Starting phenix.real_space_refine on Sun Sep 13 22:56:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9usw_64473/09_2026/9usw_64473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9usw_64473/09_2026/9usw_64473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9usw_64473/09_2026/9usw_64473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9usw_64473/09_2026/9usw_64473.map" model { file = "/net/cci-nas-00/data/ceres_data/9usw_64473/09_2026/9usw_64473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9usw_64473/09_2026/9usw_64473.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 16329 2.51 5 N 4152 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25542 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4298 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Chain: "B" Number of atoms: 4298 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Chain: "C" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "D" Number of atoms: 4298 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Chain: "E" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "F" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Time building chain proxies: 5.48, per 1000 atoms: 0.21 Number of scatterers: 25542 At special positions: 0 Unit cell: (155.61, 156.94, 136.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 4986 8.00 N 4152 7.00 C 16329 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: 2.07 Conformation dependent library (CDL) restraints added in 918.8 milliseconds 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 72 sheets defined 18.7% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 4.268A pdb=" N LEU A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.832A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.747A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.975A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 2 through 9 removed outlier: 4.085A pdb=" N LEU B 9 " --> pdb=" O ILE B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.831A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.625A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.632A pdb=" N SER B 402 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.859A pdb=" N VAL B 521 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.913A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.623A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.900A pdb=" N LEU D 9 " --> pdb=" O ILE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.959A pdb=" N ASP D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 395 removed outlier: 3.655A pdb=" N THR D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 3.959A pdb=" N TRP D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 401' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 198 through 206 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.814A pdb=" N ASP E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 removed outlier: 3.615A pdb=" N THR E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 removed outlier: 4.060A pdb=" N TRP E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR E 401 " --> pdb=" O VAL E 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 401' Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 186 through 189 Processing helix chain 'F' and resid 198 through 206 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.855A pdb=" N ASP F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP F 294 " --> pdb=" O ARG F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 395 removed outlier: 3.642A pdb=" N THR F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 401 removed outlier: 3.990A pdb=" N TRP F 400 " --> pdb=" O PRO F 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR F 401 " --> pdb=" O VAL F 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 401' Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 39 removed outlier: 4.540A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 152 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 39 removed outlier: 4.540A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.659A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 239 removed outlier: 4.948A pdb=" N LEU A 525 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE A 239 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS A 523 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.577A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.618A pdb=" N ARG A 442 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 443 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER A 454 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 445 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 299 Processing sheet with id=AB2, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.718A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 383 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 371 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE A 381 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER A 373 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N THR A 379 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40 removed outlier: 6.371A pdb=" N GLU B 211 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 71 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER B 213 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 69 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 40 removed outlier: 6.371A pdb=" N GLU B 211 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 71 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER B 213 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 69 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.087A pdb=" N SER B 102 