Starting phenix.real_space_refine on Tue Dec 31 13:00:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wm2_32598/12_2024/7wm2_32598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wm2_32598/12_2024/7wm2_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_32598/12_2024/7wm2_32598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wm2_32598/12_2024/7wm2_32598.map" model { file = "/net/cci-nas-00/data/ceres_data/7wm2_32598/12_2024/7wm2_32598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wm2_32598/12_2024/7wm2_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-5532/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: 9.79, per 1000 atoms: 0.63 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: 4.29 Conformation dependent library (CDL) restraints added in 2.1 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: 1.69 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: 4.69 Time building geometry restraints manager: 4.63 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: 1.010 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.250 Find NCS groups from input model: 1.050 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: 0.010 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- 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= 0.755 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 *********************** 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 : 1.717 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: 1.2291 time to fit residues: 581.7792 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 : 2.034 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2208 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= 0.224 Angle : 0.727 9.706 21476 Z= 0.379 Chirality : 0.046 0.180 2422 Planarity : 0.005 0.042 2688 Dihedral : 12.061 90.632 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: -0.93 (0.14), residues: 1148 sheet: -2.25 (0.49), residues: 102 loop : -1.26 (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 *********************** 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 : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: A 103 ASP cc_start: 0.7378 (t70) cc_final: 0.7093 (t0) REVERT: A 137 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6608 (tt) REVERT: A 155 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7315 (mp10) REVERT: A 162 MET cc_start: 0.8189 (tpt) cc_final: 0.7589 (mmm) REVERT: A 183 ASN cc_start: 0.6832 (m-40) cc_final: 0.6186 (t160) REVERT: A 194 LEU cc_start: 0.7696 (mt) cc_final: 0.7446 (mt) REVERT: A 232 LEU cc_start: 0.8507 (mt) cc_final: 0.8247 (mm) REVERT: A 267 MET cc_start: 0.8396 (mtt) cc_final: 0.7974 (mtm) REVERT: A 298 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.7005 (ttm-80) REVERT: A 339 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5656 (mt-10) REVERT: A 510 MET cc_start: 0.0370 (mtt) cc_final: -0.0602 (ptm) REVERT: B 46 ARG cc_start: 0.5662 (ttm-80) cc_final: 0.5284 (ttm-80) REVERT: B 83 ARG cc_start: 0.7127 (ptp-110) cc_final: 0.6756 (mtm110) REVERT: B 86 ARG cc_start: 0.6705 (mtp180) cc_final: 0.6030 (ptt180) REVERT: B 93 ASP cc_start: 0.7230 (t0) cc_final: 0.6452 (m-30) REVERT: B 105 ILE cc_start: 0.7807 (mt) cc_final: 0.7573 (mt) REVERT: B 109 PHE cc_start: 0.7067 (m-10) cc_final: 0.6793 (m-80) REVERT: B 133 ARG cc_start: 0.6791 (mtp180) cc_final: 0.6212 (mtm-85) REVERT: B 307 GLN cc_start: 0.7590 (pp30) cc_final: 0.7330 (tp40) REVERT: B 337 ASP cc_start: 0.6775 (m-30) cc_final: 0.6558 (m-30) REVERT: B 344 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: B 352 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.4530 (tmtt) REVERT: B 397 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6439 (tp30) REVERT: B 485 MET cc_start: 0.4420 (tpt) cc_final: 0.3496 (mmt) REVERT: B 495 MET cc_start: 0.6048 (ttm) cc_final: 0.5753 (tpp) REVERT: C 93 ASP cc_start: 0.7849 (t0) cc_final: 0.7504 (m-30) REVERT: C 103 ASP cc_start: 0.7500 (t70) cc_final: 0.7148 (t0) REVERT: C 113 LEU cc_start: 0.7808 (mm) cc_final: 0.7506 (tp) REVERT: C 122 ASP cc_start: 0.6573 (p0) cc_final: 0.6317 (p0) REVERT: C 151 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6925 (ppt170) REVERT: C 155 GLN cc_start: 0.7730 (mm110) cc_final: 0.7282 (mp10) REVERT: C 177 ARG cc_start: 0.6919 (mtm110) cc_final: 0.6595 (ttp-110) REVERT: C 179 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6536 (mm-30) REVERT: C 182 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7019 (ttm-80) REVERT: C 183 ASN cc_start: 0.6928 (m-40) cc_final: 0.6660 (t160) REVERT: C 194 LEU cc_start: 0.7345 (mt) cc_final: 0.7138 (mt) REVERT: C 248 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (mt) REVERT: C 267 MET cc_start: 0.8347 (mtt) cc_final: 0.8097 (mtt) REVERT: C 288 MET cc_start: 0.7827 (tpt) cc_final: 0.7421 (tpp) REVERT: C 298 ARG cc_start: 0.6709 (mtp-110) cc_final: 0.6017 (ttm-80) REVERT: C 300 ARG cc_start: 0.7057 (ptt90) cc_final: 0.6781 (ptt-90) REVERT: C 343 GLN cc_start: 0.5156 (OUTLIER) cc_final: 0.4294 (pp30) REVERT: C 388 MET cc_start: 0.5054 (mtt) cc_final: 0.4806 (mtp) REVERT: C 401 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6406 (pp) REVERT: C 494 GLU cc_start: 0.4702 (OUTLIER) cc_final: 0.4494 (mp0) REVERT: D 56 LYS cc_start: 0.6572 (tmtt) cc_final: 0.6102 (mttp) REVERT: D 86 ARG cc_start: 0.6525 (mtp180) cc_final: 0.5871 (ptt180) REVERT: D 93 ASP cc_start: 0.7213 (t0) cc_final: 0.6452 (m-30) REVERT: D 105 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7793 (pt) REVERT: D 109 PHE cc_start: 0.7457 (m-10) cc_final: 0.7225 (m-80) REVERT: D 125 LYS cc_start: 0.7472 (mmtt) cc_final: 0.6445 (tttt) REVERT: D 162 MET cc_start: 0.8617 (tpt) cc_final: 0.8016 (mmm) REVERT: D 215 ARG cc_start: 0.6495 (ptt180) cc_final: 0.6178 (mtm110) REVERT: D 294 HIS cc_start: 0.6413 (m-70) cc_final: 0.6120 (m-70) REVERT: D 307 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7125 (mm110) REVERT: D 317 HIS cc_start: 0.5192 (OUTLIER) cc_final: 0.4454 (p-80) REVERT: D 330 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6348 (mm) REVERT: D 333 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5167 (tptp) REVERT: D 348 ASP cc_start: 0.6265 (p0) cc_final: 0.5983 (p0) REVERT: D 384 LEU cc_start: 0.4387 (OUTLIER) cc_final: 0.4129 (mm) REVERT: D 395 PRO cc_start: 0.7207 (Cg_endo) cc_final: 0.6895 (Cg_exo) REVERT: D 432 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.4943 (pm20) REVERT: D 506 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.4863 (pp20) REVERT: D 510 MET cc_start: 0.4847 (tpt) cc_final: 0.4630 (tmm) outliers start: 103 outliers final: 27 residues processed: 318 average time/residue: 1.1685 time to fit residues: 413.4747 Evaluate side-chains 252 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 93 ASP 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 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 248 ILE 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 93 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 0.0570 chunk 167 optimal weight: 10.0000 chunk 57 optimal weight: 0.1980 chunk 135 optimal weight: 0.9990 overall best weight: 1.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 383 GLN ** A 402 GLN ** 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 C 472 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15846 Z= 0.255 Angle : 0.663 12.029 21476 Z= 0.342 Chirality : 0.046 0.320 2422 Planarity : 0.004 0.040 2688 Dihedral : 10.647 90.441 2269 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 6.50 % Allowed : 26.40 % 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: -0.97 (0.19), residues: 1870 helix: -0.26 (0.15), residues: 1144 sheet: -1.84 (0.49), residues: 102 loop : -0.89 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 246 HIS 0.005 0.001 HIS D 329 PHE 0.020 0.001 PHE A 409 TYR 0.023 0.002 TYR B 364 ARG 0.010 0.001 ARG B 182 *********************** 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 319 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 210 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7579 (t70) cc_final: 0.7328 (t0) REVERT: A 120 ILE cc_start: 0.7933 (mt) cc_final: 0.7667 (pp) REVERT: A 125 LYS cc_start: 0.6419 (tppt) cc_final: 0.5823 (ttmm) REVERT: A 155 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7310 (mp10) REVERT: A 162 MET cc_start: 0.8123 (tpt) cc_final: 0.7565 (mmm) REVERT: A 183 ASN cc_start: 0.6824 (m-40) cc_final: 0.6090 (t160) REVERT: A 267 MET cc_start: 0.8431 (mtt) cc_final: 0.7991 (mtm) REVERT: A 298 ARG cc_start: 0.7367 (ttp-170) cc_final: 0.6989 (ttt90) REVERT: A 339 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5665 (mt-10) REVERT: A 464 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5851 (ttp-110) REVERT: A 510 MET cc_start: 0.0113 (mtt) cc_final: -0.0679 (ptm) REVERT: B 46 ARG cc_start: 0.5697 (ttm-80) cc_final: 0.5359 (ttm-80) REVERT: B 83 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6767 (mtm110) REVERT: B 86 ARG cc_start: 0.6527 (mtp180) cc_final: 0.5805 (ptt180) REVERT: B 93 ASP cc_start: 0.7242 (t0) cc_final: 0.6493 (m-30) REVERT: B 109 PHE cc_start: 0.7045 (m-10) cc_final: 0.6796 (m-80) REVERT: B 162 MET cc_start: 0.8643 (tpt) cc_final: 0.8194 (mmm) REVERT: B 307 GLN cc_start: 0.7453 (pp30) cc_final: 0.7243 (tp40) REVERT: B 315 ARG cc_start: 0.7155 (mmm160) cc_final: 0.6612 (tmt-80) REVERT: B 317 HIS cc_start: 0.5567 (OUTLIER) cc_final: 0.4759 (p-80) REVERT: B 337 ASP cc_start: 0.6770 (m-30) cc_final: 0.6563 (m-30) REVERT: B 485 MET cc_start: 0.4373 (tpt) cc_final: 0.3537 (mmt) REVERT: B 500 MET cc_start: 0.3593 (ppp) cc_final: 0.3214 (pp-130) REVERT: C 93 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: C 103 ASP cc_start: 0.7494 (t70) cc_final: 0.7141 (t0) REVERT: C 113 LEU cc_start: 0.7815 (mm) cc_final: 0.7525 (tp) REVERT: C 151 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6895 (ppt170) REVERT: C 155 GLN cc_start: 0.7724 (mm110) cc_final: 0.7276 (mp10) REVERT: C 177 ARG cc_start: 0.6956 (mtm110) cc_final: 0.6704 (ttp-110) REVERT: C 179 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6560 (mm-30) REVERT: C 182 ARG cc_start: 0.7300 (ttm110) cc_final: 0.6893 (mtm-85) REVERT: C 183 ASN cc_start: 0.6812 (m-40) cc_final: 0.6451 (t160) REVERT: C 194 LEU cc_start: 0.7395 (mt) cc_final: 0.7188 (mt) REVERT: C 232 LEU cc_start: 0.8356 (mt) cc_final: 0.8077 (mm) REVERT: C 267 MET cc_start: 0.8424 (mtt) cc_final: 0.7979 (mtm) REVERT: C 288 MET cc_start: 0.7913 (tpt) cc_final: 0.7430 (tpp) REVERT: C 298 ARG cc_start: 0.6765 (mtp-110) cc_final: 0.6028 (ttm-80) REVERT: C 381 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4979 (mp) REVERT: C 388 MET cc_start: 0.4714 (mtt) cc_final: 0.4484 (mtp) REVERT: C 401 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6314 (pp) REVERT: C 494 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3984 (mp0) REVERT: D 56 LYS cc_start: 0.6723 (tmtt) cc_final: 0.6067 (mtmm) REVERT: D 58 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6905 (tpm170) REVERT: D 59 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6903 (pt) REVERT: D 86 ARG cc_start: 0.6334 (mtp180) cc_final: 0.5683 (ptt180) REVERT: D 93 ASP cc_start: 0.7155 (t0) cc_final: 0.6469 (m-30) REVERT: D 105 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7722 (pp) REVERT: D 108 PHE cc_start: 0.8136 (m-10) cc_final: 0.7934 (m-80) REVERT: D 109 PHE cc_start: 0.7446 (m-10) cc_final: 0.7181 (m-80) REVERT: D 115 LYS cc_start: 0.8418 (tppt) cc_final: 0.7442 (tppt) REVERT: D 125 LYS cc_start: 0.7345 (mmtt) cc_final: 0.6206 (tttt) REVERT: D 215 ARG cc_start: 0.6523 (ptt180) cc_final: 0.6120 (mtm110) REVERT: D 248 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7318 (mm) REVERT: D 294 HIS cc_start: 0.6526 (m-70) cc_final: 0.6155 (m-70) REVERT: D 330 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6294 (mm) REVERT: D 395 PRO cc_start: 0.7158 (Cg_endo) cc_final: 0.6886 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6619 (tp30) REVERT: D 400 ILE cc_start: 0.4869 (OUTLIER) cc_final: 0.4350 (tp) outliers start: 109 outliers final: 38 residues processed: 294 average time/residue: 1.1660 time to fit residues: 382.8227 Evaluate side-chains 256 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 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 