Starting phenix.real_space_refine on Sun Dec 29 00:10:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwq_10635/12_2024/6xwq_10635.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwq_10635/12_2024/6xwq_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_10635/12_2024/6xwq_10635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwq_10635/12_2024/6xwq_10635.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwq_10635/12_2024/6xwq_10635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwq_10635/12_2024/6xwq_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-5532/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: 7.03, per 1000 atoms: 0.73 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 1.5 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: 2.60 Time building geometry restraints manager: 2.99 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: 0.670 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.580 Find NCS groups from input model: 0.390 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- 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 : 1.054 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: 0.1901 time to fit residues: 51.5917 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 : 0.989 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 1.105 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8527 (tpp) cc_final: 0.8216 (tpp) REVERT: B 109 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6377 (m-10) REVERT: C 109 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5725 (m-10) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.1762 time to fit residues: 39.1050 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 63 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9747 Z= 0.335 Angle : 0.678 9.468 13265 Z= 0.338 Chirality : 0.042 0.193 1651 Planarity : 0.005 0.051 1632 Dihedral : 5.225 89.131 1368 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.88 % Allowed : 17.30 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1275 helix: 0.27 (0.17), residues: 1047 sheet: None (None), residues: 0 loop : -1.22 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 428 HIS 0.002 0.000 HIS C 334 PHE 0.013 0.002 PHE A 28 TYR 0.015 0.002 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 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8625 (tpp) cc_final: 0.8352 (tpp) REVERT: B 109 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6544 (m-10) REVERT: C 109 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.5829 (m-10) REVERT: C 365 MET cc_start: 0.8716 (tpp) cc_final: 0.8466 (tpp) outliers start: 29 outliers final: 16 residues processed: 150 average time/residue: 0.1646 time to fit residues: 37.7742 Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 A residue 358 VAL Chi-restraints excluded: chain A residue 385 LEU 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 B residue 358 VAL 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 243 LEU Chi-restraints excluded: chain C residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.3980 chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN C 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9747 Z= 0.163 Angle : 0.635 10.075 13265 Z= 0.305 Chirality : 0.039 0.139 1651 Planarity : 0.005 0.050 1632 Dihedral : 4.976 85.656 1368 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.79 % Allowed : 20.48 % Favored : 77.73 % 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: 0.43 (0.25), residues: 1275 helix: 0.60 (0.17), residues: 1050 sheet: None (None), residues: 0 loop : -0.70 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 20 HIS 0.001 0.000 HIS A 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 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8556 (tpp) cc_final: 0.8299 (tpp) REVERT: C 109 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.5735 (m-10) outliers start: 18 outliers final: 9 residues processed: 158 average time/residue: 0.1570 time to fit residues: 38.6082 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain B residue 224 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.0050 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2832 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= 0.170 Angle : 0.663 10.265 13265 Z= 0.314 Chirality : 0.041 0.179 1651 Planarity : 0.005 0.050 1632 Dihedral : 4.928 88.858 1368 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.88 % Allowed : 20.97 % Favored : 76.14 % 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: 0.66 (0.25), residues: 1275 helix: 0.86 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.000 0.000 HIS A 334 PHE 0.013 0.001 PHE C 302 TYR 0.013 0.001 TYR B 387 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 178 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: A 365 MET cc_start: 0.8563 (tpp) cc_final: 0.8359 (tpp) REVERT: B 109 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: C 109 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.5737 (m-10) outliers start: 29 outliers final: 13 residues processed: 169 average time/residue: 0.1564 time to fit residues: 41.4723 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU 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 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 C residue 35 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3066 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= 0.218 Angle : 0.694 11.469 13265 Z= 0.329 Chirality : 0.041 0.195 1651 Planarity : 0.005 0.051 1632 Dihedral : 4.864 86.254 1368 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.29 % Allowed : 22.56 % Favored : 75.15 % 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: 0.82 (0.25), residues: 1275 helix: 0.96 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 428 HIS 0.001 0.000 HIS C 334 PHE 0.014 0.001 PHE C 302 TYR 0.017 0.002 TYR B 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 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6495 (m-10) REVERT: B 109 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6442 (m-10) REVERT: B 241 LEU cc_start: 0.8936 (mt) cc_final: 0.8726 (mp) REVERT: C 109 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.5888 (m-10) outliers start: 23 outliers final: 16 residues processed: 152 average time/residue: 0.1673 time to fit residues: 39.3330 Evaluate side-chains 