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.573A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AB9, first strand: chain 'B' and resid 227 through 239 removed outlier: 4.649A pdb=" N LEU B 525 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 239 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS B 523 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.560A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 243 through 246 removed outlier: 5.856A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AC4, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.513A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC7, first strand: chain 'C' and resid 32 through 40 removed outlier: 6.273A pdb=" N GLU C 211 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 71 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER C 213 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 69 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 32 through 40 removed outlier: 6.273A pdb=" N GLU C 211 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 71 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER C 213 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 69 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 42 through 44 removed outlier: 5.741A pdb=" N SER C 102 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.532A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.668A pdb=" N GLY C 82 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 227 through 239 removed outlier: 3.513A pdb=" N SER C 227 " --> pdb=" O VAL C 535 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU C 525 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 239 " --> pdb=" O LYS C 523 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS C 523 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.514A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.537A pdb=" N ARG C 442 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 443 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 454 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 445 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AD7, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD8, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.417A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS C 383 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR C 371 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE C 381 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER C 373 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR C 379 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AE1, first strand: chain 'D' and resid 34 through 39 removed outlier: 4.229A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU D 69 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 34 through 39 removed outlier: 4.229A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.334A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 78 through 79 removed outlier: 6.677A pdb=" N VAL D 78 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AE6, first strand: chain 'D' and resid 227 through 236 removed outlier: 3.999A pdb=" N GLN D 522 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 252 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.563A pdb=" N ARG D 475 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN D 522 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 243 through 246 removed outlier: 6.663A pdb=" N SER D 504 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL D 445 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG D 506 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU D 443 " --> pdb=" O ARG D 506 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 508 " --> pdb=" O SER D 441 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE D 447 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AF1, first strand: chain 'D' and resid 296 through 299 Processing sheet with id=AF2, first strand: chain 'D' and resid 320 through 323 removed outlier: 6.489A pdb=" N ASP D 327 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE D 368 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR D 329 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY D 370 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS D 331 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR D 372 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP D 333 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE D 365 " --> pdb=" O HIS D 386 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS D 386 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA D 367 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D 384 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR D 369 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 378 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AF4, first strand: chain 'E' and resid 34 through 39 removed outlier: 4.276A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU E 69 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 34 through 39 removed outlier: 4.276A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AF7, first strand: chain 'E' and resid 78 through 79 Processing sheet with id=AF8, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AF9, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.715A pdb=" N SER E 227 " --> pdb=" O VAL E 535 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 232 through 236 removed outlier: 4.023A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 475 " --> pdb=" O VAL E 257 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 232 through 236 removed outlier: 4.023A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 252 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 243 through 246 removed outlier: 3.591A pdb=" N