500 MET Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 115 LYS 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 327 LEU Chi-restraints excluded: chain B residue 356 SER 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 104 ILE 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 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 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 105 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 C 216 ASN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3072 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= 0.194 Angle : 0.616 10.280 21476 Z= 0.319 Chirality : 0.043 0.311 2422 Planarity : 0.004 0.047 2688 Dihedral : 9.813 102.260 2239 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.36 % Allowed : 27.06 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.19), residues: 1870 helix: 0.09 (0.15), residues: 1148 sheet: -1.52 (0.50), residues: 100 loop : -0.68 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.021 0.001 PHE C 409 TYR 0.023 0.002 TYR B 364 ARG 0.008 0.000 ARG B 182 *********************** 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 296 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 206 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7601 (t70) cc_final: 0.7345 (t0) REVERT: A 122 ASP cc_start: 0.6679 (p0) cc_final: 0.6404 (p0) REVERT: A 125 LYS cc_start: 0.6457 (tppt) cc_final: 0.5927 (ttmm) REVERT: A 155 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7299 (mp10) REVERT: A 162 MET cc_start: 0.8125 (tpt) cc_final: 0.7637 (mmm) REVERT: A 183 ASN cc_start: 0.6820 (m-40) cc_final: 0.6086 (t160) REVERT: A 267 MET cc_start: 0.8446 (mtt) cc_final: 0.8018 (mtm) REVERT: A 298 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6922 (ttm-80) REVERT: A 464 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5879 (ttp-110) REVERT: A 510 MET cc_start: -0.0004 (mtt) cc_final: -0.0860 (ptm) REVERT: B 46 ARG cc_start: 0.5645 (ttm-80) cc_final: 0.5321 (ttm-80) REVERT: B 59 ILE cc_start: 0.7707 (tp) cc_final: 0.7236 (pt) REVERT: B 83 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6745 (mtm110) REVERT: B 84 LYS cc_start: 0.7811 (pttm) cc_final: 0.7585 (ptmm) REVERT: B 86 ARG cc_start: 0.6424 (mtp180) cc_final: 0.5732 (ptt180) REVERT: B 93 ASP cc_start: 0.7297 (t0) cc_final: 0.6585 (m-30) REVERT: B 109 PHE cc_start: 0.6888 (m-10) cc_final: 0.6653 (m-80) REVERT: B 248 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7768 (mt) REVERT: B 397 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: B 485 MET cc_start: 0.4305 (tpt) cc_final: 0.3597 (mmt) REVERT: B 500 MET cc_start: 0.3597 (ppp) cc_final: 0.3185 (pp-130) REVERT: C 93 ASP cc_start: 0.7838 (t0) cc_final: 0.7538 (m-30) REVERT: C 103 ASP cc_start: 0.7465 (t70) cc_final: 0.7135 (t0) REVERT: C 113 LEU cc_start: 0.7753 (mm) cc_final: 0.7477 (tp) REVERT: C 122 ASP cc_start: 0.6640 (p0) cc_final: 0.6411 (p0) REVERT: C 151 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6918 (ppt170) REVERT: C 155 GLN cc_start: 0.7740 (mm110) cc_final: 0.7294 (mp10) REVERT: C 177 ARG cc_start: 0.6986 (mtm110) cc_final: 0.6718 (ttp-110) REVERT: C 179 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6505 (mm-30) REVERT: C 182 ARG cc_start: 0.7232 (ttm110) cc_final: 0.6767 (ttm-80) REVERT: C 183 ASN cc_start: 0.6840 (m-40) cc_final: 0.6474 (t160) REVERT: C 194 LEU cc_start: 0.7375 (mt) cc_final: 0.7160 (mt) REVERT: C 232 LEU cc_start: 0.8366 (mt) cc_final: 0.8043 (mm) REVERT: C 267 MET cc_start: 0.8412 (mtt) cc_final: 0.7961 (mtm) REVERT: C 288 MET cc_start: 0.7894 (tpt) cc_final: 0.7512 (tpp) REVERT: C 298 ARG cc_start: 0.6756 (mtp-110) cc_final: 0.6051 (ttm-80) REVERT: C 388 MET cc_start: 0.4562 (mtt) cc_final: 0.4334 (mtp) REVERT: C 389 LYS cc_start: 0.6040 (mttp) cc_final: 0.5499 (mptt) REVERT: C 401 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6340 (pp) REVERT: C 494 GLU cc_start: 0.4401 (OUTLIER) cc_final: 0.4134 (mp0) REVERT: D 56 LYS cc_start: 0.6630 (tmtt) cc_final: 0.5994 (mtmm) REVERT: D 58 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6865 (tpm170) REVERT: D 59 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7051 (pt) REVERT: D 86 ARG cc_start: 0.6364 (mtp180) cc_final: 0.5712 (ptt180) REVERT: D 93 ASP cc_start: 0.7124 (t0) cc_final: 0.6536 (m-30) REVERT: D 105 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7784 (pp) REVERT: D 109 PHE cc_start: 0.7309 (m-10) cc_final: 0.7049 (m-80) REVERT: D 115 LYS cc_start: 0.8457 (tppt) cc_final: 0.7461 (tppt) REVERT: D 152 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7426 (pp) REVERT: D 215 ARG cc_start: 0.6468 (ptt180) cc_final: 0.5981 (mtm110) REVERT: D 248 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7358 (mm) REVERT: D 294 HIS cc_start: 0.6359 (m-70) cc_final: 0.5980 (m-70) REVERT: D 330 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6393 (mm) REVERT: D 395 PRO cc_start: 0.7244 (Cg_endo) cc_final: 0.6961 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4506 (tp) outliers start: 90 outliers final: 35 residues processed: 272 average time/residue: 1.1840 time to fit residues: 358.4344 Evaluate side-chains 241 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL 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 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 367 MET 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 149 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 0.0010 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3332 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= 0.181 Angle : 0.598 10.031 21476 Z= 0.309 Chirality : 0.043 0.235 2422 Planarity : 0.004 0.041 2688 Dihedral : 9.367 102.762 2232 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.89 % Allowed : 26.88 % Favored : 68.24 % 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: -0.19 (0.19), residues: 1870 helix: 0.36 (0.15), residues: 1154 sheet: -1.38 (0.50), residues: 100 loop : -0.60 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 246 HIS 0.005 0.001 HIS D 329 PHE 0.021 0.001 PHE A 409 TYR 0.022 0.002 TYR B 364 ARG 0.010 0.000 ARG B 182 *********************** 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 283 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 201 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6795 (p0) cc_final: 0.6497 (p0) REVERT: A 125 LYS cc_start: 0.6452 (tppt) cc_final: 0.5898 (ttmm) REVERT: A 162 MET cc_start: 0.8117 (tpt) cc_final: 0.7683 (mmm) REVERT: A 183 ASN cc_start: 0.6847 (m-40) cc_final: 0.6044 (t160) REVERT: A 267 MET cc_start: 0.8443 (mtt) cc_final: 0.8017 (mtm) REVERT: A 298 ARG cc_start: 0.7155 (ttp-170) cc_final: 0.6869 (ttm-80) REVERT: A 441 GLU cc_start: 0.5229 (OUTLIER) cc_final: 0.4789 (tt0) REVERT: A 464 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5866 (ttp-110) REVERT: A 510 MET cc_start: -0.0083 (mtt) cc_final: -0.0916 (ptm) REVERT: B 46 ARG cc_start: 0.5611 (ttm-80) cc_final: 0.5299 (ttm-80) REVERT: B 58 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7215 (tpt-90) REVERT: B 59 ILE cc_start: 0.7702 (tp) cc_final: 0.7264 (pt) REVERT: B 83 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6721 (mtm110) REVERT: B 86 ARG cc_start: 0.6363 (mtp180) cc_final: 0.5674 (ptt180) REVERT: B 93 ASP cc_start: 0.7286 (t0) cc_final: 0.6615 (m-30) REVERT: B 109 PHE cc_start: 0.6839 (m-10) cc_final: 0.6610 (m-80) REVERT: B 115 LYS cc_start: 0.7781 (tppt) cc_final: 0.7487 (tppt) REVERT: B 248 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7761 (mt) REVERT: B 485 MET cc_start: 0.4456 (tpt) cc_final: 0.3679 (mmt) REVERT: B 500 MET cc_start: 0.3555 (ppp) cc_final: 0.3204 (pp-130) REVERT: C 93 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: C 103 ASP cc_start: 0.7404 (t70) cc_final: 0.7104 (t0) REVERT: C 122 ASP cc_start: 0.6607 (p0) cc_final: 0.6391 (p0) REVERT: C 125 LYS cc_start: 0.8088 (tptp) cc_final: 0.7338 (mmtm) REVERT: C 155 GLN cc_start: 0.7730 (mm110) cc_final: 0.7288 (mp10) REVERT: C 177 ARG cc_start: 0.6852 (mtm110) cc_final: 0.6600 (ttp-110) REVERT: C 179 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6468 (mm-30) REVERT: C 183 ASN cc_start: 0.6863 (m-40) cc_final: 0.6477 (t160) REVERT: C 194 LEU cc_start: 0.7372 (mt) cc_final: 0.7152 (mt) REVERT: C 267 MET cc_start: 0.8409 (mtt) cc_final: 0.7966 (mtm) REVERT: C 288 MET cc_start: 0.8008 (tpt) cc_final: 0.7562 (tpp) REVERT: C 298 ARG cc_start: 0.6764 (mtp-110) cc_final: 0.6033 (ttm-80) REVERT: C 389 LYS cc_start: 0.5995 (mttp) cc_final: 0.5434 (mptt) REVERT: C 494 GLU cc_start: 0.4435 (OUTLIER) cc_final: 0.4151 (mp0) REVERT: D 56 LYS cc_start: 0.6562 (tmtt) cc_final: 0.5951 (mtmm) REVERT: D 58 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6948 (tpm170) REVERT: D 59 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7026 (pt) REVERT: D 86 ARG cc_start: 0.6381 (mtp180) cc_final: 0.5667 (ptt180) REVERT: D 93 ASP cc_start: 0.7124 (t0) cc_final: 0.6527 (m-30) REVERT: D 105 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7757 (pp) REVERT: D 109 PHE cc_start: 0.7375 (m-10) cc_final: 0.7132 (m-80) REVERT: D 115 LYS cc_start: 0.8465 (tppt) cc_final: 0.7462 (tppt) REVERT: D 152 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7399 (pp) REVERT: D 215 ARG cc_start: 0.6430 (ptt180) cc_final: 0.5944 (mtm110) REVERT: D 248 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (mm) REVERT: D 294 HIS cc_start: 0.6275 (m-70) cc_final: 0.5889 (m-70) REVERT: D 330 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6371 (mm) REVERT: D 387 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: D 395 PRO cc_start: 0.7202 (Cg_endo) cc_final: 0.6926 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4752 (OUTLIER) cc_final: 0.4503 (tp) outliers start: 82 outliers final: 34 residues processed: 262 average time/residue: 1.2682 time to fit residues: 368.1077 Evaluate side-chains 243 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 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 66 VAL Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 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 159 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL 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 311 ASN Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 387 GLU 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 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 0.0170 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 218 ASN B 307 GLN C 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15846 Z= 0.236 Angle : 0.618 9.633 21476 Z= 0.318 Chirality : 0.044 0.209 2422 Planarity : 0.004 0.050 2688 Dihedral : 8.957 89.537 2227 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.18 % Allowed : 26.46 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.15), residues: 1152 sheet: -1.29 (0.50), residues: 100 loop : -0.51 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 PHE 0.014 0.001 PHE B 272 TYR 0.025 0.002 TYR B 364 ARG 0.012 0.000 ARG D 182 *********************** 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 286 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 199 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.6471 (tppt) cc_final: 0.5866 (ttmm) REVERT: A 162 MET cc_start: 0.8105 (tpt) cc_final: 0.7422 (mmm) REVERT: A 183 ASN cc_start: 0.6880 (m-40) cc_final: 0.6037 (t160) REVERT: A 267 MET cc_start: 0.8463 (mtt) cc_final: 0.8022 (mtm) REVERT: A 298 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6878 (ttm-80) REVERT: A 432 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6500 (tt0) REVERT: A 441 GLU cc_start: 0.5164 (OUTLIER) cc_final: 0.4739 (tt0) REVERT: A 464 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5948 (ttp-110) REVERT: A 497 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5950 (p0) REVERT: A 510 MET cc_start: -0.0101 (mtt) cc_final: -0.0984 (ptm) REVERT: B 46 ARG cc_start: 0.5606 (ttm-80) cc_final: 0.5311 (ttm-80) REVERT: B 58 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7356 (tpt-90) REVERT: B 59 ILE cc_start: 0.7687 (tp) cc_final: 0.7238 (pt) REVERT: B 83 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6757 (mtm110) REVERT: B 86 ARG cc_start: 0.6415 (mtp180) cc_final: 0.5752 (ptt180) REVERT: B 93 ASP cc_start: 0.7227 (t0) cc_final: 0.6571 (m-30) REVERT: B 109 PHE cc_start: 0.6797 (m-10) cc_final: 0.6577 (m-80) REVERT: B 115 LYS cc_start: 0.7882 (tppt) cc_final: 0.7601 (tppt) REVERT: B 190 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7211 (mmm160) REVERT: B 248 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7844 (mt) REVERT: B 315 ARG cc_start: 0.7060 (mmm160) cc_final: 0.5924 (tpt170) REVERT: B 397 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6830 (tp30) REVERT: B 485 MET cc_start: 0.4494 (tpt) cc_final: 0.3749 (mmt) REVERT: B 500 MET cc_start: 0.3515 (ppp) cc_final: 0.3148 (pp-130) REVERT: C 53 TYR cc_start: 0.8043 (m-80) cc_final: 0.6789 (m-80) REVERT: C 58 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.5592 (mpt-90) REVERT: C 93 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: C 103 ASP cc_start: 0.7400 (t70) cc_final: 0.7110 (t0) REVERT: C 113 LEU cc_start: 0.7900 (mm) cc_final: 0.7618 (tp) REVERT: C 122 ASP cc_start: 0.6596 (p0) cc_final: 0.6390 (p0) REVERT: C 155 GLN cc_start: 0.7705 (mm110) cc_final: 0.7309 (mp10) REVERT: C 177 ARG cc_start: 0.6868 (mtm110) cc_final: 0.6574 (ttp-110) REVERT: C 179 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6901 (mm-30) REVERT: C 183 ASN cc_start: 0.6875 (m-40) cc_final: 0.6416 (t160) REVERT: C 185 ASN cc_start: 0.6774 (m-40) cc_final: 0.5919 (t0) REVERT: C 194 LEU cc_start: 0.7368 (mt) cc_final: 0.7140 (mt) REVERT: C 232 LEU cc_start: 0.8269 (mt) cc_final: 0.8047 (mm) REVERT: C 267 MET cc_start: 0.8431 (mtt) cc_final: 0.7954 (mtm) REVERT: C 288 MET cc_start: 0.7935 (tpt) cc_final: 0.7489 (tpp) REVERT: C 298 ARG cc_start: 0.6780 (mtp-110) cc_final: 0.6152 (ttm-80) REVERT: C 389 LYS cc_start: 0.6071 (mttp) cc_final: 0.5493 (mptt) REVERT: C 432 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6657 (pp20) REVERT: C 494 GLU cc_start: 0.4298 (OUTLIER) cc_final: 0.3975 (mp0) REVERT: D 56 LYS cc_start: 0.6666 (tmtt) cc_final: 0.5891 (mtmm) REVERT: D 58 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6996 (tpm170) REVERT: D 59 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7013 (pt) REVERT: D 86 ARG cc_start: 0.6293 (mtp180) cc_final: 0.5571 (ptt180) REVERT: D 93 ASP cc_start: 0.7151 (t0) cc_final: 0.6567 (m-30) REVERT: D 109 PHE cc_start: 0.7372 (m-10) cc_final: 0.7126 (m-80) REVERT: D 115 LYS cc_start: 0.8520 (tppt) cc_final: 0.8090 (mptp) REVERT: D 215 ARG cc_start: 0.6499 (ptt180) cc_final: 0.5941 (mtm110) REVERT: D 248 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7556 (mt) REVERT: D 294 HIS cc_start: 0.6397 (m-70) cc_final: 0.5989 (m-70) REVERT: D 317 HIS cc_start: 0.4916 (OUTLIER) cc_final: 0.4136 (p-80) REVERT: D 330 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6216 (mm) REVERT: D 395 PRO cc_start: 0.7217 (Cg_endo) cc_final: 0.6947 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4751 (OUTLIER) cc_final: 0.4503 (tp) outliers start: 87 outliers final: 39 residues processed: 265 average time/residue: 1.2377 time to fit residues: 364.6382 Evaluate side-chains 253 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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 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 380 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 420 VAL 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 141 VAL 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 327 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU 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 159 LEU 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 421 ASP Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU 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 330 LEU Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 307 GLN C 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15846 Z= 0.250 Angle : 0.637 17.039 21476 Z= 0.324 Chirality : 0.044 0.218 2422 Planarity : 0.004 0.045 2688 Dihedral : 8.849 95.642 2225 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.18 % Allowed : 27.06 % 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: 0.01 (0.19), residues: 1870 helix: 0.47 (0.15), residues: 1150 sheet: -1.11 (0.51), residues: 100 loop : -0.45 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 PHE 0.014 0.001 PHE D 272 TYR 0.024 0.002 TYR D 364 ARG 0.012 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 195 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.6559 (tppt) cc_final: 0.6011 (ttmm) REVERT: A 162 MET cc_start: 0.8164 (tpt) cc_final: 0.7687 (mmm) REVERT: A 183 ASN cc_start: 0.6890 (m-40) cc_final: 0.6233 (t160) REVERT: A 267 MET cc_start: 0.8471 (mtt) cc_final: 0.8028 (mtm) REVERT: A 298 ARG cc_start: 0.7185 (ttp-170) cc_final: 0.6874 (ttm-80) REVERT: A 432 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: A 441 GLU cc_start: 0.5099 (OUTLIER) cc_final: 0.4681 (tt0) REVERT: A 451 LEU cc_start: 0.4758 (OUTLIER) cc_final: 0.4518 (mt) REVERT: A 464 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.5884 (ttp-110) REVERT: A 510 MET cc_start: -0.0413 (mtt) cc_final: -0.1267 (ptm) REVERT: B 46 ARG cc_start: 0.5601 (ttm-80) cc_final: 0.5317 (ttm-80) REVERT: B 58 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7403 (tpt-90) REVERT: B 59 ILE cc_start: 0.7532 (tp) cc_final: 0.7115 (pt) REVERT: B 83 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6687 (mtm110) REVERT: B 86 ARG cc_start: 0.6406 (mtp180) cc_final: 0.5739 (ptt180) REVERT: B 93 ASP cc_start: 0.7232 (t0) cc_final: 0.6595 (m-30) REVERT: B 109 PHE cc_start: 0.6772 (m-10) cc_final: 0.6557 (m-80) REVERT: B 115 LYS cc_start: 0.7918 (tppt) cc_final: 0.7667 (tppt) REVERT: B 190 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7236 (mmm160) REVERT: B 248 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 397 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: B 485 MET cc_start: 0.4314 (tpt) cc_final: 0.3696 (mmt) REVERT: B 500 MET cc_start: 0.3512 (ppp) cc_final: 0.3227 (pp-130) REVERT: C 58 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.5587 (mpt-90) REVERT: C 93 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: C 103 ASP cc_start: 0.7493 (t70) cc_final: 0.7211 (t0) REVERT: C 120 