Starting phenix.real_space_refine on Thu Jul 2 19:42:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r10_14226/07_2026/7r10_14226.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Zn 1 6.06 5 S 51 5.16 5 C 6286 2.51 5 N 1620 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9823 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4923 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 32, 'TRANS': 589} Chain breaks: 4 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.89, per 1000 atoms: 0.19 Number of scatterers: 9823 At special positions: 0 Unit cell: (94.864, 108.878, 164.934, 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) Zn 1 29.99 S 51 16.00 O 1865 8.00 N 1620 7.00 C 6286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.07 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 432 " " NAG D 906 " - " ASN D 546 " " NAG D 907 " - " ASN D 103 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 310.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 13 sheets defined 36.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.684A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 173 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.668A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 224' Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 265 through 268 removed outlier: 4.357A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 275 through 281 removed outlier: 3.650A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.677A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.799A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.771A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.940A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.651A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.584A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.887A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.633A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.009A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.661A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.939A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.847A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.815A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143 removed outlier: 5.622A pdb=" N LEU A 244 " --> pdb=" O VAL A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.898A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.534A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1146 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: 1.26 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3104 1.34 - 1.46: 2360 1.46 - 1.58: 4545 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 10083 Sorted by residual: bond pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.24e-02 6.50e+03 9.76e+00 bond pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.11e+00 bond pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.22e-02 6.72e+03 9.01e+00 bond pdb=" N LYS A 529 " pdb=" CA LYS A 529 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.27e+00 bond pdb=" N ASP A 290 " pdb=" CA ASP A 290 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.24e-02 6.50e+03 7.73e+00 ... (remaining 10078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 13281 1.31 - 2.62: 313 2.62 - 3.93: 102 3.93 - 5.24: 9 5.24 - 6.54: 3 Bond angle restraints: 13708 Sorted by residual: angle pdb=" CA CYS A 291 " pdb=" C CYS A 291 " pdb=" O CYS A 291 " ideal model delta sigma weight residual 120.55 116.78 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" CA PHE A 318 " pdb=" C PHE A 318 " pdb=" O PHE A 318 " ideal model delta sigma weight residual 121.55 117.93 3.62 1.06e+00 8.90e-01 1.17e+01 angle pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" O SER A 591 " ideal model delta sigma weight residual 121.55 118.37 3.18 1.06e+00 8.90e-01 9.00e+00 angle pdb=" CA ILE A 332 " pdb=" C ILE A 332 " pdb=" O ILE A 332 " ideal model delta sigma weight residual 121.09 117.94 3.15 1.06e+00 8.90e-01 8.82e+00 angle pdb=" CA ARG A 319 " pdb=" C ARG A 319 " pdb=" O ARG A 319 " ideal model delta sigma weight residual 121.16 117.98 3.18 1.12e+00 7.97e-01 8.06e+00 ... (remaining 13703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5368 17.52 - 35.04: 426 35.04 - 52.57: 75 52.57 - 70.09: 14 70.09 - 87.61: 10 Dihedral angle restraints: 5893 sinusoidal: 2355 harmonic: 3538 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.14 67.14 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 