ARG E 442 " --> pdb=" O VAL E 508 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE E 447 " --> pdb=" O VAL E 451 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL E 451 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AG5, first strand: chain 'E' and resid 296 through 299 Processing sheet with id=AG6, first strand: chain 'E' and resid 320 through 323 removed outlier: 6.546A pdb=" N ASP E 327 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE E 368 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR E 329 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY E 370 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS E 331 " --> pdb=" O GLY E 370 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR E 372 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP E 333 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE E 365 " --> pdb=" O HIS E 386 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS E 386 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA E 367 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE E 384 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR E 369 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG E 378 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 349 through 350 Processing sheet with id=AG8, first strand: chain 'F' and resid 34 through 40 removed outlier: 4.096A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU F 69 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 34 through 40 removed outlier: 4.096A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 42 through 44 removed outlier: 3.578A pdb=" N ILE F 178 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR F 179 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 100 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR F 181 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL F 98 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR F 183 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.528A pdb=" N VAL F 78 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.735A pdb=" N GLY F 82 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 227 through 236 removed outlier: 3.860A pdb=" N GLN F 522 " --> pdb=" O TYR F 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 252 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 475 through 478 removed outlier: 6.619A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN F 522 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 243 through 246 removed outlier: 6.774A pdb=" N LEU F 443 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER F 454 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL F 445 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP F 450 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 296 through 299 removed outlier: 3.612A pdb=" N SER F 299 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 340 " --> pdb=" O SER F 299 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 320 through 323 removed outlier: 6.345A pdb=" N ASP F 327 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE F 368 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR F 329 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY F 370 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS F 331 " --> pdb=" O GLY F 370 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR F 372 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP F 333 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS F 383 " --> pdb=" O THR F 369 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR F 371 " --> pdb=" O PHE F 381 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N PHE F 381 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER F 373 " --> pdb=" O THR F 379 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR F 379 " --> pdb=" O SER F 373 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 349 through 350 1003 hydrogen bonds defined for protein. 2649 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: 5.19 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7985 1.34 - 1.45: 3818 1.45 - 1.57: 14162 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 26091 Sorted by residual: bond pdb=" N ILE C 190 " pdb=" CA ILE C 190 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.27e+01 bond pdb=" N GLY E 41 " pdb=" CA GLY E 41 " ideal model delta sigma weight residual 1.445 1.476 -0.031 1.01e-02 9.80e+03 9.41e+00 bond pdb=" N ILE E 192 " pdb=" CA ILE E 192 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.31e+00 bond pdb=" N VAL C 207 " pdb=" CA VAL C 207 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 8.98e+00 bond pdb=" N VAL D 191 " pdb=" CA VAL D 191 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.84e+00 ... (remaining 26086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 34656 1.35 - 2.70: 641 2.70 - 4.05: 171 4.05 - 5.39: 16 5.39 - 6.74: 3 Bond angle restraints: 35487 Sorted by residual: angle pdb=" CA GLY D 82 " pdb=" C GLY D 82 " pdb=" O GLY D 82 " ideal model delta sigma weight residual 121.86 118.18 3.68 1.04e+00 9.25e-01 1.26e+01 angle pdb=" N GLN D 539 " pdb=" CA GLN D 539 " pdb=" C GLN D 539 " ideal model delta sigma weight residual 110.91 106.91 4.00 1.17e+00 7.31e-01 1.17e+01 angle pdb=" CA GLN D 539 " pdb=" CB GLN D 539 " pdb=" CG GLN D 539 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLY A 430 " pdb=" C GLY A 430 " pdb=" O GLY A 430 " ideal model delta sigma weight residual 122.65 118.60 4.05 1.28e+00 6.10e-01 1.00e+01 angle pdb=" CA ASP F 198 " pdb=" C ASP F 198 " pdb=" O ASP F 198 " ideal model delta sigma weight residual 122.64 118.70 3.94 1.25e+00 6.40e-01 9.93e+00 ... (remaining 35482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14027 17.95 - 35.89: 1307 35.89 - 53.84: 282 53.84 - 