Starting phenix.real_space_refine on Sun Jun 15 04:08:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o12_49995/06_2025/9o12_49995.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o12_49995/06_2025/9o12_49995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o12_49995/06_2025/9o12_49995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o12_49995/06_2025/9o12_49995.map" model { file = "/net/cci-nas-00/data/ceres_data/9o12_49995/06_2025/9o12_49995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o12_49995/06_2025/9o12_49995.cif" } resolution = 4.3 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= 0.002 sd= 0.012 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5520 2.51 5 N 1356 2.21 5 O 1444 1.98 5 H 8772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17136 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "B" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "D" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Time building chain proxies: 8.14, per 1000 atoms: 0.48 Number of scatterers: 17136 At special positions: 0 Unit cell: (118.137, 122.595, 78.758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1444 8.00 N 1356 7.00 C 5520 6.00 H 8772 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 2 sheets defined 81.7% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 169 through 181 removed outlier: 4.182A pdb=" N LYS A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 226 through 251 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 280 removed outlier: 3.564A pdb=" N ILE A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 314 through 354 removed outlier: 3.729A pdb=" N GLN A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASN A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 376 removed outlier: 4.491A pdb=" N TRP A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.795A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.663A pdb=" N ILE A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 4.227A pdb=" N ARG B 172 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 209 removed outlier: 4.098A pdb=" N LEU B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 250 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.733A pdb=" N PHE B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 280 removed outlier: 4.637A pdb=" N ASP B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Proline residue: B 272 - end of helix removed outlier: 4.109A pdb=" N THR B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 277 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.870A pdb=" N ARG B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 4.171A pdb=" N ILE B 304 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 removed outlier: 4.406A pdb=" N ARG B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 354 removed outlier: 4.538A pdb=" N GLY B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 387 through 407 removed outlier: 3.789A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.548A pdb=" N ILE B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 175 through 181 Processing helix chain 'C' and resid 185 through 209 removed outlier: 4.017A pdb=" N LYS C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 250 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.665A pdb=" N LYS C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 280 Proline residue: C 272 - end of helix removed outlier: 4.128A pdb=" N PHE C 278 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 280 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 288 through 299 removed outlier: 3.958A pdb=" N ARG C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 314 removed outlier: 3.882A pdb=" N ILE C 304 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 354 removed outlier: 5.583A pdb=" N ASN C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 375 removed outlier: 3.872A pdb=" N TRP C 369 " --> pdb=" O PRO C 365 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.676A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 402 " --> pdb=" O CYS C 398 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 425 removed outlier: 3.822A pdb=" N ILE C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.690A pdb=" N LEU D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 209 removed outlier: 4.060A pdb=" N LEU D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 213 removed outlier: 5.981A pdb=" N GLU D 213 " --> pdb=" O THR D 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 210 through 213' Processing helix chain 'D' and resid 226 through 251 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.806A pdb=" N GLY D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 281 removed outlier: 5.237A pdb=" N ASP D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Proline residue: D 272 - end of helix removed outlier: 3.776A pdb=" N THR D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 removed outlier: 3.768A pdb=" N VAL D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 314 through 332 removed outlier: 3.624A pdb=" N PHE D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 354 removed outlier: 