ILE cc_start: 0.7969 (tt) cc_final: 0.7572 (mp) REVERT: C 155 GLN cc_start: 0.7699 (mm110) cc_final: 0.7313 (mp10) REVERT: C 177 ARG cc_start: 0.6864 (mtm110) cc_final: 0.6585 (ttp-110) REVERT: C 183 ASN cc_start: 0.6841 (m-40) cc_final: 0.6329 (t160) REVERT: C 185 ASN cc_start: 0.6668 (m-40) cc_final: 0.5853 (t0) REVERT: C 194 LEU cc_start: 0.7364 (mt) cc_final: 0.7143 (mt) REVERT: C 232 LEU cc_start: 0.8271 (mt) cc_final: 0.8038 (mm) REVERT: C 267 MET cc_start: 0.8421 (mtt) cc_final: 0.7968 (mtm) REVERT: C 288 MET cc_start: 0.7933 (tpt) cc_final: 0.7483 (tpp) REVERT: C 298 ARG cc_start: 0.6778 (mtp-110) cc_final: 0.6150 (ttm-80) REVERT: C 494 GLU cc_start: 0.4292 (OUTLIER) cc_final: 0.3950 (mp0) REVERT: D 58 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7242 (tpt-90) REVERT: D 59 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7049 (pt) REVERT: D 86 ARG cc_start: 0.6412 (mtp180) cc_final: 0.5663 (ptt180) REVERT: D 93 ASP cc_start: 0.7151 (t0) cc_final: 0.6572 (m-30) REVERT: D 109 PHE cc_start: 0.7268 (m-10) cc_final: 0.7010 (m-80) REVERT: D 115 LYS cc_start: 0.8502 (tppt) cc_final: 0.8059 (mptp) REVERT: D 215 ARG cc_start: 0.6405 (ptt180) cc_final: 0.5900 (mtm110) REVERT: D 248 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7639 (mt) REVERT: D 294 HIS cc_start: 0.6431 (m-70) cc_final: 0.6023 (m-70) REVERT: D 317 HIS cc_start: 0.4903 (OUTLIER) cc_final: 0.4140 (p-80) REVERT: D 330 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6198 (mm) REVERT: D 387 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7142 (pt0) REVERT: D 395 PRO cc_start: 0.7280 (Cg_endo) cc_final: 0.7013 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4908 (OUTLIER) cc_final: 0.4607 (tp) outliers start: 87 outliers final: 43 residues processed: 263 average time/residue: 1.2695 time to fit residues: 371.2650 Evaluate side-chains 248 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 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 420 VAL 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 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 318 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU 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 113 LEU 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 421 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 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 330 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 472 ASN D 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 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 0.038 15846 Z= 0.209 Angle : 0.612 12.429 21476 Z= 0.313 Chirality : 0.043 0.201 2422 Planarity : 0.004 0.048 2688 Dihedral : 8.723 97.739 2225 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.77 % Allowed : 27.47 % 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: 0.11 (0.19), residues: 1870 helix: 0.57 (0.15), residues: 1158 sheet: -1.10 (0.51), residues: 100 loop : -0.46 (0.25), residues: 612 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 D 272 TYR 0.025 0.002 TYR B 364 ARG 0.013 0.000 ARG B 182 *********************** 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 269 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 189 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5114 (ppt170) REVERT: A 162 MET cc_start: 0.8165 (tpt) cc_final: 0.7696 (mmm) REVERT: A 183 ASN cc_start: 0.6884 (m-40) cc_final: 0.6218 (t160) REVERT: A 267 MET cc_start: 0.8469 (mtt) cc_final: 0.8027 (mtm) REVERT: A 298 ARG cc_start: 0.7195 (ttp-170) cc_final: 0.6831 (ttt90) REVERT: A 300 ARG cc_start: 0.6899 (ptt90) cc_final: 0.6675 (ptt-90) REVERT: A 432 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6369 (tt0) REVERT: A 441 GLU cc_start: 0.5094 (OUTLIER) cc_final: 0.4665 (tt0) REVERT: A 451 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.4466 (mt) REVERT: A 464 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5831 (ttp-110) REVERT: A 510 MET cc_start: -0.0464 (mtt) cc_final: -0.1266 (ptm) REVERT: B 46 ARG cc_start: 0.5561 (ttm-80) cc_final: 0.5268 (ttm-80) REVERT: B 58 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7362 (tpt-90) REVERT: B 59 ILE cc_start: 0.7533 (tp) cc_final: 0.7132 (pt) REVERT: B 83 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6698 (mtm110) REVERT: B 86 ARG cc_start: 0.6322 (mtp180) cc_final: 0.5620 (ptt180) REVERT: B 93 ASP cc_start: 0.7211 (t0) cc_final: 0.6590 (m-30) REVERT: B 109 PHE cc_start: 0.6757 (m-10) cc_final: 0.6551 (m-80) REVERT: B 115 LYS cc_start: 0.7907 (tppt) cc_final: 0.7649 (tppt) REVERT: B 162 MET cc_start: 0.8643 (tpt) cc_final: 0.8309 (mmm) REVERT: B 190 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7514 (mmm160) REVERT: B 248 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7699 (mt) REVERT: B 317 HIS cc_start: 0.5403 (OUTLIER) cc_final: 0.4571 (p-80) REVERT: B 397 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: B 485 MET cc_start: 0.4355 (tpt) cc_final: 0.3771 (mmt) REVERT: B 500 MET cc_start: 0.3499 (ppp) cc_final: 0.3166 (pp-130) REVERT: C 93 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: C 103 ASP cc_start: 0.7424 (t70) cc_final: 0.7160 (t0) REVERT: C 155 GLN cc_start: 0.7693 (mm110) cc_final: 0.7281 (mp10) REVERT: C 177 ARG cc_start: 0.6729 (mtm110) cc_final: 0.6468 (ttp-110) REVERT: C 183 ASN cc_start: 0.6930 (m-40) cc_final: 0.6371 (t160) REVERT: C 185 ASN cc_start: 0.6503 (m-40) cc_final: 0.5756 (t0) REVERT: C 194 LEU cc_start: 0.7343 (mt) cc_final: 0.7119 (mt) REVERT: C 232 LEU cc_start: 0.8277 (mt) cc_final: 0.8033 (mm) REVERT: C 267 MET cc_start: 0.8429 (mtt) cc_final: 0.8086 (mtt) REVERT: C 288 MET cc_start: 0.7992 (tpt) cc_final: 0.7477 (tpp) REVERT: C 298 ARG cc_start: 0.6743 (mtp-110) cc_final: 0.6023 (ttm-80) REVERT: C 494 GLU cc_start: 0.4386 (OUTLIER) cc_final: 0.4098 (mp0) REVERT: D 56 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5423 (mtmm) REVERT: D 58 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7224 (mmt90) REVERT: D 59 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7027 (pt) REVERT: D 86 ARG cc_start: 0.6334 (mtp180) cc_final: 0.5595 (ptt180) REVERT: D 93 ASP cc_start: 