc_start: -0.0277 (mtt) cc_final: -0.1180 (ptm) REVERT: B 46 ARG cc_start: 0.5518 (ttm-80) cc_final: 0.5220 (ttm-80) REVERT: B 58 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7693 (mmt90) REVERT: B 59 ILE cc_start: 0.7878 (tp) cc_final: 0.7550 (pt) REVERT: B 83 ARG cc_start: 0.7778 (ptp-110) cc_final: 0.7380 (mtm110) REVERT: B 86 ARG cc_start: 0.6609 (mtp180) cc_final: 0.5741 (ptt180) REVERT: B 93 ASP cc_start: 0.7842 (t0) cc_final: 0.7200 (m-30) REVERT: B 109 PHE cc_start: 0.7355 (m-10) cc_final: 0.7135 (m-80) REVERT: B 115 LYS cc_start: 0.7891 (tppt) cc_final: 0.7670 (tppt) REVERT: B 190 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8308 (mmm160) REVERT: B 248 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8682 (mt) REVERT: B 315 ARG cc_start: 0.7076 (mmm160) cc_final: 0.5927 (tpt170) REVERT: B 397 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: B 400 ILE cc_start: 0.5275 (OUTLIER) cc_final: 0.5019 (tp) REVERT: B 485 MET cc_start: 0.4631 (tpt) cc_final: 0.3834 (mmt) REVERT: B 500 MET cc_start: 0.3534 (ppp) cc_final: 0.3303 (pp-130) REVERT: C 103 ASP cc_start: 0.7812 (t70) cc_final: 0.7555 (t0) REVERT: C 125 LYS cc_start: 0.8107 (tptp) cc_final: 0.7428 (mmtm) REVERT: C 155 GLN cc_start: 0.7890 (mm110) cc_final: 0.7453 (mp10) REVERT: C 177 ARG cc_start: 0.7384 (mtm110) cc_final: 0.7178 (ttp-110) REVERT: C 179 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6988 (mm-30) REVERT: C 183 ASN cc_start: 0.7148 (m-40) cc_final: 0.6652 (t160) REVERT: C 185 ASN cc_start: 0.7003 (m-40) cc_final: 0.6239 (t0) REVERT: C 230 ASN cc_start: 0.6321 (m110) cc_final: 0.5934 (p0) REVERT: C 288 MET cc_start: 0.9029 (tpt) cc_final: 0.8740 (tpp) REVERT: C 298 ARG cc_start: 0.7597 (mtp-110) cc_final: 0.7034 (ttm-80) REVERT: C 494 GLU cc_start: 0.4476 (OUTLIER) cc_final: 0.4168 (mp0) REVERT: C 511 LEU cc_start: 0.2883 (OUTLIER) cc_final: 0.2644 (mt) REVERT: C 513 ARG cc_start: -0.1233 (OUTLIER) cc_final: -0.1599 (ppt-90) REVERT: D 56 LYS cc_start: 0.6854 (tmtt) cc_final: 0.6052 (mtmm) REVERT: D 58 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7552 (tpt-90) REVERT: D 59 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7550 (pt) REVERT: D 86 ARG cc_start: 0.6590 (mtp180) cc_final: 0.5720 (ptt180) REVERT: D 93 ASP cc_start: 0.7791 (t0) cc_final: 0.7195 (m-30) REVERT: D 109 PHE cc_start: 0.7841 (m-10) cc_final: 0.7599 (m-80) REVERT: D 115 LYS cc_start: 0.8551 (tppt) cc_final: 0.8107 (mptp) REVERT: D 152 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7344 (pp) REVERT: D 215 ARG cc_start: 0.7278 (ptt180) cc_final: 0.6612 (mtm110) REVERT: D 248 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8451 (mm) REVERT: D 294 HIS cc_start: 0.6731 (m-70) cc_final: 0.6408 (m-70) REVERT: D 317 HIS cc_start: 0.5020 (OUTLIER) cc_final: 0.4258 (p-80) REVERT: D 395 PRO cc_start: 0.7504 (Cg_endo) cc_final: 0.7241 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5290 (OUTLIER) cc_final: 0.4969 (tp) REVERT: D 495 MET cc_start: 0.5162 (pp-130) cc_final: 0.4848 (pp-130) REVERT: D 500 MET cc_start: 0.5565 (OUTLIER) cc_final: 0.5257 (tmm) outliers start: 73 outliers final: 33 residues processed: 257 average time/residue: 1.1736 time to fit residues: 334.8126 Evaluate side-chains 241 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 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 441 GLU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 248 ILE 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 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 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 383 GLN 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 494 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 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 400 ILE Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 160 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 133 optimal weight: 0.0170 chunk 14 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.226622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140039 restraints weight = 15911.347| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.22 r_work: 0.3188 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15846 Z= 0.135 Angle : 0.604 12.783 21476 Z= 0.308 Chirality : 0.042 0.204 2422 Planarity : 0.004 0.049 2688 Dihedral : 8.306 83.906 2223 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.41 % Allowed : 27.