Starting phenix.real_space_refine on Thu Feb 13 21:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwq_10635/02_2025/6xwq_10635.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwq_10635/02_2025/6xwq_10635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xwq_10635/02_2025/6xwq_10635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwq_10635/02_2025/6xwq_10635.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwq_10635/02_2025/6xwq_10635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwq_10635/02_2025/6xwq_10635.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 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 48 5.16 5 C 6309 2.51 5 N 1549 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9572 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "B" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Chain: "C" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 265 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 265 " occ=0.50 Time building chain proxies: 7.18, per 1000 atoms: 0.75 Number of scatterers: 9572 At special positions: 0 Unit cell: (105.248, 108.284, 81.972, 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 48 16.00 O 1666 8.00 N 1549 7.00 C 6309 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: 2.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 36 removed outlier: 3.644A pdb=" N ALA A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.722A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.532A pdb=" N VAL A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 110 removed outlier: 4.029A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 171 Processing helix chain 'A' and resid 175 through 223 removed outlier: 3.621A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 3.869A pdb=" N ALA A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 257 removed outlier: 3.667A pdb=" N VAL A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 5.499A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.527A pdb=" N GLU A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.566A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.953A pdb=" N LEU A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.869A pdb=" N ILE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.978A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 419 removed outlier: 4.255A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 13 through 36 removed outlier: 3.670A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.776A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 Processing helix chain 'B' and resid 76 through 110 removed outlier: 3.749A pdb=" N ARG B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 153 through 171 Processing helix chain 'B' and resid 175 through 223 removed outlier: 3.591A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.563A pdb=" N ILE B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 257 removed outlier: 3.735A pdb=" N VAL B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.040A pdb=" N ASP B 269 " --> pdb=" O AARG B 265 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 304 through 313 removed outlier: 4.210A pdb=" N THR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.747A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 354 removed outlier: 4.035A pdb=" N LEU B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.872A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 419 removed outlier: 3.640A pdb=" N LEU B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.693A pdb=" N ASP C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 36 removed outlier: 3.591A pdb=" N LEU C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.799A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 76 through 110 removed outlier: 3.950A pdb=" N TYR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 175 through 223 removed outlier: 3.881A pdb=" N SER C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.529A pdb=" N ALA C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 216 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 257 removed outlier: 3.652A pdb=" N VAL C 233 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 