71.79: 49 71.79 - 89.73: 22 Dihedral angle restraints: 15687 sinusoidal: 6171 harmonic: 9516 Sorted by residual: dihedral pdb=" CA ASP C 438 " pdb=" CB ASP C 438 " pdb=" CG ASP C 438 " pdb=" OD1 ASP C 438 " ideal model delta sinusoidal sigma weight residual -30.00 -89.79 59.79 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP E 501 " pdb=" CB ASP E 501 " pdb=" CG ASP E 501 " pdb=" OD1 ASP E 501 " ideal model delta sinusoidal sigma weight residual -30.00 -87.55 57.55 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA PRO C 144 " pdb=" C PRO C 144 " pdb=" N ASN C 145 " pdb=" CA ASN C 145 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 15684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3157 0.049 - 0.098: 593 0.098 - 0.147: 337 0.147 - 0.196: 11 0.196 - 0.246: 6 Chirality restraints: 4104 Sorted by residual: chirality pdb=" CA ILE E 192 " pdb=" N ILE E 192 " pdb=" C ILE E 192 " pdb=" CB ILE E 192 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG F 193 " pdb=" N ARG F 193 " pdb=" C ARG F 193 " pdb=" CB ARG F 193 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ARG D 193 " pdb=" N ARG D 193 " pdb=" C ARG D 193 " pdb=" CB ARG D 193 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4101 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 193 " 0.349 9.50e-02 1.11e+02 1.56e-01 1.50e+01 pdb=" NE ARG E 193 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG E 193 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG E 193 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 193 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 143 " -0.049 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO C 144 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 144 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 144 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 193 " -0.174 9.50e-02 1.11e+02 7.80e-02 3.75e+00 pdb=" NE ARG D 193 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 193 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG D 193 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 193 " -0.006 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 711 2.71 - 3.25: 24455 3.25 - 3.80: 40054 3.80 - 4.35: 52888 4.35 - 4.90: 91085 Nonbonded interactions: 209193 Sorted by model distance: nonbonded pdb=" OH TYR E 359 " pdb=" OD1 ASP E 392 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP F 267 " pdb=" OG SER F 398 " model vdw 2.162 3.040 nonbonded pdb=" OD1 ASP C 267 " pdb=" OG SER C 398 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR D 453 " pdb=" OE1 GLU D 455 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP B 438 " pdb=" NH2 ARG B 475 " model vdw 2.238 3.120 ... (remaining 209188 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 547) selection = (chain 'B' and resid 15 through 547) selection = chain 'C' selection = (chain 'D' and resid 15 through 547) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.66 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.290 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26091 Z= 0.177 Angle : 0.491 6.744 35487 Z= 0.286 Chirality : 0.048 0.246 4104 Planarity : 0.004 0.156 4527 Dihedral : 14.729 89.733 9561 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3183 helix: 0.38 (0.25), residues: 489 sheet: 0.84 (0.17), residues: 945 loop : -0.03 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 378 TYR 0.010 0.001 TYR C 283 PHE 0.019 0.001 BPHE E 357 TRP 0.005 0.001 TRP B 108 HIS 0.008 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.18 (26091) covalent geometry : angle 0.49066 / 0.29 (35487) hydrogen bonds : bond 0.17782 / 11.71 ( 885) hydrogen bonds : angle 8.05440 / 5.65 ( 2649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: B 377 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7806 (mmmt) REVERT: D 404 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7631 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1748 time to fit residues: 90.6252 Evaluate side-chains 310 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 424 ASN D 104 ASN E 515 ASN F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098482 restraints weight = 34900.753| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.09 r_work: 0.2974 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 26091 Z= 0.314 Angle : 0.577 6.787 35487 Z= 0.306 Chirality : 0.051 0.161 4104 Planarity : 0.004 0.050 4527 Dihedral : 4.070 18.019 3498 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.16 % Allowed : 14.64 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3183 helix: -0.17 (0.24), residues: 519 sheet: 0.38 (0.17), residues: 933 loop : -0.21 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 404 TYR 0.018 0.002 TYR E 359 PHE 0.018 0.002 PHE E 199 TRP 0.012 0.002 TRP B 108 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.31 (26091) covalent geometry : angle 0.57655 / 0.31 (35487) hydrogen bonds : bond 0.04519 / 3.00 ( 885) hydrogen bonds : angle 5.77503 / 4.05 ( 2649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 320 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: A 380 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6905 (mp) REVERT: B 404 ARG cc_start: 0.8011 (mpp80) cc_final: 0.7724 (mpp80) REVERT: C 138 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8705 (mm) REVERT: C 230 GLU cc_start: 0.8521 (mp0) cc_final: 0.8262 (mp0) REVERT: D 536 SER cc_start: 0.8862 (m) cc_final: 0.8448 (p) REVERT: E 177 LYS cc_start: 0.8988 (tttt) cc_final: 0.8586 (tmmt) REVERT: E 267 ASP cc_start: 0.8413 (t0) cc_final: 0.8161 (t0) REVERT: E 378 ARG cc_start: 0.8823 (mtm110) cc_final: 0.8620 (mtm110) REVERT: F 220 LYS cc_start: 0.7993 (mptt) cc_final: 0.7633 (mmtm) outliers start: 64 outliers final: 42 residues processed: 363 average