32.40 60.60 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -38.84 -47.16 1 1.00e+01 1.00e-02 3.07e+01 ... (remaining 5890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1147 0.044 - 0.087: 233 0.087 - 0.131: 103 0.131 - 0.174: 9 0.174 - 0.218: 2 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 143 " pdb=" N VAL A 143 " pdb=" C VAL A 143 " pdb=" CB VAL A 143 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 1491 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 35 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLU D 35 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU D 35 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA D 36 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 479 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 289 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C VAL A 289 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 289 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 290 " -0.012 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 176 2.68 - 3.24: 9263 3.24 - 3.79: 14875 3.79 - 4.35: 19540 4.35 - 4.90: 32679 Nonbonded interactions: 76533 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.131 2.230 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.277 3.040 nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 2.292 3.120 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.296 3.040 nonbonded pdb=" O ASN D 53 " pdb=" ND2 ASN D 58 " model vdw 2.334 3.120 ... (remaining 76528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 0.039 10105 Z= 0.187 Angle : 0.524 6.545 13755 Z= 0.293 Chirality : 0.043 0.218 1494 Planarity : 0.003 0.054 1760 Dihedral : 13.186 87.611 3582 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.47 % Allowed : 0.19 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1196 helix: 2.25 (0.28), residues: 388 sheet: 0.80 (0.38), residues: 182 loop : -0.87 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.012 0.001 TYR A 265 PHE 0.010 0.001 PHE D 512 TRP 0.012 0.001 TRP A 353 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.19 (10083) covalent geometry : angle 0.51629 / 0.29 (13708) SS BOND : bond 0.00983 / 0.52 ( 13) SS BOND : angle 1.26653 / 0.70 ( 26) hydrogen bonds : bond 0.12487 / 8.25 ( 416) hydrogen bonds : angle 5.13874 / 3.79 ( 1146) metal coordination : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : bond 0.00365 / 0.21 ( 7) link_NAG-ASN : angle 1.91630 / 1.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 MET cc_start: 0.9308 (ttp) cc_final: 0.9051 (tmm) REVERT: D 270 MET cc_start: 0.8684 (tpp) cc_final: 0.8242 (tpp) REVERT: A 177 MET cc_start: 0.4589 (ttm) cc_final: 0.4306 (mtm) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.0866 time to fit residues: 8.8188 Evaluate side-chains 40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 319 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0870 chunk 117 optimal weight: 7.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.076320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049734 restraints weight = 45348.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049276 restraints weight = 28329.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049436 restraints weight = 24112.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049608 restraints weight = 21960.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049715 restraints weight = 20008.559| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10105 Z= 0.102 Angle : 0.512 10.018 13755 Z= 0.257 Chirality : 0.042 0.175 1494 Planarity : 0.004 0.060 1760 Dihedral : 4.527 57.430 1316 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.84 % Allowed : 4.21 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1196 helix: 2.17 (0.27), residues: 385 sheet: 0.93 (0.39), residues: 161 loop : -0.88 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.011 0.001 TYR A 612 PHE 0.011 0.001 PHE D 230 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10083) covalent geometry : angle 0.50634 / 0.26 (13708) SS BOND : bond 0.00164 / 0.11 ( 13) SS BOND : angle 0.52978 / 0.33 ( 26) hydrogen bonds : bond 0.03717 / 2.42 ( 416) hydrogen bonds : angle 4.48167 / 3.33 ( 1146) metal coordination : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : bond 0.00375 / 0.21 ( 7) link_NAG-ASN : angle 1.99419 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8835 (tpp) cc_final: 0.8563 (tpt) REVERT: D 190 MET cc_start: 0.9383 (ttp) cc_final: 