278 removed outlier: 5.360A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 3.597A pdb=" N GLU C 293 " --> pdb=" O ARG C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.567A pdb=" N PHE C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 313 removed outlier: 4.315A pdb=" N THR C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.661A pdb=" N LEU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 removed outlier: 3.965A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 removed outlier: 3.919A pdb=" N ILE C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 381 through 420 removed outlier: 4.054A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 393 " --> pdb=" O MET C 389 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 4.335A pdb=" N TRP C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2976 1.34 - 1.46: 1339 1.46 - 1.57: 5336 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 9747 Sorted by residual: bond pdb=" CA VAL C 373 " pdb=" CB VAL C 373 " ideal model delta sigma weight residual 1.527 1.543 -0.017 1.31e-02 5.83e+03 1.61e+00 bond pdb=" CG1 ILE B 18 " pdb=" CD1 ILE B 18 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.08e-01 bond pdb=" CB VAL C 200 " pdb=" CG2 VAL C 200 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.41e-01 bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.11e-01 bond pdb=" N ARG C 278 " pdb=" CA ARG C 278 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 6.28e-01 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 12839 1.46 - 2.91: 350 2.91 - 4.37: 59 4.37 - 5.82: 13 5.82 - 7.28: 4 Bond angle restraints: 13265 Sorted by residual: angle pdb=" N VAL B 211 " pdb=" CA VAL B 211 " pdb=" C VAL B 211 " ideal model delta sigma weight residual 113.07 108.39 4.68 1.36e+00 5.41e-01 1.19e+01 angle pdb=" C LEU B 6 " pdb=" N ARG B 7 " pdb=" CA ARG B 7 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LEU A 6 " pdb=" N ARG A 7 " pdb=" CA ARG A 7 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.31e+00 angle pdb=" C VAL C 246 " pdb=" N ILE C 247 " pdb=" CA ILE C 247 " ideal model delta sigma weight residual 121.84 118.82 3.02 1.13e+00 7.83e-01 7.12e+00 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 115.66 111.75 3.91 1.56e+00 4.11e-01 6.29e+00 ... (remaining 13260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5224 17.65 - 35.30: 437 35.30 - 52.95: 70 52.95 - 70.60: 7 70.60 - 88.25: 10 Dihedral angle restraints: 5748 sinusoidal: 2135 harmonic: 3613 Sorted by residual: dihedral pdb=" CA GLN A 128 " pdb=" C GLN A 128 " pdb=" N PRO A 129 " pdb=" CA PRO A 129 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLN B 128 " pdb=" C GLN B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLN C 128 " pdb=" C GLN C 128 " pdb=" N PRO C 129 " pdb=" CA PRO C 129 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 934 0.028 - 0.056: 495 0.056 - 0.085: 155 0.085 - 0.113: 55 0.113 - 0.141: 12 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA LEU B 284 " pdb=" N LEU B 284 " pdb=" C LEU B 284 " pdb=" CB LEU B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1648 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 207 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 208 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO C 208 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 207 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B 208 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " -0.030 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 277 2.72 - 3.26: 10782 3.26 - 3.81: 15857 3.81 - 4.35: 18939 4.35 - 4.90: 32473 Nonbonded interactions: 78328 Sorted by model distance: nonbonded pdb=" OH TYR B 9 " pdb=" O GLN B 205 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR A 402 " pdb=" N ASP A 501 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR C 402 " pdb=" N ASP C 501 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR B 402 " pdb=" N ASP B 501 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN A 313 " pdb=" OD1 ASP A 409 " model vdw 2.302 3.120 ... (remaining 78323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 264 or resid 266 through 430 or resid 501)) selection = (chain 'B' and (resid 5 through 264 or resid 266 through 430 or resid 501)) selection = (chain 'C' and (resid 5 through 264 or resid 266 through 430 or resid 501)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.630 Find NCS groups from input model: 0.430 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 0.035 9747 Z= 0.206 Angle : 0.609 7.275 13265 Z= 0.346 Chirality : 0.039 0.141 1651 Planarity : 0.005 0.057 1632 Dihedral : 13.417 88.247 3454 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.54 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.21), residues: 1275 helix: -1.55 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 428 HIS 0.001 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.013 0.001 TYR B 387 ARG 0.003 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 LEU cc_start: 0.8706 (mt) cc_final: 0.8488 (mp) REVERT: C 271 MET cc_start: 0.7915 (mtp) cc_final: 0.7667 (mtp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1866 time to fit residues: 50.3294 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 138 ASN A 174 ASN A 321 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 138 ASN B 174 ASN B 340 GLN C 110 ASN C 138 ASN C 174 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053404 restraints weight = 51370.883| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.94 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9747 Z= 0.314 Angle : 0.695 10.919 13265 Z= 0.345 Chirality : 0.042 0.197 1651 Planarity : 0.005 0.053 1632 Dihedral : 5.209 82.351 1368 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.09 % Allowed : 15.21 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1275 helix: -0.22 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -1.63 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 428 HIS 0.002 0.001 HIS C 334 PHE 0.013 0.002 PHE A 28 TYR 0.017 0.002 TYR B 387 ARG 0.007 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7618 (ttm-80) REVERT: A 271 MET cc_start: 0.9013 (mtm) cc_final: 0.8689 (mtm) REVERT: A 321 GLN cc_start: 0.9143 (mt0) cc_final: 0.8739 (mm-40) REVERT: A 365 MET cc_start: 0.9343 (tpp) cc_final: 0.8865 (tpp) REVERT: A 399 MET cc_start: 0.8742 (mmm) cc_final: 0.8248 (mmt) REVERT: B 109 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6555 (m-10) REVERT: B 219 MET cc_start: 0.9164 (mmp) cc_final: 0.8729 (tpp) REVERT: C 61 MET cc_start: 0.8612 (tpp) cc_final: 0.8274 (mmt) REVERT: C 90 TYR cc_start: 0.8875 (t80) cc_final: 0.8654 (t80) REVERT: C 109 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.5899 (m-10) REVERT: C 321 GLN cc_start: 0.9165 (mt0) cc_final: 0.8914 (mm-40) REVERT: C 324 THR cc_start: 0.9268 (m) cc_final: 0.9027 (p) REVERT: C 399 MET cc_start: 0.8771 (mmm) cc_final: 0.8230 (mmt) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.1631 time to fit residues: 36.3637 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN C 330 ASN C 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.077760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061590 restraints weight = 58545.300| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 5.44 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9747 Z= 0.204 Angle : 0.622 10.401 13265 Z= 0.303 Chirality : 0.040 0.194 1651 Planarity : 0.005 0.051 1632 Dihedral : 5.068 88.003 1368 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.29 % Allowed : 16.80 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1275 helix: 0.35 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -0.94 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 20 HIS 0.000 0.000 HIS A 334 PHE 0.012 0.001 PHE C 302 TYR 0.013 0.001 TYR B 387 ARG 0.005 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7603 (ttm-80) REVERT: A 271 MET cc_start: 0.9004 (mtm) cc_final: 0.8685 (mtm) REVERT: A 321 GLN cc_start: 0.9102 (mt0) cc_final: 0.8585 (mm-40) REVERT: A 365 MET cc_start: 0.9379 (tpp) cc_final: 0.8967 (tpp) REVERT: A 399 MET cc_start: 0.8478 (mmm) cc_final: 0.8090 (mmt) REVERT: B 109 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: B 219 MET cc_start: 0.9212 (mmp) cc_final: 0.8789 (tpp) REVERT: C 19 LEU cc_start: 0.9314 (tt) cc_final: 0.9079 (pp) REVERT: C 61 MET cc_start: 0.8580 (tpp) cc_final: 