time/residue: 0.1629 time to fit residues: 93.7008 Evaluate side-chains 332 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 118 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 191 optimal weight: 0.5980 chunk 279 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 100 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102438 restraints weight = 34451.928| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.11 r_work: 0.3050 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26091 Z= 0.107 Angle : 0.433 5.233 35487 Z= 0.232 Chirality : 0.047 0.153 4104 Planarity : 0.003 0.035 4527 Dihedral : 3.635 16.283 3498 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.42 % Allowed : 15.79 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3183 helix: 0.19 (0.25), residues: 492 sheet: 0.39 (0.17), residues: 903 loop : -0.10 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 59 TYR 0.010 0.001 TYR D 520 PHE 0.018 0.001 BPHE B 357 TRP 0.009 0.001 TRP B 108 HIS 0.004 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (26091) covalent geometry : angle 0.43263 / 0.23 (35487) hydrogen bonds : bond 0.03241 / 2.12 ( 885) hydrogen bonds : angle 5.13914 / 3.60 ( 2649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 342 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6996 (mp) REVERT: B 33 MET cc_start: 0.9030 (tpt) cc_final: 0.8693 (tpp) REVERT: B 311 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7618 (tp30) REVERT: C 74 GLU cc_start: 0.8287 (mp0) cc_final: 0.7545 (mp0) REVERT: C 134 GLU cc_start: 0.7980 (tp30) cc_final: 0.7355 (tp30) REVERT: C 209 VAL cc_start: 0.8994 (t) cc_final: 0.8438 (m) REVERT: C 230 GLU cc_start: 0.8304 (mp0) cc_final: 0.8090 (mp0) REVERT: C 317 GLU cc_start: 0.7934 (pp20) cc_final: 0.7655 (pp20) REVERT: C 385 SER cc_start: 0.7629 (m) cc_final: 0.7416 (t) REVERT: C 407 TYR cc_start: 0.7592 (m-80) cc_final: 0.7371 (m-80) REVERT: C 462 ILE cc_start: 0.8675 (mm) cc_final: 0.8311 (mm) REVERT: D 165 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8350 (mt-10) REVERT: D 218 MET cc_start: 0.8415 (mtt) cc_final: 0.8191 (mtt) REVERT: D 536 SER cc_start: 0.8763 (m) cc_final: 0.8421 (p) REVERT: E 177 LYS cc_start: 0.8983 (tttt) cc_final: 0.8682 (tmmt) REVERT: E 267 ASP cc_start: 0.8385 (t0) cc_final: 0.8085 (t0) REVERT: F 220 LYS cc_start: 0.8063 (mptt) cc_final: 0.7597 (mmtm) REVERT: F 538 ASP cc_start: 0.7987 (m-30) cc_final: 0.7742 (p0) outliers start: 42 outliers final: 33 residues processed: 372 average time/residue: 0.1842 time to fit residues: 108.3040 Evaluate side-chains 355 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 321 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 436 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 319 optimal weight: 3.9990 chunk 313 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 162 optimal weight: 0.1980 chunk 265 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 HIS ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN F 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103055 restraints weight = 34350.898| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.11 r_work: 0.3059 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26091 Z= 0.104 Angle : 0.422 5.331 35487 Z= 0.225 Chirality : 0.046 0.162 4104 Planarity : 0.003 0.035 4527 Dihedral : 3.485 15.754 3498 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.10 % Allowed : 15.79 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3183 helix: 0.26 (0.25), residues: 495 sheet: 0.44 (0.17), residues: 933 loop : -0.09 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 378 TYR 0.010 0.001 TYR B 342 PHE 0.015 0.001 BPHE E 357 TRP 0.007 0.001 TRP B 108 HIS 0.003 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (26091) covalent geometry : angle 0.42162 / 0.22 (35487) hydrogen bonds : bond 0.02985 / 1.97 ( 885) hydrogen bonds : angle 4.90333 / 3.43 ( 2649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 380 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6977 (mp) REVERT: A 520 TYR cc_start: 0.8333 (m-80) cc_final: 0.8128 (m-80) REVERT: B 33 MET cc_start: 0.9043 (tpt) cc_final: 0.8722 (tpp) REVERT: B 311 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7579 (tp30) REVERT: B 349 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7570 (ppp) REVERT: C 74 GLU cc_start: 0.8264 (mp0) cc_final: 0.7560 (mp0) REVERT: C 134 GLU cc_start: 0.7992 (tp30) cc_final: 0.7329 (tp30) REVERT: C 209 VAL cc_start: 0.9046 (t) cc_final: 0.8544 (m) REVERT: C 462 ILE cc_start: 0.8679 (mm) cc_final: 0.8326 (mm) REVERT: C 504 SER cc_start: 0.8668 (t) cc_final: 0.8431 (p) REVERT: D 165 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8405 (mt-10) REVERT: D 536 SER cc_start: 0.8774 (m) cc_final: 0.8427 (p) REVERT: D 539 GLN cc_start: 0.6760 (tm-30) cc_final: 0.6549 (tm-30) REVERT: E 177 LYS cc_start: 0.9025 (tttt) cc_final: 0.8638 (tmmt) REVERT: E 267 ASP cc_start: 0.8421 (t0) cc_final: 0.8117 (t0) REVERT: E 378 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8497 (mtm110) REVERT: E 498 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6935 (tpt170) REVERT: F 81 MET cc_start: 0.7984 (mtp) cc_final: 0.7646 (mtm) REVERT: F 198 ASP cc_start: 0.8442 (t0) cc_final: 0.7993 (t0) REVERT: F 220 LYS cc_start: 0.8156 (mptt) cc_final: 0.7699 (mmtm) REVERT: F 538 ASP cc_start: 0.7979 (m-30) cc_final: 0.7762 (p0) outliers start: 62 outliers final: 46 residues processed: 382 average time/residue: 0.1858 time to fit residues: 112.1168 Evaluate side-chains 363 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 267 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN D 3 ASN F 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100319 restraints weight = 34380.971| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.10 