0.8968 (tmm) REVERT: D 270 MET cc_start: 0.8504 (tpp) cc_final: 0.8033 (tpp) REVERT: D 303 ASP cc_start: 0.6879 (p0) cc_final: 0.6656 (p0) REVERT: D 360 MET cc_start: 0.8343 (mtm) cc_final: 0.8097 (ttp) REVERT: A 258 TRP cc_start: 0.5105 (p-90) cc_final: 0.4865 (p-90) REVERT: A 266 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.8325 (m-80) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.0911 time to fit residues: 6.2654 Evaluate side-chains 40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 36 optimal weight: 0.0020 chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 98 GLN A 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.075848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049784 restraints weight = 45433.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049048 restraints weight = 29343.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049222 restraints weight = 25906.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049457 restraints weight = 22788.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049557 restraints weight = 20555.273| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10105 Z= 0.111 Angle : 0.489 7.547 13755 Z= 0.247 Chirality : 0.041 0.171 1494 Planarity : 0.003 0.052 1760 Dihedral : 4.082 54.903 1311 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.66 % Allowed : 6.18 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1196 helix: 2.14 (0.27), residues: 385 sheet: 0.91 (0.39), residues: 159 loop : -0.84 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.015 0.001 TYR A 612 PHE 0.010 0.001 PHE D 230 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10083) covalent geometry : angle 0.48272 / 0.25 (13708) SS BOND : bond 0.00161 / 0.11 ( 13) SS BOND : angle 0.49102 / 0.31 ( 26) hydrogen bonds : bond 0.03518 / 2.31 ( 416) hydrogen bonds : angle 4.38118 / 3.25 ( 1146) metal coordination : bond 0.00082 / 0.04 ( 2) link_NAG-ASN : bond 0.00284 / 0.16 ( 7) link_NAG-ASN : angle 2.11033 / 1.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8895 (tpp) cc_final: 0.8524 (tpt) REVERT: D 190 MET cc_start: 0.9357 (ttp) cc_final: 0.8944 (tmm) REVERT: D 249 MET cc_start: 0.8132 (mmt) cc_final: 0.7922 (mmt) REVERT: D 270 MET cc_start: 0.8526 (tpp) cc_final: 0.8050 (tpp) REVERT: D 303 ASP cc_start: 0.6882 (p0) cc_final: 0.6623 (p0) REVERT: D 360 MET cc_start: 0.8389 (mtm) cc_final: 0.8181 (ttp) REVERT: D 376 MET cc_start: 0.9024 (tpp) cc_final: 0.8804 (mmm) REVERT: A 258 TRP cc_start: 0.5101 (p-90) cc_final: 0.4804 (p-90) REVERT: A 266 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8469 (m-80) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.0791 time to fit residues: 5.0895 Evaluate side-chains 36 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.076456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050372 restraints weight = 45818.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049702 restraints weight = 29840.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049729 restraints weight = 24048.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049952 restraints weight = 22420.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050006 restraints weight = 20820.642| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10105 Z= 0.084 Angle : 0.466 6.789 13755 Z= 0.233 Chirality : 0.040 0.175 1494 Planarity : 0.003 0.035 1760 Dihedral : 3.949 54.433 1311 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.66 % Allowed : 7.58 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1196 helix: 2.21 (0.27), residues: 385 sheet: 0.97 (0.39), residues: 159 loop : -0.80 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.016 0.001 TYR A 612 PHE 0.008 0.001 PHE D 504 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.08 (10083) covalent geometry : angle 0.45867 / 0.23 (13708) SS BOND : bond 0.00120 / 0.08 ( 13) SS BOND : angle 0.39295 / 0.26 ( 26) hydrogen bonds : bond 0.03070 / 2.03 ( 416) hydrogen bonds : angle 4.21228 / 3.12 ( 1146) metal coordination : bond 0.00082 / 0.04 ( 2) link_NAG-ASN : bond 0.00307 / 0.18 ( 7) link_NAG-ASN : angle 2.12426 / 1.