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1870 helix: 0.68 (0.15), residues: 1154 sheet: -1.14 (0.51), residues: 100 loop : -0.37 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 PHE 0.011 0.001 PHE B 272 TYR 0.024 0.001 TYR B 364 ARG 0.014 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 818) hydrogen bonds : angle 4.36876 ( 2361) covalent geometry : bond 0.00303 (15846) covalent geometry : angle 0.60433 (21476) *********************** 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 261 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7177 (tmm) cc_final: 0.6806 (tmm) REVERT: A 119 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7041 (mt) REVERT: A 125 LYS cc_start: 0.6653 (tppt) cc_final: 0.6092 (ttmm) REVERT: A 162 MET cc_start: 0.8754 (tpt) cc_final: 0.8174 (mmm) REVERT: A 183 ASN cc_start: 0.7200 (m-40) cc_final: 0.6372 (t160) REVERT: A 267 MET cc_start: 0.9097 (mtt) cc_final: 0.8804 (mtm) REVERT: A 298 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7494 (ttm-80) REVERT: A 300 ARG cc_start: 0.7716 (ptt90) cc_final: 0.7503 (ptt-90) REVERT: A 356 SER cc_start: 0.7573 (t) cc_final: 0.7233 (p) REVERT: A 432 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: A 441 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.5131 (tt0) REVERT: A 451 LEU cc_start: 0.4781 (OUTLIER) cc_final: 0.4532 (mt) REVERT: A 464 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6502 (ttp-110) REVERT: A 497 ASP cc_start: 0.6234 (OUTLIER) cc_final: 0.5993 (p0) REVERT: A 510 MET cc_start: -0.0277 (mtt) cc_final: -0.1158 (ptm) REVERT: B 46 ARG cc_start: 0.5561 (ttm-80) cc_final: 0.5276 (ttm-80) REVERT: B 58 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7729 (mmt90) REVERT: B 59 ILE cc_start: 0.7923 (tp) cc_final: 0.7578 (pt) REVERT: B 83 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7409 (mtm110) REVERT: B 86 ARG cc_start: 0.6634 (mtp180) cc_final: 0.5798 (ptt180) REVERT: B 93 ASP cc_start: 0.7855 (t0) cc_final: 0.7240 (m-30) REVERT: B 109 PHE cc_start: 0.7360 (m-10) cc_final: 0.7140 (m-80) REVERT: B 190 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8384 (mtp180) REVERT: B 248 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8701 (mt) REVERT: B 397 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7059 (tp30) REVERT: B 400 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.5055 (tp) REVERT: B 485 MET cc_start: 0.4498 (tpt) cc_final: 0.3853 (mmt) REVERT: B 500 MET cc_start: 0.3534 (ppp) cc_final: 0.3305 (pp-130) REVERT: C 103 ASP cc_start: 0.7916 (t70) cc_final: 0.7671 (t0) REVERT: C 155 GLN cc_start: 0.7897 (mm110) cc_final: 0.7437 (mp10) REVERT: C 177 ARG cc_start: 0.7414 (mtm110) cc_final: 0.7200 (ttp-110) REVERT: C 179 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7272 (mm-30) REVERT: C 183 ASN cc_start: 0.7142 (m-40) cc_final: 0.6619 (t160) REVERT: C 185 ASN cc_start: 0.6849 (m-40) cc_final: 0.6156 (t0) REVERT: C 230 ASN cc_start: 0.6375 (m110) cc_final: 0.6018 (p0) REVERT: C 232 LEU cc_start: 0.8695 (mt) cc_final: 0.8482 (mm) REVERT: C 288 MET cc_start: 0.9055 (tpt) cc_final: 0.8775 (tpp) REVERT: C 298 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7010 (ttm-80) REVERT: C 494 GLU cc_start: 0.4475 (OUTLIER) cc_final: 0.4179 (mp0) REVERT: C 511 LEU cc_start: 0.2862 (OUTLIER) cc_final: 0.2651 (mt) REVERT: C 513 ARG cc_start: -0.1213 (OUTLIER) cc_final: -0.1685 (ppt-90) REVERT: D 58 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7582 (tpt-90) REVERT: D 59 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7566 (pt) REVERT: D 86 ARG cc_start: 0.6579 (mtp180) cc_final: 0.5721 (ptt180) REVERT: D 93 ASP cc_start: 0.7817 (t0) cc_final: 0.7242 (m-30) REVERT: D 109 PHE cc_start: 0.7782 (m-10) cc_final: 0.7529 (m-80) REVERT: D 115 LYS cc_start: 0.8538 (tppt) cc_final: 0.8078 (mptp) REVERT: D 215 ARG cc_start: 0.7243 (ptt180) cc_final: 0.6617 (mmm160) REVERT: D 294 HIS cc_start: 0.6773 (m-70) cc_final: 0.6409 (m-70) REVERT: D 317 HIS cc_start: 0.4930 (OUTLIER) cc_final: 0.4168 (p-80) REVERT: D 330 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6592 (mm) REVERT: D 387 