3.987A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 376 removed outlier: 4.187A pdb=" N TRP D 369 " --> pdb=" O PRO D 365 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 407 removed outlier: 3.517A pdb=" N CYS D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 425 removed outlier: 3.768A pdb=" N ILE D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN D 423 " --> pdb=" O PHE D 419 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA2, first strand: chain 'D' and resid 215 through 217 560 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8752 1.03 - 1.23: 20 1.23 - 1.42: 3452 1.42 - 1.61: 5028 1.61 - 1.81: 68 Bond restraints: 17320 Sorted by residual: bond pdb=" N CYS D 167 " pdb=" CA CYS D 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N CYS C 167 " pdb=" CA CYS C 167 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N CYS B 167 " pdb=" CA CYS B 167 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N CYS A 167 " pdb=" CA CYS A 167 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N CYS D 167 " pdb=" H CYS D 167 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 17315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 28779 0.92 - 1.83: 2557 1.83 - 2.75: 109 2.75 - 3.66: 23 3.66 - 4.58: 24 Bond angle restraints: 31492 Sorted by residual: angle pdb=" N ILE D 364 " pdb=" CA ILE D 364 " pdb=" C ILE D 364 " ideal model delta sigma weight residual 112.35 108.58 3.77 1.20e+00 6.94e-01 9.86e+00 angle pdb=" C ILE B 409 " pdb=" CA ILE B 409 " pdb=" CB ILE B 409 " ideal model delta sigma weight residual 114.00 110.70 3.30 1.31e+00 5.83e-01 6.34e+00 angle pdb=" CA ILE B 409 " pdb=" C ILE B 409 " pdb=" N PRO B 410 " ideal model delta sigma weight residual 120.83 119.34 1.49 6.10e-01 2.69e+00 5.93e+00 angle pdb=" CA ILE D 364 " pdb=" C ILE D 364 " pdb=" N PRO D 365 " ideal model delta sigma weight residual 120.83 119.56 1.27 6.10e-01 2.69e+00 4.36e+00 angle pdb=" CA PHE A 361 " pdb=" C PHE A 361 " pdb=" N LYS A 362 " ideal model delta sigma weight residual 114.76 117.00 -2.24 1.14e+00 7.69e-01 3.86e+00 ... (remaining 31487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 7596 17.62 - 35.24: 320 35.24 - 52.85: 99 52.85 - 70.47: 32 70.47 - 88.09: 13 Dihedral angle restraints: 8060 sinusoidal: 4384 harmonic: 3676 Sorted by residual: dihedral pdb=" CA ALA B 406 " pdb=" C ALA B 406 " pdb=" N LEU B 407 " pdb=" CA LEU B 407 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ALA C 406 " pdb=" C ALA C 406 " pdb=" N LEU C 407 " pdb=" CA LEU C 407 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE B 301 " pdb=" C ILE B 301 " pdb=" N MET B 302 " pdb=" CA MET B 302 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 874 0.023 - 0.047: 234 0.047 - 0.070: 139 0.070 - 0.094: 91 0.094 - 0.117: 26 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA PRO C 272 " pdb=" N PRO C 272 " pdb=" C PRO C 272 " pdb=" CB PRO C 272 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA PRO B 410 " pdb=" N PRO B 410 " pdb=" C PRO B 410 " pdb=" CB PRO B 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA PRO A 410 " pdb=" N PRO A 410 " pdb=" C PRO A 410 " pdb=" CB PRO A 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 1361 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 407 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 408 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 278 " -0.011 2.00e-02 2.50e+03 7.05e-03 1.49e+00 pdb=" CG PHE A 278 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 278 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 278 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 278 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 278 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 278 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 278 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 278 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 278 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 278 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 278 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 271 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 272 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.015 5.00e-02 4.00e+02 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 601 2.16 - 2.77: 33819 2.77 - 3.38: 47738 3.38 - 3.99: 53912 3.99 - 4.60: 87873 Nonbonded interactions: 223943 Sorted by model distance: nonbonded pdb=" OE2 GLU B 353 " pdb=" H LYS B 386 " model vdw 1.550 2.450 nonbonded pdb=" OD1 ASN B 226 " pdb=" H LEU B 229 " model vdw 1.556 2.450 nonbonded pdb=" O ILE A 411 " pdb="HD21 ASN A 415 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLU D 330 " pdb=" H GLU D 330 " model vdw 1.573 2.450 nonbonded pdb=" O LEU C 211 " pdb=" H GLN C 215 " model vdw 1.582 2.450 ... (remaining 223938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.300 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.240 Find NCS groups from input model: 0.400 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 0.033 8548 Z= 0.140 Angle : 0.473 4.538 11572 Z= 0.275 Chirality : 0.036 0.117 1364 Planarity : 0.003 0.039 1408 Dihedral : 10.075 88.089 3140 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.19 % Allowed : 2.05 % Favored : 96.77 % 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: 1.53 (0.28), residues: 1036 helix: 1.61 (0.20), residues: 753 sheet: None (None), residues: 0 loop : -0.51 (0.42), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.021 0.001 PHE A 278 TYR 0.008 0.001 TYR B 328 ARG 0.002 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.15750 ( 560) hydrogen bonds : angle 5.91319 ( 1578) covalent geometry : bond 0.00272 ( 8548) covalent geometry : angle 0.47304 (11572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 310 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8718 (mp) cc_final: 0.8402 (mp) REVERT: A 388 LEU cc_start: 0.8138 (tp) cc_final: 0.7937 (tt) REVERT: A 392 ILE cc_start: 0.8155 (mt) cc_final: 0.7754 (tp) REVERT: C 194 ILE cc_start: 0.8490 (mm) cc_final: 0.8110 (mm) REVERT: C 413 VAL cc_start: 0.8334 (t) cc_final: 0.8075 (t) REVERT: D 299 PHE cc_start: 0.8264 (m-80) cc_final: 0.8022 (m-10) REVERT: D 412 ILE cc_start: 0.8838 (mt) cc_final: 0.8605 (tp) outliers start: 11 outliers final: 9 residues processed: 316 average time/residue: 0.5255 time to fit residues: 215.3202 Evaluate side-chains 228 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097500 restraints weight = 78047.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101107 restraints weight = 44868.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.103607 restraints weight = 30926.692| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8548 Z= 0.146 Angle : 0.558 5.300 11572 Z= 0.318 Chirality : 0.038 0.148 1364 Planarity : 0.004 0.035 1408 Dihedral : 4.322 18.911 1112 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 1.30 (0.27), residues: 1036 helix: 1.45 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.023 0.002 PHE B 368 TYR 0.011 0.002 TYR C 328 ARG 0.010 0.001 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.05464 ( 560) hydrogen bonds : angle 4.82941 ( 1578) covalent geometry : bond 0.00299 ( 8548) covalent geometry : angle 0.55787 (11572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 PHE cc_start: 0.8784 (m-80) cc_final: 0.8569 (m-80) REVERT: B 202 SER cc_start: 0.9351 (t) cc_final: 0.9005 (m) REVERT: B 243 GLU cc_start: 0.8218 (pp20) cc_final: 0.7956 (pp20) REVERT: B 356 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8644 (mp0) REVERT: C 194 ILE cc_start: 0.9763 (mm) cc_final: 0.9366 (mm) REVERT: C 242 MET cc_start: 0.9195 (ttm) cc_final: 0.8840 (mmt) REVERT: C 291 ASN cc_start: 0.8218 (m-40) cc_final: 0.7899 (m-40) REVERT: D 214 LEU cc_start: 0.9126 (mt) cc_final: 0.8807 (mt) REVERT: D 299 PHE cc_start: 0.9589 (m-80) cc_final: 0.9187 (m-10) REVERT: D 353 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8574 (mm-30) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.5183 time to fit residues: 183.6994 Evaluate side-chains 216 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 34 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 0.0670 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.6722 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.113831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086421 restraints weight = 84963.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089727 restraints weight = 46106.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.092055 restraints weight = 30595.652| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8548 Z= 0.125 Angle : 0.514 4.730 11572 Z= 0.289 Chirality : 0.038 0.154 1364 Planarity : 0.004 0.036 1408 Dihedral : 4.305 18.494 1112 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.32 (0.27), residues: 1036 helix: 1.41 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.60 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.021 0.002 PHE C 416 TYR 0.008 0.001 TYR D 384 ARG 0.007 0.000 ARG D 326 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 560) hydrogen bonds : angle 4.53516 ( 1578) covalent geometry : bond 0.00261 ( 8548) covalent geometry : angle 0.51401 (11572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 SER cc_start: 0.9243 (t) cc_final: 0.9028 (m) REVERT: B 243 GLU cc_start: 0.8275 (pp20) cc_final: 0.7989 (pp20) REVERT: B 407 LEU cc_start: 0.9647 (mp) cc_final: 0.9310 (tt) REVERT: D 299 PHE cc_start: 0.9611 (m-80) cc_final: 0.9166 (m-10) REVERT: D 353 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8269 (mm-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.5260 time to fit residues: 184.3366 Evaluate side-chains 217 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 9.9990 chunk 27 optimal weight: 0.0170 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.124893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097361 restraints weight = 78878.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100942 restraints weight = 46007.