r_work: 0.3000 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26091 Z= 0.212 Angle : 0.488 5.543 35487 Z= 0.258 Chirality : 0.048 0.156 4104 Planarity : 0.004 0.045 4527 Dihedral : 3.744 16.347 3498 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.77 % Allowed : 15.42 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3183 helix: 0.08 (0.24), residues: 510 sheet: 0.19 (0.17), residues: 903 loop : -0.13 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 193 TYR 0.012 0.001 TYR E 359 PHE 0.018 0.001 PHE C 199 TRP 0.009 0.001 TRP B 108 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (26091) covalent geometry : angle 0.48779 / 0.26 (35487) hydrogen bonds : bond 0.03537 / 2.34 ( 885) hydrogen bonds : angle 5.13901 / 3.59 ( 2649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 317 time to evaluate : 1.127 Fit side-chains REVERT: A 380 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6932 (mp) REVERT: B 33 MET cc_start: 0.9190 (tpt) cc_final: 0.8913 (tpp) REVERT: B 143 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.6691 (t) REVERT: B 146 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7061 (p0) REVERT: B 311 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7628 (tp30) REVERT: B 348 LEU cc_start: 0.8912 (mt) cc_final: 0.8630 (mt) REVERT: C 74 GLU cc_start: 0.8345 (mp0) cc_final: 0.7603 (mp0) REVERT: C 134 GLU cc_start: 0.8043 (tp30) cc_final: 0.7380 (tp30) REVERT: C 209 VAL cc_start: 0.9001 (t) cc_final: 0.8508 (m) REVERT: C 462 ILE cc_start: 0.8700 (mm) cc_final: 0.8362 (mm) REVERT: D 536 SER cc_start: 0.8789 (m) cc_final: 0.8419 (p) REVERT: D 539 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6725 (tm-30) REVERT: E 103 CYS cc_start: 0.8624 (m) cc_final: 0.8406 (p) REVERT: E 177 LYS cc_start: 0.9101 (tttt) cc_final: 0.8642 (tmmt) REVERT: E 267 ASP cc_start: 0.8467 (t0) cc_final: 0.8133 (t0) REVERT: E 378 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8539 (mtm110) REVERT: E 498 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6997 (tpt170) REVERT: F 81 MET cc_start: 0.7919 (mtp) cc_final: 0.7580 (mtm) REVERT: F 198 ASP cc_start: 0.8374 (t0) cc_final: 0.8167 (t0) outliers start: 82 outliers final: 61 residues processed: 375 average time/residue: 0.1858 time to fit residues: 109.4886 Evaluate side-chains 361 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 296 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 512 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 115 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101324 restraints weight = 34285.117| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.13 r_work: 0.3017 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26091 Z= 0.148 Angle : 0.450 5.433 35487 Z= 0.239 Chirality : 0.047 0.152 4104 Planarity : 0.003 0.041 4527 Dihedral : 3.639 15.659 3498 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.57 % Allowed : 16.02 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3183 helix: 0.12 (0.24), residues: 510 sheet: 0.17 (0.17), residues: 903 loop : -0.10 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 378 TYR 0.011 0.001 TYR D 520 PHE 0.020 0.001 PHE C 199 TRP 0.009 0.001 TRP B 108 HIS 0.002 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (26091) covalent geometry : angle 0.44996 / 0.24 (35487) hydrogen bonds : bond 0.03142 / 2.07 ( 885) hydrogen bonds : angle 4.97593 / 3.48 ( 2649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 316 time to evaluate : 1.032 Fit side-chains REVERT: A 380 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6977 (mp) REVERT: B 33 MET cc_start: 0.9152 (tpt) cc_final: 0.8873 (tpp) REVERT: B 143 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.6741 (p) REVERT: B 311 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7576 (tp30) REVERT: B 348 LEU cc_start: 0.8870 (mt) cc_final: 0.8658 (mt) REVERT: B 349 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7441 (ppp) REVERT: C 134 GLU cc_start: 0.8009 (tp30) cc_final: 0.7359 (tp30) REVERT: C 462 ILE cc_start: 0.8708 (mm) cc_final: 0.8372 (mm) REVERT: D 536 SER cc_start: 0.8772 (m) cc_final: 0.8424 (p) REVERT: E 177 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8634 (tmmt) REVERT: E 267 ASP cc_start: 0.8414 (t0) cc_final: 0.8051 (t0) REVERT: E 378 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8385 (mtm110) REVERT: E 498 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6973 (tpt170) REVERT: F 81 MET cc_start: 0.7929 (mtp) cc_final: 0.7581 (mtm) REVERT: F 198 ASP cc_start: 0.8356 (t0) cc_final: 0.8043 (t0) outliers start: 76 outliers final: 62 residues processed: 368 average time/residue: 0.1782 time to fit residues: 104.4342 Evaluate side-chains 378 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 512 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 147 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 ASN D 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101125 restraints weight = 34221.998| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.09 r_work: 0.3016 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26091 Z= 0.158 Angle : 0.461 6.509 35487 Z= 0.244 Chirality : 0.047 0.148 4104 Planarity : 0.004 0.037 4527 Dihedral : 3.643 15.529 3498 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.81 % Allowed : 15.99 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3183 helix: 0.09 (0.24), residues: 513 sheet: 0.09 (0.17), residues: 903 loop : -0.12 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 378 TYR 0.011 0.001 TYR D 520 PHE 0.020 0.001 PHE C 199 TRP 0.008 0.001 TRP B 108 HIS 0.002 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (26091) covalent geometry : angle 0.46140 / 0.24 (35487) hydrogen bonds : bond 0.03186 / 2.10 ( 885) hydrogen