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7491 (pt0) REVERT: D 395 PRO cc_start: 0.7522 (Cg_endo) cc_final: 0.7253 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.5076 (tp) REVERT: D 495 MET cc_start: 0.5241 (pp-130) cc_final: 0.4855 (tmm) REVERT: D 500 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.5147 (tmm) outliers start: 74 outliers final: 41 residues processed: 248 average time/residue: 1.2507 time to fit residues: 347.1750 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 : 1.596 ------------------------------------------------------------------------------- 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 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 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 248 ILE 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 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 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 243 SER 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 366 LEU Chi-restraints excluded: chain D residue 400 ILE 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 148 optimal weight: 5.9990 chunk 56 optimal weight: 0.0030 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN C 472 ASN D 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.227939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141752 restraints weight = 16066.346| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.20 r_work: 0.3245 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15846 Z= 0.120 Angle : 0.593 10.921 21476 Z= 0.303 Chirality : 0.042 0.198 2422 Planarity : 0.004 0.054 2688 Dihedral : 8.074 84.748 2223 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.87 % Allowed : 28.84 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1870 helix: 0.77 (0.15), residues: 1168 sheet: -0.96 (0.50), residues: 104 loop : -0.38 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 135 HIS 0.005 0.001 HIS D 329 PHE 0.010 0.001 PHE C 231 TYR 0.023 0.001 TYR B 364 ARG 0.015 0.000 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 818) hydrogen bonds : angle 4.28775 ( 2361) covalent geometry : bond 0.00257 (15846) covalent geometry : angle 0.59317 (21476) *********************** 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 249 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7121 (tmm) cc_final: 0.6770 (tmm) REVERT: A 119 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6944 (mt) REVERT: A 125 LYS cc_start: 0.6665 (tppt) cc_final: 0.6103 (ttmm) REVERT: A 162 MET cc_start: 0.8763 (tpt) cc_final: 0.8189 (mmm) REVERT: A 183 ASN cc_start: 0.7165 (m-40) cc_final: 0.6495 (t160) REVERT: A 267 MET cc_start: 0.9093 (mtt) cc_final: 0.8775 (mtm) REVERT: A 298 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7458 (ttt180) REVERT: A 356 SER cc_start: 0.7615 (t) cc_final: 0.7222 (p) REVERT: A 441 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5137 (tt0) REVERT: A 451 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4571 (mt) REVERT: A 464 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6412 (ttp-110) REVERT: A 497 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.6010 (p0) REVERT: A 510 MET cc_start: -0.0307 (mtt) cc_final: -0.1214 (ptm) REVERT: B 46 ARG cc_start: 0.5645 (ttm-80) cc_final: 0.5255 (ttm-80) REVERT: B 58 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7713 (mmt90) REVERT: B 59 ILE cc_start: 0.7857 (tp) cc_final: 0.7550 (pt) REVERT: B 83 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7416 (mtm110) REVERT: B 86 ARG cc_start: 0.6546 (mtp180) cc_final: 0.5682 (ptt180) REVERT: B 93 ASP cc_start: 0.7834 (t0) cc_final: 0.7228 (m-30) REVERT: B 109 PHE cc_start: 0.7328 (m-10) cc_final: 0.7119 (m-80) REVERT: B 190 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8366 (mmm160) REVERT: B 317 HIS cc_start: 0.5479 (OUTLIER) cc_final: 0.4642 (p-80) REVERT: B 327 LEU cc_start: 0.7117 (mt) cc_final: 0.6867 (mt) REVERT: B 397 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: B 400 ILE cc_start: 0.5335 (OUTLIER) cc_final: 0.5107 (tp) REVERT: B 485 MET cc_start: 0.4472 (tpt) cc_final: 0.3820 (mmt) REVERT: B 500 MET cc_start: 0.3546 (ppp) cc_final: 0.3311 (pp-130) REVERT: C 103 ASP cc_start: 0.7857 (t70) cc_final: 0.7652 (t0) REVERT: C 155 