0.8293 (mmt) REVERT: C 90 TYR cc_start: 0.8871 (t80) cc_final: 0.8652 (t80) REVERT: C 97 MET cc_start: 0.8872 (mmm) cc_final: 0.8483 (mmm) REVERT: C 109 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: C 321 GLN cc_start: 0.9146 (mt0) cc_final: 0.8841 (mm-40) REVERT: C 324 THR cc_start: 0.9290 (m) cc_final: 0.9074 (p) REVERT: C 365 MET cc_start: 0.9423 (tpp) cc_final: 0.9120 (tpp) REVERT: C 399 MET cc_start: 0.8625 (mmm) cc_final: 0.8205 (mmt) outliers start: 23 outliers final: 12 residues processed: 160 average time/residue: 0.1609 time to fit residues: 39.5108 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.073641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058185 restraints weight = 48045.803| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.75 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9747 Z= 0.170 Angle : 0.620 10.070 13265 Z= 0.297 Chirality : 0.039 0.182 1651 Planarity : 0.005 0.050 1632 Dihedral : 4.976 89.847 1368 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.99 % Allowed : 18.89 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1275 helix: 0.73 (0.17), residues: 1041 sheet: None (None), residues: 0 loop : -0.61 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.001 0.000 HIS C 334 PHE 0.014 0.001 PHE C 302 TYR 0.013 0.001 TYR B 387 ARG 0.005 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8845 (mmm) cc_final: 0.8548 (mpp) REVERT: A 107 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7567 (ttm-80) REVERT: A 137 LEU cc_start: 0.9413 (mp) cc_final: 0.9203 (pp) REVERT: A 271 MET cc_start: 0.8948 (mtm) cc_final: 0.8653 (mtm) REVERT: A 365 MET cc_start: 0.9356 (tpp) cc_final: 0.9018 (tpp) REVERT: A 389 MET cc_start: 0.9405 (ptm) cc_final: 0.9183 (ptt) REVERT: A 399 MET cc_start: 0.8417 (mmm) cc_final: 0.8056 (mmt) REVERT: B 50 ASP cc_start: 0.9243 (t70) cc_final: 0.8971 (m-30) REVERT: B 365 MET cc_start: 0.9319 (tpp) cc_final: 0.9049 (tpp) REVERT: B 399 MET cc_start: 0.8487 (mtp) cc_final: 0.8284 (mmt) REVERT: C 97 MET cc_start: 0.8757 (mmm) cc_final: 0.8450 (mmm) REVERT: C 109 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.5940 (m-10) REVERT: C 365 MET cc_start: 0.9371 (tpp) cc_final: 0.9066 (tpp) REVERT: C 399 MET cc_start: 0.8593 (mmm) cc_final: 0.8299 (mmt) outliers start: 20 outliers final: 12 residues processed: 165 average time/residue: 0.1784 time to fit residues: 44.9965 Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 overall best weight: 2.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055267 restraints weight = 68009.973| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 5.92 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9747 Z= 0.238 Angle : 0.650 9.889 13265 Z= 0.314 Chirality : 0.041 0.195 1651 Planarity : 0.005 0.050 1632 Dihedral : 4.946 89.010 1368 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.08 % Allowed : 20.68 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1275 helix: 0.90 (0.17), residues: 1044 sheet: None (None), residues: 0 loop : -0.37 (0.46), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 428 HIS 0.001 0.000 HIS C 334 PHE 0.014 0.001 PHE C 302 TYR 0.015 0.002 TYR C 90 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7570 (ttm-80) REVERT: A 109 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6784 (m-10) REVERT: A 137 LEU cc_start: 0.9420 (mp) cc_final: 0.9143 (pp) REVERT: A 271 MET cc_start: 0.8987 (mtm) cc_final: 0.8688 (mtm) REVERT: A 321 GLN cc_start: 0.9188 (mt0) cc_final: 0.8848 (mm-40) REVERT: A 365 MET cc_start: 0.9385 (tpp) cc_final: 0.9047 (tpp) REVERT: A 399 MET cc_start: 0.8423 (mmm) cc_final: 0.8062 (mmt) REVERT: B 107 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7442 (ttm-80) REVERT: B 109 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6728 (m-10) REVERT: B 365 MET cc_start: 0.9332 (tpp) cc_final: 0.9069 (tpp) REVERT: C 97 MET cc_start: 0.8837 (mmm) cc_final: 0.8477 (mmm) REVERT: C 107 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7456 (ttm-80) REVERT: C 109 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6171 (m-10) REVERT: C 365 MET cc_start: 0.9444 (tpp) cc_final: 0.9197 (tpp) REVERT: C 399 MET cc_start: 0.8674 (mmm) cc_final: 0.8396 (mmt) outliers start: 31 outliers final: 19 residues processed: 160 average time/residue: 0.1868 time to fit residues: 44.5725 Evaluate side-chains 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055039 restraints weight = 70044.166| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 6.00 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9747 Z= 0.198 Angle : 0.641 10.044 13265 Z= 0.305 Chirality : 0.040 0.155 1651 Planarity : 0.004 0.051 1632 Dihedral : 4.875 89.372 1368 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.58 % Allowed : 21.37 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1275 helix: 0.98 (0.17), residues: 1050 sheet: None (None), residues: 0 loop : -0.56 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 20 HIS 0.000 0.000 HIS C 334 PHE 0.014 0.001 PHE C 302 TYR 0.015 0.002 TYR C 90 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.143 Fit side-chains REVERT: A 107 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7573 (ttm-80) REVERT: A 137 LEU cc_start: 0.9397 (mp) cc_final: 0.9178 (pp) REVERT: A 271 MET cc_start: 0.8971 (mtp) cc_final: 0.8671 (mtm) REVERT: A 321 GLN cc_start: 0.9168 (mt0) cc_final: 0.8801 (mm-40) REVERT: A 365 MET cc_start: 0.9361 (tpp) cc_final: 0.9015 (tpp) REVERT: B 50 ASP cc_start: 0.9294 (t70) cc_final: 0.9044 (m-30) REVERT: B 107 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7334 (ttm-80) REVERT: B 109 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6696 (m-10) REVERT: B 241 LEU cc_start: 0.9575 (mt) cc_final: 0.9261 (mp) REVERT: B 272 ILE cc_start: 0.8947 (mm) cc_final: 0.8730 (mp) REVERT: B 365 MET cc_start: 0.9315 (tpp) cc_final: 0.9025 (tpp) REVERT: C 19 LEU cc_start: 0.9286 (tt) cc_final: 0.9063 (pp) REVERT: C 97 MET cc_start: 0.8739 (mmm) cc_final: 0.8531 (mmm) REVERT: C 107 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7457 (ttm-80) REVERT: C 109 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: C 365 MET cc_start: 0.9379 (tpp) cc_final: 0.9145 (tpp) REVERT: C 399 MET cc_start: 0.8574 (mmm) cc_final: 0.8328 (mmt) outliers start: 26 outliers final: 18 residues processed: 165 average time/residue: 0.1848 time to fit residues: 45.3910 Evaluate side-chains 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 117 optimal weight: 0.0040 chunk 23 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.075036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057314 restraints weight = 87062.874| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 6.73 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9747 Z= 0.162 Angle : 0.648 11.729 13265 Z= 0.304 Chirality : 0.040 0.148 1651 Planarity : 0.004 0.051 1632 Dihedral : 4.801 89.361 1368 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.39 % Allowed : 22.56 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1275 helix: 1.15 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 20 HIS 0.000 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.013 0.001 TYR C 90 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8826 (mmm) cc_final: 0.8581 (mpp) REVERT: A 107 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7645 (ttm-80) REVERT: A 109 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: A 137 LEU cc_start: 0.9374 (mp) cc_final: 0.9164 (pp) REVERT: A 271 MET cc_start: 0.8972 (mtm) cc_final: 0.8688 (mtm) REVERT: A 321 GLN cc_start: 0.9138 (mt0) cc_final: 0.8769 (mm-40) REVERT: A 365 MET cc_start: 0.9348 (tpp) cc_final: 0.9074 (tpp) REVERT: B 50 ASP cc_start: 0.9232 (t70) cc_final: 0.8998 (m-30) REVERT: B 107 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7275 (ttm-80) REVERT: B 109 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6769 (m-10) REVERT: B 241 LEU cc_start: 0.9551 (mt) cc_final: 0.9255 (mp) REVERT: B 272 ILE cc_start: 0.8926 (mm) cc_final: 0.8694 (mp) REVERT: B 365 MET cc_start: 0.9331 (tpp) cc_final: 0.9086 (tpp) REVERT: B 399 MET cc_start: 0.8415 (mtp) cc_final: 0.8118 (mmt) REVERT: C 19 LEU cc_start: 0.9236 (tt) cc_final: 0.8977 (pp) REVERT: C 107 ARG cc_start: 0.7849 (mtm110) cc_final: 0.7426 (ttm-80) REVERT: C 109 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6190 (m-10) REVERT: C 365 MET cc_start: 0.9417 (tpp) cc_final: 0.9187 (tpp) REVERT: C 399 MET cc_start: 0.8447 (mmm) cc_final: 0.8214 (mmt) outliers start: 24 outliers final: 17 residues processed: 178 average time/residue: 0.1812 time to fit residues: 48.6157 Evaluate side-chains 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.074885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058035 restraints weight = 65060.260| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 5.75 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9747 Z= 0.178 Angle : 0.672 11.894 13265 Z= 0.311 Chirality : 0.040 0.162 1651 Planarity : 0.004 0.051 1632 Dihedral : 4.620 81.327 1368 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.39 % Allowed : 23.86 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1275 helix: 1.25 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 428 HIS 0.000 0.000 HIS A 334 PHE 0.013 0.001 PHE C 302 TYR 0.015 0.001 TYR A 90 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.9290 (tt) cc_final: 0.8744 (pp) REVERT: A 107 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7645 (ttm-80) REVERT: A 109 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: A 137 LEU cc_start: 0.9372 (mp) cc_final: 0.9160 (pp) REVERT: A 271 MET cc_start: 0.8925 (mtp) cc_final: 0.8628 (mtm) REVERT: A 321 GLN cc_start: 0.9155 (mt0) cc_final: 0.8798 (mm-40) REVERT: A 365 MET cc_start: 0.9338 (tpp) cc_final: 0.9056 (tpp) REVERT: A 389 MET cc_start: 0.9394 (ptm) cc_final: 0.9138 (ptt) REVERT: B 107 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7274 (ttm-80) REVERT: B 109 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: B 110 ASN cc_start: 0.8865 (t0) cc_final: 0.8538 (t0) REVERT: B 241 LEU cc_start: 0.9591 (mt) cc_final: 0.9293 (mp) REVERT: B 272 ILE cc_start: 0.8934 (mm) cc_final: 0.8694 (mp) REVERT: B 330 ASN cc_start: 0.8945 (m-40) cc_final: 0.8695 (t0) REVERT: B 365 MET cc_start: 0.9342 (tpp) cc_final: 0.9099 (tpp) REVERT: B 399 MET cc_start: 0.8471 (mtp) cc_final: 0.8160 (mmt) REVERT: C 19 LEU cc_start: 0.9228 (tt) cc_final: 0.8976 (pp) REVERT: C 107 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7408 (ttm-80) REVERT: C 109 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6215 (m-10) REVERT: C 272 ILE cc_start: 0.8960 (mm) cc_final: 0.8758 (mp) REVERT: C 365 MET cc_start: 0.9386 (tpp) cc_final: 0.9164 (tpp) REVERT: C 399 MET cc_start: 0.8441 (mmm) cc_final: 0.8188 (mmt) outliers start: 24 outliers final: 15 residues processed: 165 average time/residue: 0.1844 time to fit residues: 45.7760 Evaluate side-chains 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 0.0570 chunk 121 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 overall best weight: 2.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.073794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.056465 restraints weight = 74467.889| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 6.13 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9747 Z= 0.228 Angle : 0.681 13.336 13265 Z= 0.319 Chirality : 0.041 0.183 1651 Planarity : 0.004 0.051 1632 Dihedral : 4.596 78.386 1368 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.39 % Allowed : 24.45 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1275 helix: 1.17 (0.17), residues: 1053 sheet: None (None), residues: 0 loop : -0.65 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 16 HIS 0.001 0.000 HIS C 34 PHE 0.013 0.001 PHE C 302 TYR 0.018 0.002 TYR C 90 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.094 Fit side-chains REVERT: A 59 LEU cc_start: 0.9206 (tp) cc_final: 0.8706 (tt) REVERT: A 107 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7688 (ttm-80) REVERT: A 109 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: A 137 LEU cc_start: 0.9398 (mp) cc_final: 0.9162 (pp) REVERT: A 321 GLN cc_start: 0.9155 (mt0) cc_final: 0.8772 (mm-40) REVERT: A 365 MET cc_start: 0.9343 (tpp) cc_final: 0.9049 (tpp) REVERT: B 107 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7361 (ttm-80) REVERT: B 109 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: B 110 ASN cc_start: 0.8857 (t0) cc_final: 0.8591 (t0) REVERT: B 241 LEU cc_start: 0.9610 (mt) cc_final: 0.9322 (mp) REVERT: B 365 MET