bonds : angle 4.97539 / 3.47 ( 2649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 322 time to evaluate : 1.061 Fit side-chains REVERT: A 17 LYS cc_start: 0.8490 (mptt) cc_final: 0.8185 (tptt) REVERT: A 380 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6976 (mp) REVERT: B 33 MET cc_start: 0.9165 (tpt) cc_final: 0.8892 (tpp) REVERT: B 348 LEU cc_start: 0.8894 (mt) cc_final: 0.8663 (mt) REVERT: B 349 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7452 (ppp) REVERT: C 134 GLU cc_start: 0.7995 (tp30) cc_final: 0.7342 (tp30) REVERT: C 462 ILE cc_start: 0.8710 (mm) cc_final: 0.8378 (mm) REVERT: D 218 MET cc_start: 0.8489 (mtt) cc_final: 0.8283 (mtt) REVERT: D 484 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8685 (mmtm) REVERT: D 536 SER cc_start: 0.8821 (m) cc_final: 0.8484 (p) REVERT: D 539 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6748 (tm-30) REVERT: E 177 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8642 (tmmt) REVERT: E 267 ASP cc_start: 0.8420 (t0) cc_final: 0.8037 (t0) REVERT: E 378 ARG cc_start: 0.8730 (mtm110) cc_final: 0.8359 (mtm110) REVERT: E 498 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6990 (tpt170) REVERT: F 81 MET cc_start: 0.7904 (mtp) cc_final: 0.7555 (mtm) REVERT: F 198 ASP cc_start: 0.8346 (t0) cc_final: 0.7891 (t0) outliers start: 83 outliers final: 68 residues processed: 380 average time/residue: 0.1800 time to fit residues: 109.3274 Evaluate side-chains 384 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 312 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 512 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 146 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 306 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 ASN C 97 HIS D 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102283 restraints weight = 34241.370| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.10 r_work: 0.3034 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26091 Z= 0.121 Angle : 0.441 6.226 35487 Z= 0.234 Chirality : 0.047 0.147 4104 Planarity : 0.003 0.044 4527 Dihedral : 3.526 14.968 3498 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.30 % Allowed : 16.63 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3183 helix: 0.25 (0.25), residues: 495 sheet: 0.10 (0.17), residues: 912 loop : -0.07 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 193 TYR 0.011 0.001 TYR B 342 PHE 0.019 0.001 PHE C 199 TRP 0.008 0.001 TRP B 108 HIS 0.002 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (26091) covalent geometry : angle 0.44140 / 0.23 (35487) hydrogen bonds : bond 0.02928 / 1.93 ( 885) hydrogen bonds : angle 4.84266 / 3.38 ( 2649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 328 time to evaluate : 1.089 Fit side-chains REVERT: A 17 LYS cc_start: 0.8523 (mptt) cc_final: 0.8213 (tptt) REVERT: A 380 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6987 (mp) REVERT: B 33 MET cc_start: 0.9125 (tpt) cc_final: 0.8835 (tpp) REVERT: B 248 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 348 LEU cc_start: 0.8889 (mt) cc_final: 0.8673 (mt) REVERT: B 349 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7428 (ppp) REVERT: B 404 ARG cc_start: 0.7850 (mpp80) cc_final: 0.7492 (mpp80) REVERT: C 134 GLU cc_start: 0.7975 (tp30) cc_final: 0.7327 (tp30) REVERT: C 425 ASP cc_start: 0.8607 (t0) cc_final: 0.8371 (t0) REVERT: C 462 ILE cc_start: 0.8694 (mm) cc_final: 0.8362 (mm) REVERT: D 165 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8390 (mt-10) REVERT: D 218 MET cc_start: 0.8548 (mtt) cc_final: 0.8342 (mtt) REVERT: D 484 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8566 (mmtm) REVERT: D 536 SER cc_start: 0.8808 (m) cc_final: 0.8475 (p) REVERT: D 539 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6772 (tm-30) REVERT: E 177 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8662 (tmmt) REVERT: E 267 ASP cc_start: 0.8389 (t0) cc_final: 0.8084 (t0) REVERT: E 378 ARG cc_start: 0.8746 (mtm110) cc_final: 0.8408 (mtm110) REVERT: E 470 SER cc_start: 0.8442 (t) cc_final: 0.8094 (m) REVERT: E 498 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7056 (tpt170) REVERT: F 81 MET cc_start: 0.7898 (mtp) cc_final: 0.7549 (mtm) REVERT: F 198 ASP cc_start: 0.8288 (t0) cc_final: 0.7815 (t0) outliers start: 68 outliers final: 58 residues processed: 373 average time/residue: 0.1824 time to fit residues: 107.7452 Evaluate side-chains 380 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 512 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 84 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 ASN D 3 ASN F 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.099846 restraints weight = 34643.992| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.98 r_work: 0.2975 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 26091 Z= 0.237 Angle : 0.513 6.188 35487 Z= 0.271 Chirality : 0.049 0.154 4104 Planarity : 0.004 0.039 4527 Dihedral : 3.816 15.934 3498 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.50 % Allowed : 16.63 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3183 helix: -0.21 (0.24), residues: 537 sheet: 0.01 (0.17), residues: 900 loop : -0.21 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.014 0.001 TYR E 520 PHE 0.021 0.002 PHE C 199 TRP 0.009 0.001 TRP B 108 HIS 0.004 0.001 HIS D 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (26091) covalent geometry : angle 0.51338 / 0.27 (35487) hydrogen bonds : bond 0.03536 / 2.34 ( 885) hydrogen bonds : angle 5.12714 / 3.58 ( 2649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 317 time to evaluate : 1.078 Fit side-chains REVERT: A 17 LYS cc_start: 0.8541 (mptt) cc_final: 0.8285 (tptt) REVERT: A 137 ASP cc_start: 0.7940 (m-30) cc_final: 0.7292 (m-30) REVERT: A 380 