GLN cc_start: 0.7849 (mm110) cc_final: 0.7371 (mp10) REVERT: C 179 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7217 (mm-30) REVERT: C 183 ASN cc_start: 0.7134 (m-40) cc_final: 0.6620 (t160) REVERT: C 185 ASN cc_start: 0.7034 (m-40) cc_final: 0.6330 (t0) REVERT: C 230 ASN cc_start: 0.6358 (m110) cc_final: 0.5992 (p0) REVERT: C 288 MET cc_start: 0.9044 (tpt) cc_final: 0.8774 (tpp) REVERT: C 298 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7043 (ttm-80) REVERT: C 494 GLU cc_start: 0.4510 (OUTLIER) cc_final: 0.4210 (mp0) REVERT: C 510 MET cc_start: 0.0865 (ttt) cc_final: 0.0590 (ttm) REVERT: C 511 LEU cc_start: 0.2917 (OUTLIER) cc_final: 0.2652 (mt) REVERT: C 513 ARG cc_start: -0.1053 (OUTLIER) cc_final: -0.1606 (ppt90) REVERT: D 58 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7683 (mmt90) REVERT: D 86 ARG cc_start: 0.6569 (mtp180) cc_final: 0.5725 (ptt180) REVERT: D 93 ASP cc_start: 0.7761 (t0) cc_final: 0.7217 (m-30) REVERT: D 109 PHE cc_start: 0.7789 (m-10) cc_final: 0.7553 (m-80) REVERT: D 115 LYS cc_start: 0.8529 (tppt) cc_final: 0.8066 (mptp) REVERT: D 215 ARG cc_start: 0.7193 (ptt180) cc_final: 0.6609 (mmm160) REVERT: D 294 HIS cc_start: 0.6659 (m-70) cc_final: 0.6320 (m-70) REVERT: D 317 HIS cc_start: 0.4788 (OUTLIER) cc_final: 0.4046 (p-80) REVERT: D 387 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7603 (pt0) REVERT: D 395 PRO cc_start: 0.7569 (Cg_endo) cc_final: 0.7308 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.5122 (tp) REVERT: D 495 MET cc_start: 0.5421 (pp-130) cc_final: 0.5131 (tmm) REVERT: D 500 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5162 (tmm) outliers start: 65 outliers final: 34 residues processed: 238 average time/residue: 1.2206 time to fit residues: 321.7400 Evaluate side-chains 232 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 358 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 248 ILE 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 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 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 366 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 14 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.0020 chunk 148 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.227359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142236 restraints weight = 15960.828| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.71 r_work: 0.3205 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3900 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= 0.128 Angle : 0.604 11.307 21476 Z= 0.307 Chirality : 0.042 0.200 2422 Planarity : 0.004 0.055 2688 Dihedral : 7.993 84.585 2223 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.16 % Allowed : 29.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1870 helix: 0.78 (0.15), residues: 1174 sheet: -0.85 (0.51), residues: 104 loop : -0.40 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 246 HIS 0.006 0.001 HIS B 294 PHE 0.019 0.001 PHE C 409 TYR 0.025 0.001 TYR B 364 ARG 0.015 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 818) hydrogen bonds : angle 4.29698 ( 2361) covalent geometry : bond 0.00284 (15846) covalent geometry : angle 0.60423 (21476) ********************** 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 238 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7127 (tmm) cc_final: 0.6753 (tmm) REVERT: A 119 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6940 (mt) REVERT: A 125 LYS cc_start: 0.6651 (tppt) cc_final: 0.6092 (ttmm) REVERT: A 162 MET cc_start: 0.8769 (tpt) cc_final: 0.8445 (mmm) REVERT: A 183 ASN cc_start: 0.7170 (m-40) cc_final: 0.6469 (t160) REVERT: A 267 MET cc_start: 0.9102 (mtt) cc_final: 0.8816 (mtm) REVERT: A 298 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7466 (ttt180) REVERT: A 356 SER cc_start: 0.7624 (t) cc_final: 0.7205 (p) REVERT: A 441 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5171 (tt0) REVERT: A 451 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4566 (mt) REVERT: A 510 MET cc_start: 0.0270 (mtt) cc_final: -0.0727 (ptm) REVERT: B 46 ARG cc_start: 0.5625 (ttm-80) cc_final: 0.5269 (ttm-80) REVERT: B 58 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7726 (mmt90) REVERT: B 59 ILE cc_start: 0.7918 (tp) cc_final: 0.7641 (pt) REVERT: B 83 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7428 (mtm110) REVERT: B 86 ARG cc_start: 0.6507 (mtp180) cc_final: 0.5641 (ptt180) REVERT: B 93 ASP cc_start: 0.7799 (t0) cc_final: 0.7198 (m-30) REVERT: B 109 PHE cc_start: 0.7343 (m-10) cc_final: 0.7135 (m-80) REVERT: B 190 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8395 (mmm160) REVERT: B 248 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8709 (mt) REVERT: B 317 HIS cc_start: 0.5438 (OUTLIER) cc_final: 0.4592 (p-80) REVERT: B 327 LEU cc_start: 0.7054 (mt) cc_final: 0.6805 (mt) REVERT: B 397 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: B 400 ILE cc_start: 0.5344 (OUTLIER) cc_final: 0.5111 (tp) REVERT: B 485 MET cc_start: 0.4473 (tpt) cc_final: 0.3829 (mmt) REVERT: C 155 GLN cc_start: 0.7858 (mm110) cc_final: 0.7378 (mp10) REVERT: C 179 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 183 ASN cc_start: 0.7191 (m-40) cc_final: 0.6632 (t160) REVERT: C 185 ASN cc_start: 0.6999 (m-40) cc_final: 0.6305 (t0) REVERT: C 230 ASN cc_start: 0.6390 (m110) cc_final: 0.6039 (p0) REVERT: C 288 MET cc_start: 0.9056 (tpt) cc_final: 0.8762 (tpp) REVERT: C 298 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.7032 (ttm-80) REVERT: C 494 GLU cc_start: 0.4526 (OUTLIER) cc_final: 0.4239 (mp0) REVERT: C 511 LEU cc_start: 0.2941 (OUTLIER) cc_final: 0.2705 (mt) REVERT: C 513 ARG cc_start: -0.1132 (OUTLIER) cc_final: -0.1669 (ppt90) REVERT: D 58 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7511 (tpt-90) REVERT: D 86 ARG cc_start: 0.6569 (mtp180) cc_final: 0.5724 (ptt180) REVERT: D 93 ASP cc_start: 0.7781 (t0) cc_final: 0.7223 (m-30) REVERT: D 109 PHE cc_start: 0.7852 (m-10) cc_final: 0.7628 (m-80) REVERT: D 115 LYS cc_start: 0.8571 (tppt) cc_final: 0.8121 (mptp) REVERT: D 215 ARG cc_start: 0.7066 (ptt180) cc_final: 0.6506 (mmm160) REVERT: D 294 HIS cc_start: 0.6721 (m-70) cc_final: 0.6362 (m-70) REVERT: D 317 HIS cc_start: 0.4662 (OUTLIER) cc_final: 0.3971 (p-80) REVERT: D 330 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6446 (mm) REVERT: D 387 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7562 (pt0) REVERT: D 395 PRO cc_start: 0.7577 (Cg_endo) cc_final: 0.7314 (Cg_exo) REVERT: D 400 ILE cc_start: 0.5509 (OUTLIER) cc_final: 0.5127 (tp) REVERT: D 465 MET cc_start: 0.7217 (tpt) cc_final: 0.6739 (tmm) REVERT: D 495 MET cc_start: 0.5411 (pp-130) cc_final: 0.5111 (tmm) REVERT: D 500 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5146 (tmm) outliers start: 53 outliers final: 30 residues processed: 231 average time/residue: 1.1496 time to fit residues: 295.6405 Evaluate side-chains 231 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL 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 358 ILE 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 441 GLU Chi-restraints excluded: chain A residue 451 LEU 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 83 ARG Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 248 ILE 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 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 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 513 ARG Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.227793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137447 restraints weight = 15919.629| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.16 r_work: 0.3204 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15846 Z= 0.128 Angle : 0.615 11.423 21476 Z= 0.312 Chirality : 0.042 0.211 2422 Planarity : 0.004 0.058 2688 Dihedral : 7.892 84.593 2223 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.04 % Allowed : 29.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1870 helix: 0.82 (0.15), residues: 1174 sheet: -0.90 (0.56), residues: 90 loop : -0.35 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 135 HIS 0.006 0.001 HIS D 329 PHE 0.021 0.001 PHE C 409 TYR 0.026 0.001 TYR D 364 ARG 0.015 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 818) hydrogen bonds : angle 4.28564 ( 2361) covalent geometry : bond 0.00281 (15846) covalent geometry : angle 0.61521 (21476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15924.25 seconds wall clock time: 273 minutes 31.13 seconds (16411.13 seconds total)