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.103385 restraints weight = 31997.122| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8548 Z= 0.162 Angle : 0.517 4.605 11572 Z= 0.295 Chirality : 0.038 0.163 1364 Planarity : 0.004 0.034 1408 Dihedral : 4.356 18.594 1112 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 1.10 (0.27), residues: 1036 helix: 1.28 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.020 0.001 PHE C 416 TYR 0.014 0.002 TYR A 380 ARG 0.002 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 560) hydrogen bonds : angle 4.59740 ( 1578) covalent geometry : bond 0.00320 ( 8548) covalent geometry : angle 0.51652 (11572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.9238 (m-80) cc_final: 0.9013 (m-10) REVERT: A 392 ILE cc_start: 0.9610 (mt) cc_final: 0.9252 (tp) REVERT: B 202 SER cc_start: 0.9242 (t) cc_final: 0.8986 (m) REVERT: B 243 GLU cc_start: 0.8501 (pp20) cc_final: 0.8187 (pp20) REVERT: B 340 MET cc_start: 0.9484 (mtp) cc_final: 0.9256 (mmm) REVERT: D 299 PHE cc_start: 0.9638 (m-80) cc_final: 0.9243 (m-10) REVERT: D 353 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8708 (mm-30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.5472 time to fit residues: 180.4002 Evaluate side-chains 206 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.081893 restraints weight = 87595.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084987 restraints weight = 48726.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087197 restraints weight = 32783.407| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8548 Z= 0.217 Angle : 0.555 4.465 11572 Z= 0.324 Chirality : 0.038 0.157 1364 Planarity : 0.004 0.034 1408 Dihedral : 4.488 20.897 1112 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 0.61 (0.26), residues: 1036 helix: 0.94 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -1.04 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.022 0.002 PHE C 198 TYR 0.023 0.002 TYR C 380 ARG 0.003 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 560) hydrogen bonds : angle 4.82200 ( 1578) covalent geometry : bond 0.00411 ( 8548) covalent geometry : angle 0.55482 (11572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.9825 (mm) cc_final: 0.9619 (mm) REVERT: A 368 PHE cc_start: 0.9259 (m-80) cc_final: 0.9059 (m-10) REVERT: A 392 ILE cc_start: 0.9612 (mt) cc_final: 0.9262 (tp) REVERT: B 202 SER cc_start: 0.9324 (t) cc_final: 0.9055 (m) REVERT: B 243 GLU cc_start: 0.8607 (pp20) cc_final: 0.8245 (pp20) REVERT: B 340 MET cc_start: 0.9511 (mtp) cc_final: 0.9289 (mmm) REVERT: C 308 LEU cc_start: 0.9342 (tp) cc_final: 0.9137 (tp) REVERT: D 299 PHE cc_start: 0.9666 (m-80) cc_final: 0.9223 (m-10) REVERT: D 353 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8460 (mm-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5303 time to fit residues: 168.9966 Evaluate side-chains 197 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082740 restraints weight = 86434.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.085970 restraints weight = 47068.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088203 restraints weight = 31386.343| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8548 Z= 0.127 Angle : 0.499 5.281 11572 Z= 0.282 Chirality : 0.037 0.155 1364 Planarity : 0.003 0.034 1408 Dihedral : 4.320 19.144 1112 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.01 (0.27), residues: 1036 helix: 1.24 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.024 0.001 PHE A 198 TYR 0.012 0.001 TYR A 380 ARG 0.002 0.000 ARG D 303 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 560) hydrogen bonds : angle 4.44446 ( 1578) covalent geometry : bond 0.00255 ( 8548) covalent geometry : angle 0.49922 (11572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.9235 (m-80) cc_final: 0.8959 (m-10) REVERT: A 392 ILE cc_start: 0.9606 (mt) cc_final: 0.9251 (tp) REVERT: A 415 ASN cc_start: 0.9211 (m-40) cc_final: 0.8864 (m110) REVERT: B 202 SER cc_start: 0.9270 (t) cc_final: 0.9032 (m) REVERT: B 340 MET cc_start: 0.9510 (mtp) cc_final: 0.9176 (mmm) REVERT: C 306 ARG cc_start: 0.9546 (ttt-90) cc_final: 0.9108 (ttp-170) REVERT: D 299 PHE cc_start: 0.9648 (m-80) cc_final: 0.9192 (m-10) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.6077 time to fit residues: 204.5075 Evaluate side-chains 205 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082190 restraints weight = 87014.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.085283 restraints weight = 48143.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.087410 restraints weight = 32369.354| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8548 Z= 0.174 Angle : 0.522 4.377 11572 Z= 0.299 Chirality : 0.038 0.173 1364 Planarity : 0.004 0.033 1408 Dihedral : 4.352 19.875 1112 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 0.83 (0.27), residues: 1036 helix: 1.13 (0.19), residues: 767 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.028 0.002 PHE C 198 TYR 0.016 0.002 TYR A 380 ARG 0.006 0.000 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 560) hydrogen bonds : angle 4.56527 ( 1578) covalent geometry : bond 0.00337 ( 8548) covalent geometry : angle 0.52191 (11572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.9240 (m-80) cc_final: 0.8994 (m-10) REVERT: A 392 ILE cc_start: 0.9615 (mt) cc_final: 0.9286 (tp) REVERT: B 202 SER cc_start: 0.9270 (t) cc_final: 0.9053 (m) REVERT: B 340 MET cc_start: 0.9542 (mtp) cc_final: 0.9208 (mmm) REVERT: C 306 ARG cc_start: 0.9553 (ttt-90) cc_final: 0.9110 (ttp-170) REVERT: D 299 PHE cc_start: 0.9651 (m-80) cc_final: 0.9177 (m-10) REVERT: D 353 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8469 (mm-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5306 time to fit residues: 171.1526 Evaluate side-chains 200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 overall best weight: 1.