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7044 (mp) REVERT: B 33 MET cc_start: 0.9189 (tpt) cc_final: 0.8953 (tpp) REVERT: B 348 LEU cc_start: 0.8935 (mt) cc_final: 0.8730 (mt) REVERT: B 349 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7477 (ppp) REVERT: B 404 ARG cc_start: 0.7859 (mpp80) cc_final: 0.7507 (mpp80) REVERT: C 317 GLU cc_start: 0.7940 (pp20) cc_final: 0.7666 (pp20) REVERT: C 349 MET cc_start: 0.8928 (ptm) cc_final: 0.8583 (ptm) REVERT: C 361 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8444 (tp) REVERT: C 462 ILE cc_start: 0.8765 (mm) cc_final: 0.8436 (mm) REVERT: D 146 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: D 484 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8694 (mmtm) REVERT: D 536 SER cc_start: 0.8859 (m) cc_final: 0.8484 (p) REVERT: D 539 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7078 (tm-30) REVERT: E 177 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8715 (tmmt) REVERT: E 267 ASP cc_start: 0.8446 (t0) cc_final: 0.8080 (t0) REVERT: E 498 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6951 (tpt170) REVERT: F 81 MET cc_start: 0.7897 (mtp) cc_final: 0.7560 (mtm) REVERT: F 198 ASP cc_start: 0.8377 (t0) cc_final: 0.8155 (t0) outliers start: 74 outliers final: 61 residues processed: 370 average time/residue: 0.1832 time to fit residues: 107.2706 Evaluate side-chains 373 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 306 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 339 MET Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 512 MET Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 292 optimal weight: 0.0570 chunk 220 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 319 optimal weight: 0.9980 chunk 269 optimal weight: 0.5980 chunk 277 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 ASN D 3 ASN E 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102837 restraints weight = 34179.778| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.12 r_work: 0.3039 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26091 Z= 0.108 Angle : 0.442 6.216 35487 Z= 0.234 Chirality : 0.046 0.150 4104 Planarity : 0.003 0.042 4527 Dihedral : 3.528 15.095 3498 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.76 % Allowed : 17.58 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3183 helix: 0.26 (0.25), residues: 495 sheet: 0.06 (0.17), residues: 912 loop : -0.08 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.016 0.001 TYR C 407 PHE 0.019 0.001 BPHE E 357 TRP 0.008 0.001 TRP B 108 HIS 0.003 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (26091) covalent geometry : angle 0.44176 / 0.23 (35487) hydrogen bonds : bond 0.02831 / 1.86 ( 885) hydrogen bonds : angle 4.82577 / 3.37 ( 2649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6366 Ramachandran restraints generated. 3183 Oldfield, 0 Emsley, 3183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 1.108 Fit side-chains REVERT: A 17 LYS cc_start: 0.8515 (mptt) cc_final: 0.8245 (tptt) REVERT: A 380 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6984 (mp) REVERT: B 33 MET cc_start: 0.9104 (tpt) cc_final: 0.8813 (tpp) REVERT: B 248 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 349 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7774 (ppp) REVERT: B 404 ARG cc_start: 0.7808 (mpp80) cc_final: 0.7511 (mpp80) REVERT: C 17 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7779 (mmmt) REVERT: C 134 GLU cc_start: 0.7817 (tp30) cc_final: 0.7230 (tp30) REVERT: C 349 MET cc_start: 0.8846 (ptm) cc_final: 0.8534 (ptm) REVERT: C 425 ASP cc_start: 0.8620 (t0) cc_final: 0.8394 (t0) REVERT: C 462 ILE cc_start: 0.8688 (mm) cc_final: 0.8360 (mm) REVERT: D 75 LEU cc_start: 0.8999 (mt) cc_final: 0.8748 (mt) REVERT: D 165 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8398 (mt-10) REVERT: D 484 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8548 (mmtm) REVERT: D 536 SER cc_start: 0.8803 (m) cc_final: 0.8468 (p) REVERT: E 50 ASN cc_start: 0.7861 (p0) cc_final: 0.7641 (t0) REVERT: E 177 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8671 (tmmt) REVERT: E 267 ASP cc_start: 0.8381 (t0) cc_final: 0.8049 (t0) REVERT: F 81 MET cc_start: 0.7887 (mtp) cc_final: 0.7535 (mtm) REVERT: F 198 ASP cc_start: 0.8290 (t0) cc_final: 0.7821 (t0) outliers start: 52 outliers final: 47 residues processed: 361 average time/residue: 0.1865 time to fit residues: 106.2243 Evaluate side-chains 373 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 512 MET Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 74 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 214 optimal weight: 0.4980 chunk 174 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 2 ASN D 3 ASN E 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103227 restraints weight = 33938.437| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.97 r_work: 0.3048 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26091 Z= 0.108 Angle : 0.443 7.652 35487 Z= 0.233 Chirality : 0.046 0.148 4104 Planarity : 0.004 0.044 4527 Dihedral : 3.452 18.801 3498 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.79 % Allowed : 17.44 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3183 helix: 0.30 (0.25), residues: 495 sheet: 0.14 (0.17), residues: 903 loop : -0.06 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 378 TYR 0.015 0.001 TYR C 407 PHE 0.021 0.001 BPHE B 357 TRP 0.009 0.001 TRP B 108 HIS 0.002 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (26091) covalent geometry : angle 0.44322 / 0.23 (35487) hydrogen bonds : bond 0.02792 / 1.83 ( 885) hydrogen bonds : angle 4.72940 / 3.30 ( 2649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7473.26 seconds wall clock time: 128 minutes 55.02 seconds (7735.02 seconds total)