cc_start: 0.9359 (tpp) cc_final: 0.9111 (tpp) REVERT: B 399 MET cc_start: 0.8470 (mtp) cc_final: 0.8189 (mmt) REVERT: C 107 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7436 (ttm-80) REVERT: C 109 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: C 272 ILE cc_start: 0.8978 (mm) cc_final: 0.8771 (mp) REVERT: C 365 MET cc_start: 0.9374 (tpp) cc_final: 0.9153 (tpp) REVERT: C 399 MET cc_start: 0.8585 (mmm) cc_final: 0.8264 (mmt) outliers start: 24 outliers final: 17 residues processed: 155 average time/residue: 0.2033 time to fit residues: 47.4141 Evaluate side-chains 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 chunk 113 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.075638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058146 restraints weight = 76349.297| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 6.37 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9747 Z= 0.164 Angle : 0.698 13.294 13265 Z= 0.317 Chirality : 0.040 0.173 1651 Planarity : 0.004 0.051 1632 Dihedral : 4.539 77.550 1368 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.99 % Allowed : 25.15 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1275 helix: 1.23 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 20 HIS 0.001 0.000 HIS C 334 PHE 0.013 0.001 PHE C 302 TYR 0.015 0.001 TYR A 90 ARG 0.003 0.000 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9540 (tmm) cc_final: 0.9334 (ppp) REVERT: A 59 LEU cc_start: 0.9069 (tp) cc_final: 0.8663 (tt) REVERT: A 80 LEU cc_start: 0.9259 (tt) cc_final: 0.8765 (pp) REVERT: A 90 TYR cc_start: 0.8950 (t80) cc_final: 0.8487 (t80) REVERT: A 107 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7595 (ttm-80) REVERT: A 109 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: A 137 LEU cc_start: 0.9353 (mp) cc_final: 0.9139 (pp) REVERT: A 271 MET cc_start: 0.8856 (mtp) cc_final: 0.8601 (mtt) REVERT: A 321 GLN cc_start: 0.9127 (mt0) cc_final: 0.8729 (mm-40) REVERT: A 365 MET cc_start: 0.9305 (tpp) cc_final: 0.9101 (tpp) REVERT: A 368 MET cc_start: 0.9280 (tpp) cc_final: 0.8804 (tpp) REVERT: A 399 MET cc_start: 0.8366 (mmt) cc_final: 0.7822 (mmp) REVERT: B 107 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7287 (ttm-80) REVERT: B 109 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6670 (m-10) REVERT: B 110 ASN cc_start: 0.8848 (t0) cc_final: 0.8555 (t0) REVERT: B 241 LEU cc_start: 0.9593 (mt) cc_final: 0.9291 (mp) REVERT: B 272 ILE cc_start: 0.8960 (mm) cc_final: 0.8717 (mp) REVERT: B 365 MET cc_start: 0.9327 (tpp) cc_final: 0.9084 (tpp) REVERT: B 399 MET cc_start: 0.8398 (mtp) cc_final: 0.8080 (mmt) REVERT: C 19 LEU cc_start: 0.9211 (tt) cc_final: 0.8973 (pp) REVERT: C 107 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7469 (ttm-80) REVERT: C 109 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6162 (m-10) REVERT: C 271 MET cc_start: 0.8680 (mtp) cc_final: 0.8421 (mtm) REVERT: C 272 ILE cc_start: 0.8920 (mm) cc_final: 0.8713 (mp) REVERT: C 365 MET cc_start: 0.9387 (tpp) cc_final: 0.9168 (tpp) REVERT: C 399 MET cc_start: 0.8420 (mmm) cc_final: 0.8097 (mmt) outliers start: 20 outliers final: 13 residues processed: 167 average time/residue: 0.1737 time to fit residues: 43.4688 Evaluate side-chains 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.0010 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.074816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057021 restraints weight = 79587.756| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 6.51 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9747 Z= 0.195 Angle : 0.703 14.590 13265 Z= 0.319 Chirality : 0.041 0.179 1651 Planarity : 0.004 0.050 1632 Dihedral : 4.447 76.406 1368 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.09 % Allowed : 26.24 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1275 helix: 1.20 (0.17), residues: 1050 sheet: None (None), residues: 0 loop : -0.74 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 428 HIS 0.000 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.015 0.001 TYR C 90 ARG 0.003 0.000 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.33 seconds wall clock time: 65 minutes 13.19 seconds (3913.19 seconds total)