0.7142 (t0) cc_final: 0.6590 (m-30) REVERT: D 109 PHE cc_start: 0.7248 (m-10) cc_final: 0.6995 (m-80) REVERT: D 115 LYS cc_start: 0.8499 (tppt) cc_final: 0.8060 (mptp) REVERT: D 215 ARG cc_start: 0.6336 (ptt180) cc_final: 0.5874 (mmm160) REVERT: D 248 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7615 (mt) REVERT: D 294 HIS cc_start: 0.6360 (m-70) cc_final: 0.5950 (m-70) REVERT: D 317 HIS cc_start: 0.4879 (OUTLIER) cc_final: 0.4116 (p-80) REVERT: D 330 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6151 (mm) REVERT: D 387 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7162 (pt0) REVERT: D 395 PRO cc_start: 0.7284 (Cg_endo) cc_final: 0.7020 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4923 (OUTLIER) cc_final: 0.4632 (tp) outliers start: 80 outliers final: 41 residues processed: 252 average time/residue: 1.2741 time to fit residues: 355.1166 Evaluate side-chains 250 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 420 VAL 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 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 318 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU 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 159 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 56 LYS 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 51 optimal weight: 0.0870 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3746 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= 0.216 Angle : 0.615 10.786 21476 Z= 0.315 Chirality : 0.043 0.207 2422 Planarity : 0.004 0.053 2688 Dihedral : 8.690 102.313 2225 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.29 % Allowed : 27.89 % 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: 0.18 (0.19), residues: 1870 helix: 0.62 (0.15), residues: 1158 sheet: -0.95 (0.51), residues: 104 loop : -0.44 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 246 HIS 0.006 0.001 HIS D 329 PHE 0.012 0.001 PHE D 272 TYR 0.024 0.002 TYR B 364 ARG 0.014 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 191 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5121 (ppt170) REVERT: A 162 MET cc_start: 0.8156 (tpt) cc_final: 0.7697 (mmm) REVERT: A 183 ASN cc_start: 0.6899 (m-40) cc_final: 0.6234 (t160) REVERT: A 267 MET cc_start: 0.8469 (mtt) cc_final: 0.8019 (mtm) REVERT: A 298 ARG cc_start: 0.7171 (ttp-170) cc_final: 0.6844 (ttt90) REVERT: A 300 ARG cc_start: 0.6755 (ptt90) cc_final: 0.6538 (ptt-90) REVERT: A 432 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6183 (tt0) REVERT: A 441 GLU cc_start: 0.5100 (OUTLIER) cc_final: 0.4680 (tt0) REVERT: A 451 LEU cc_start: 0.4681 (OUTLIER) cc_final: 0.4457 (mt) REVERT: A 464 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5859 (ttp-110) REVERT: A 510 MET cc_start: 0.0051 (mtt) cc_final: -0.0800 (ptm) REVERT: B 46 ARG cc_start: 0.5668 (ttm-80) cc_final: 0.5306 (ttm-80) REVERT: B 58 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7381 (mmt90) REVERT: B 59 ILE cc_start: 0.7529 (tp) cc_final: 0.7124 (pt) REVERT: B 83 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6716 (mtm110) REVERT: B 86 ARG cc_start: 0.6166 (mtp180) cc_final: 0.5500 (ptt180) REVERT: B 93 ASP cc_start: 0.7085 (t0) cc_final: 0.6483 (m-30) REVERT: B 109 PHE cc_start: 0.6752 (m-10) cc_final: 0.6550 (m-80) REVERT: B 115 LYS cc_start: 0.7884 (tppt) cc_final: 0.7638 (tppt) REVERT: B 162 MET cc_start: 0.8635 (tpt) cc_final: 0.8306 (mmm) REVERT: B 190 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7522 (mmm160) REVERT: B 248 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7703 (mt) REVERT: B 317 HIS cc_start: 0.5379 (OUTLIER) cc_final: 0.4591 (p-80) REVERT: B 397 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: B 485 MET cc_start: 0.4299 (tpt) cc_final: 0.3696 (mmt) REVERT: C 58 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5508 (mpt-90) REVERT: C 93 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: C 103 ASP cc_start: 0.7420 (t70) cc_final: 0.7171 (t0) REVERT: C 155 GLN cc_start: 0.7630 (mm110) cc_final: 0.7221 (mp10) REVERT: C 183 ASN cc_start: 0.6912 (m-40) cc_final: 0.6303 (t160) REVERT: C 185 ASN cc_start: 0.6930 (m-40) cc_final: 0.6137 (t0) REVERT: C 194 LEU cc_start: 0.7342 (mt) cc_final: 0.7117 (mt) REVERT: C 232 LEU cc_start: 0.8309 (mt) cc_final: 0.8091 (mm) REVERT: C 267 MET cc_start: 0.8428 (mtt) cc_final: 0.7965 (mtm) REVERT: C 288 MET cc_start: 0.7998 (tpt) cc_final: 0.7477 (tpp) REVERT: C 298 ARG cc_start: 0.6743 (mtp-110) cc_final: 0.6130 (ttm-80) REVERT: C 494 GLU cc_start: 0.4412 (OUTLIER) cc_final: 0.4125 (mp0) REVERT: D 56 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5434 (mtmm) REVERT: D 58 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7187 (mmt90) REVERT: D 59 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.7023 (pt) REVERT: D 86 ARG cc_start: 0.6364 (mtp180) cc_final: 0.5628 (ptt180) REVERT: D 93 ASP cc_start: 0.7142 (t0) cc_final: 0.6591 (m-30) REVERT: D 109 PHE cc_start: 0.7258 (m-10) cc_final: 0.7007 (m-80) REVERT: D 115 LYS cc_start: 0.8536 (tppt) cc_final: 0.8088 (mptp) REVERT: D 215 ARG cc_start: 0.6371 (ptt180) cc_final: 0.5917 (mmm160) REVERT: D 248 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7660 (mt) REVERT: D 294 HIS cc_start: 0.6393 (m-70) cc_final: 0.5983 (m-70) REVERT: D 317 HIS cc_start: 0.4730 (OUTLIER) cc_final: 0.4003 (p-80) REVERT: D 330 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6155 (mm) REVERT: D 387 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7229 (pt0) REVERT: D 395 PRO cc_start: 0.7278 (Cg_endo) cc_final: 0.7014 (Cg_exo) REVERT: D 400 ILE cc_start: 0.4943 (OUTLIER) cc_final: 0.4649 (tp) outliers start: 72 outliers final: 38 residues processed: 244 average time/residue: 1.2797 time to fit residues: 346.0330 Evaluate side-chains 246 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 420 VAL 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 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 314 HIS Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU 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 159 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 56 LYS 