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU 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 301 ILE 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 61 MET 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 13 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9747 Z= 0.169 Angle : 0.686 11.099 13265 Z= 0.321 Chirality : 0.041 0.172 1651 Planarity : 0.004 0.051 1632 Dihedral : 4.758 86.673 1368 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 23.06 % Favored : 74.65 % 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: 1.08 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 20 HIS 0.000 0.000 HIS A 334 PHE 0.014 0.001 PHE C 302 TYR 0.017 0.001 TYR B 90 ARG 0.003 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 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6453 (m-10) REVERT: B 109 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6364 (m-10) REVERT: B 272 ILE cc_start: 0.8547 (mm) cc_final: 0.8307 (mp) REVERT: C 109 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.5781 (m-10) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.1574 time to fit residues: 38.9910 Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 403 MET 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 61 MET 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 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9747 Z= 0.172 Angle : 0.712 11.861 13265 Z= 0.329 Chirality : 0.041 0.177 1651 Planarity : 0.004 0.050 1632 Dihedral : 4.640 82.922 1368 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 0.98 (0.25), residues: 1275 helix: 1.09 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.001 0.000 HIS A 334 PHE 0.015 0.001 PHE B 242 TYR 0.018 0.001 TYR A 90 ARG 0.004 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 176 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: B 109 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6396 (m-10) REVERT: B 110 ASN cc_start: 0.8343 (t0) cc_final: 0.8052 (t0) REVERT: B 272 ILE cc_start: 0.8517 (mm) cc_final: 0.8286 (mp) REVERT: C 109 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.5894 (m-10) REVERT: C 272 ILE cc_start: 0.8617 (mm) cc_final: 0.8411 (mp) outliers start: 24 outliers final: 16 residues processed: 166 average time/residue: 0.1604 time to fit residues: 41.7939 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 : 1.112 ------------------------------------------------------------------------------- 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 137 LEU 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 224 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3569 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= 0.207 Angle : 0.729 13.411 13265 Z= 0.336 Chirality : 0.041 0.178 1651 Planarity : 0.005 0.051 1632 Dihedral : 4.636 80.182 1368 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.39 % Allowed : 24.65 % Favored : 72.96 % 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: 1.16 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.03 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 428 HIS 0.001 0.000 HIS C 34 PHE 0.014 0.001 PHE C 302 TYR 0.018 0.002 TYR C 90 ARG 0.004 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 166 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: A 272 ILE cc_start: 0.8676 (mm) cc_final: 0.8449 (mp) REVERT: B 109 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6455 (m-10) REVERT: B 110 ASN cc_start: 0.8345 (t0) cc_final: 0.8072 (t0) REVERT: B 272 ILE cc_start: 0.8549 (mm) cc_final: 0.8323 (mp) REVERT: C 109 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.5951 (m-10) REVERT: C 272 ILE cc_start: 0.8602 (mm) cc_final: 0.8388 (mp) outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 0.1905 time to fit residues: 46.1289 Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 137 LEU 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 61 MET 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 73 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 83 optimal weight: 0.0670 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9747 Z= 0.241 Angle : 0.737 10.649 13265 Z= 0.343 Chirality : 0.042 0.183 1651 Planarity : 0.005 0.051 1632 Dihedral : 4.579 78.270 1368 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.19 % Allowed : 24.45 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1275 helix: 1.17 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 16 HIS 0.001 0.000 HIS C 334 PHE 0.012 0.001 PHE C 302 TYR 0.021 0.002 TYR C 90 ARG 0.004 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 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.050 Fit side-chains REVERT: A 109 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6471 (m-10) REVERT: A 272 ILE cc_start: 0.8673 (mm) cc_final: 0.8448 (mp) REVERT: B 109 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: B 110 ASN cc_start: 0.8312 (t0) cc_final: 0.8032 (t0) REVERT: B 137 LEU cc_start: 0.8944 (pp) cc_final: 0.8686 (pt) REVERT: C 109 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.5873 (m-10) outliers start: 22 outliers final: 17 residues processed: 152 average time/residue: 0.1768 time to fit residues: 41.6769 Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 188 VAL 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 C residue 51 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 114 ASN 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 30 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.075091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058189 restraints weight = 82373.748| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 6.36 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3687 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= 0.175 Angle : 0.757 16.130 13265 Z= 0.342 Chirality : 0.042 0.184 1651 Planarity : 0.004 0.050 1632 Dihedral : 4.569 77.805 1368 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.79 % Allowed : 25.05 % 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: 0.95 (0.25), residues: 1275 helix: 1.11 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.21 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 20 HIS 0.000 0.000 HIS A 34 PHE 0.013 0.001 PHE C 302 TYR 0.018 0.001 TYR A 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: 1787.47 seconds wall clock time: 33 minutes 39.30 seconds (2019.30 seconds total)