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084781 restraints weight = 88324.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087980 restraints weight = 47655.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090241 restraints weight = 31473.363| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8548 Z= 0.106 Angle : 0.490 5.085 11572 Z= 0.271 Chirality : 0.037 0.161 1364 Planarity : 0.003 0.035 1408 Dihedral : 4.187 18.602 1112 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.34 (0.27), residues: 1036 helix: 1.45 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.003 0.001 HIS C 231 PHE 0.018 0.001 PHE A 368 TYR 0.014 0.001 TYR D 380 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 560) hydrogen bonds : angle 4.20994 ( 1578) covalent geometry : bond 0.00226 ( 8548) covalent geometry : angle 0.49027 (11572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9614 (mt) cc_final: 0.9282 (tp) REVERT: A 415 ASN cc_start: 0.9239 (m-40) cc_final: 0.8883 (m110) REVERT: B 202 SER cc_start: 0.9294 (t) cc_final: 0.9054 (m) REVERT: B 340 MET cc_start: 0.9524 (mtp) cc_final: 0.9196 (mmm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.5747 time to fit residues: 193.6505 Evaluate side-chains 202 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084834 restraints weight = 88746.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.087973 restraints weight = 47893.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090125 restraints weight = 32000.675| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8548 Z= 0.157 Angle : 0.521 5.633 11572 Z= 0.294 Chirality : 0.038 0.152 1364 Planarity : 0.004 0.032 1408 Dihedral : 4.267 20.025 1112 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.16 (0.27), residues: 1036 helix: 1.38 (0.19), residues: 767 sheet: None (None), residues: 0 loop : -0.91 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 239 HIS 0.003 0.001 HIS C 231 PHE 0.019 0.002 PHE A 198 TYR 0.018 0.002 TYR C 380 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 560) hydrogen bonds : angle 4.39795 ( 1578) covalent geometry : bond 0.00316 ( 8548) covalent geometry : angle 0.52122 (11572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9619 (mt) cc_final: 0.9291 (tp) REVERT: A 415 ASN cc_start: 0.9203 (m-40) cc_final: 0.8853 (m110) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.5209 time to fit residues: 168.7352 Evaluate side-chains 204 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.112352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085373 restraints weight = 87155.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088607 restraints weight = 46989.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.090881 restraints weight = 30984.533| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8548 Z= 0.105 Angle : 0.493 5.966 11572 Z= 0.272 Chirality : 0.037 0.162 1364 Planarity : 0.003 0.034 1408 Dihedral : 4.132 17.899 1112 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.41 (0.27), residues: 1036 helix: 1.51 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 176 HIS 0.002 0.000 HIS C 231 PHE 0.019 0.002 PHE A 368 TYR 0.018 0.001 TYR B 380 ARG 0.002 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 560) hydrogen bonds : angle 4.13376 ( 1578) covalent geometry : bond 0.00231 ( 8548) covalent geometry : angle 0.49343 (11572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ILE cc_start: 0.9613 (mt) cc_final: 0.9282 (tp) REVERT: A 415 ASN cc_start: 0.9215 (m-40) cc_final: 0.8874 (m110) REVERT: D 199 ILE cc_start: 0.9632 (mm) cc_final: 0.9424 (mm) REVERT: D 380 TYR cc_start: 0.7818 (p90) cc_final: 0.7395 (p90) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.5138 time to fit residues: 175.1124 Evaluate side-chains 215 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.110939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083724 restraints weight = 85866.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.086978 restraints weight = 46680.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089169 restraints weight = 30969.567| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8548 Z= 0.113 Angle : 0.505 5.936 11572 Z= 0.276 Chirality : 0.038 0.168 1364 Planarity : 0.003 0.033 1408 Dihedral : 4.133 18.592 1112 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.36 (0.27), residues: 1036 helix: 1.45 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 239 HIS 0.002 0.000 HIS C 231 PHE 0.017 0.002 PHE A 368 TYR 0.020 0.001 TYR D 380 ARG 0.004 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 560) hydrogen bonds : angle 4.12107 ( 1578) covalent geometry : bond 0.00259 ( 8548) covalent geometry : angle 0.50529 (11572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6511.59 seconds wall clock time: 114 minutes 46.48 seconds (6886.48 seconds total)