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 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 400 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3852 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= 0.191 Angle : 0.614 10.265 21476 Z= 0.313 Chirality : 0.042 0.211 2422 Planarity : 0.004 0.057 2688 Dihedral : 8.255 83.364 2223 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.11 % Allowed : 28.31 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.34 (0.20), residues: 1870 helix: 0.74 (0.15), residues: 1152 sheet: -0.94 (0.50), residues: 108 loop : -0.34 (0.26), residues: 610 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 0.011 0.001 PHE C 231 TYR 0.025 0.001 TYR B 364 ARG 0.015 0.000 ARG D 182 ********************** 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 258 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5116 (ppt170) REVERT: A 162 MET cc_start: 0.8154 (tpt) cc_final: 0.7702 (mmm) REVERT: A 183 ASN cc_start: 0.6895 (m-40) cc_final: 0.6214 (t160) REVERT: A 267 MET cc_start: 0.8465 (mtt) cc_final: 0.8032 (mtm) REVERT: A 298 ARG cc_start: 0.7156 (ttp-170) cc_final: 0.6836 (ttt180) REVERT: A 300 ARG cc_start: 0.6736 (ptt90) cc_final: 0.6526 (ptt-90) REVERT: A 432 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6281 (tt0) REVERT: A 441 GLU cc_start: 0.5036 (OUTLIER) cc_final: 0.4647 (tt0) REVERT: A 451 LEU cc_start: 0.4722 (OUTLIER) cc_final: 0.4515 (mt) REVERT: A 464 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5791 (ttp-110) REVERT: A 510 MET cc_start: 0.0124 (mtt) cc_final: -0.0826 (ptm) REVERT: B 46 ARG cc_start: 0.5659 (ttm-80) cc_final: 0.5307 (ttm-80) REVERT: B 58 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7373 (mmt90) REVERT: B 59 ILE cc_start: 0.7609 (tp) cc_final: 0.7267 (pt) REVERT: B 83 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6706 (mtm110) REVERT: B 86 ARG cc_start: 0.6114 (mtp180) cc_final: 0.5405 (ptt180) REVERT: B 93 ASP cc_start: 0.7053 (t0) cc_final: 0.6467 (m-30) REVERT: B 115 LYS cc_start: 0.7842 (tppt) cc_final: 0.7610 (tppt) REVERT: B 162 MET cc_start: 0.8634 (tpt) cc_final: 0.8312 (mmm) REVERT: B 190 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7482 (mmm160) REVERT: B 317 HIS cc_start: 0.5396 (OUTLIER) cc_final: 0.4600 (p-80) REVERT: B 327 LEU cc_start: 0.6798 (mt) cc_final: 0.6583 (mt) REVERT: B 397 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: B 485 MET cc_start: 0.4290 (tpt) cc_final: 0.3698 (mmt) REVERT: B 500 MET cc_start: 0.3936 (ppp) cc_final: 0.3143 (tpt) REVERT: C 58 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.5414 (mpt-90) REVERT: C 93 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: C 103 ASP cc_start: 0.7370 (t70) cc_final: 0.7142 (t0) REVERT: C 113 LEU cc_start: 0.8244 (mm) cc_final: 0.7907 (tp) REVERT: C 125 LYS cc_start: 0.8131 (tptp) cc_final: 0.7465 (mmtm) REVERT: C 155 GLN cc_start: 0.7619 (mm110) cc_final: 0.7217 (mp10) REVERT: C 183 ASN cc_start: 0.6949 (m-40) cc_final: 0.6341 (t160) REVERT: C 185 ASN cc_start: 0.6880 (m-40) cc_final: 0.6086 (t0) REVERT: C 194 LEU cc_start: 0.7332 (mt) cc_final: 0.7105 (mt) REVERT: C 232 LEU cc_start: 0.8302 (mt) cc_final: 0.8071 (mm) REVERT: C 267 MET cc_start: 0.8424 (mtt) cc_final: 0.7976 (mtm) REVERT: C 288 MET cc_start: 0.8031 (tpt) cc_final: 0.7529 (tpp) REVERT: C 298 ARG cc_start: 0.6742 (mtp-110) cc_final: 0.6050 (ttm-80) REVERT: C 494 GLU cc_start: 0.4403 (OUTLIER) cc_final: 0.4142 (mp0) REVERT: D 56 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5323 (mtmm) REVERT: D 58 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7171 (mmt90) REVERT: D 59 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.7059 (pt) REVERT: D 86 ARG cc_start: 0.6293 (mtp180) cc_final: 0.5587 (ptt180) REVERT: D 93 ASP cc_start: 0.7053 (t0) cc_final: 0.6501 (m-30) REVERT: D 109 PHE cc_start: 0.7259 (m-10) cc_final: 0.7017 (m-80) REVERT: D 215 ARG cc_start: 0.6391 (ptt180) cc_final: 0.5924 (mmm160) REVERT: D 294 HIS cc_start: 0.6382 (m-70) cc_final: 0.5974 (m-70) REVERT: D 317 HIS cc_start: 0.4648 (OUTLIER) cc_final: 0.3954 (p-80) REVERT: D 330 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6089 (mm) REVERT: D 387 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7199 (pt0) REVERT: D 395 PRO cc_start: 0.7282 (Cg_endo) cc_final: 0.7021 (Cg_exo) REVERT: D 397 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: D 400 ILE cc_start: 0.4959 (OUTLIER) cc_final: 0.4668 (tp) outliers start: 69 outliers final: 38 residues processed: 241 average time/residue: 1.2891 time to fit residues: 343.3638 Evaluate side-chains 246 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 420 VAL 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 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 338 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 GLU 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 159 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain D residue 56 LYS 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 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 356 SER Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.0170 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN C 472 ASN D 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.231708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.152506 restraints weight = 16051.124| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.50 r_work: 0.3260 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15846 Z= 0.157 Angle : 0.598 10.084 21476 Z= 0.306 Chirality : 0.042 0.204 2422 Planarity : 0.004 0.061 2688 Dihedral : 8.084 83.781 2223 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.40 % Allowed : 29.08 % 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: 0.42 (0.20), residues: 1870 helix: 0.81 (0.15), residues: 1168 sheet: -0.89 (0.50), residues: 108 loop : -0.37 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 135 HIS 0.005 0.001 HIS D 329 PHE 0.023 0.001 PHE C 409 TYR 0.024 0.001 TYR B 364 ARG 0.015 0.000 ARG B 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6123.73 seconds wall clock time: 111 minutes 30.81 seconds (6690.81 seconds total)