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8892 (tpp) cc_final: 0.8526 (tpt) REVERT: D 190 MET cc_start: 0.9379 (ttp) cc_final: 0.9126 (tmm) REVERT: D 270 MET cc_start: 0.8417 (tpp) cc_final: 0.7936 (tpp) REVERT: D 303 ASP cc_start: 0.7051 (p0) cc_final: 0.6796 (p0) REVERT: D 332 MET cc_start: 0.8191 (ppp) cc_final: 0.7855 (tmm) REVERT: D 360 MET cc_start: 0.8371 (mtm) cc_final: 0.8106 (ttp) REVERT: A 177 MET cc_start: 0.2169 (mtp) cc_final: 0.1931 (mtp) REVERT: A 266 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8548 (m-80) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 0.0794 time to fit residues: 5.2366 Evaluate side-chains 35 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 0.0040 chunk 72 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.075861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049407 restraints weight = 45595.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048412 restraints weight = 33232.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048661 restraints weight = 25427.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048969 restraints weight = 22699.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049083 restraints weight = 20641.069| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10105 Z= 0.100 Angle : 0.467 8.719 13755 Z= 0.234 Chirality : 0.040 0.162 1494 Planarity : 0.003 0.034 1760 Dihedral : 3.896 54.072 1311 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.75 % Allowed : 8.33 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1196 helix: 2.23 (0.27), residues: 386 sheet: 1.09 (0.39), residues: 158 loop : -0.78 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.017 0.001 TYR A 612 PHE 0.007 0.001 PHE D 369 TRP 0.013 0.001 TRP A 258 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (10083) covalent geometry : angle 0.46012 / 0.23 (13708) SS BOND : bond 0.00128 / 0.09 ( 13) SS BOND : angle 0.44127 / 0.27 ( 26) hydrogen bonds : bond 0.03150 / 2.09 ( 416) hydrogen bonds : angle 4.16880 / 3.09 ( 1146) metal coordination : bond 0.00054 / 0.03 ( 2) link_NAG-ASN : bond 0.00278 / 0.16 ( 7) link_NAG-ASN : angle 2.09974 / 1.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8928 (tpp) cc_final: 0.8561 (tpt) REVERT: D 190 MET cc_start: 0.9376 (ttp) cc_final: 0.9122 (tmm) REVERT: D 270 MET cc_start: 0.8446 (tpp) cc_final: 0.7978 (tpp) REVERT: D 303 ASP cc_start: 0.7152 (p0) cc_final: 0.6871 (p0) REVERT: D 332 MET cc_start: 0.8077 (ppp) cc_final: 0.7780 (tmm) REVERT: D 360 MET cc_start: 0.8354 (mtm) cc_final: 0.8111 (ttp) REVERT: A 177 MET cc_start: 0.2170 (mtp) cc_final: 0.1926 (mtp) REVERT: A 266 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8459 (m-80) outliers start: 8 outliers final: 4 residues processed: 41 average time/residue: 0.0830 time to fit residues: 5.2574 Evaluate side-chains 37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 105 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.075906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049676 restraints weight = 45555.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049026 restraints weight = 29793.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049170 restraints weight = 23706.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049365 restraints weight = 22835.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049445 restraints weight = 20083.351| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10105 Z= 0.095 Angle : 0.460 8.533 13755 Z= 0.230 Chirality : 0.040 0.163 1494 Planarity : 0.003 0.034 1760 Dihedral : 3.871 53.868 1311 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.84 % Allowed : 8.52 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1196 helix: 2.23 (0.27), residues: 387 sheet: 1.15 (0.40), residues: 154 loop : -0.78 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.012 0.001 TYR A 612 PHE 0.008 0.001 PHE D 369 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (10083) covalent geometry : angle 0.45314 / 0.23 (13708) SS BOND : bond 0.00121 / 0.08 ( 13) SS BOND : angle 0.42228 / 0.27 ( 26) hydrogen bonds : bond 0.03074 / 2.04 ( 416) hydrogen bonds : angle 4.12325 / 3.05 ( 1146) metal coordination : bond 0.00063 / 0.03 ( 2) link_NAG-ASN : bond 0.00300 / 0.17 ( 7) link_NAG-ASN : angle 2.12574 / 1.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.9005 (tpp) cc_final: 0.8638 (tpt) REVERT: D 190 MET cc_start: 0.9376 (ttp) cc_final: 0.9123 (tmm) REVERT: D 248 LEU cc_start: 0.9265 (tp) cc_final: 0.9033 (tp) REVERT: D 270 MET cc_start: 0.8430 (tpp) cc_final: 0.7941 (tpp) REVERT: D 303 ASP cc_start: 0.7209 (p0) cc_final: 0.6898 (p0) REVERT: D 332 MET cc_start: 0.8079 (ppp) cc_final: 0.7840 (tmm) REVERT: D 360 MET cc_start: 0.8410 (mtm) cc_final: 0.8062 (ttp) REVERT: D 375 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8286 (mp0) REVERT: A 177 MET cc_start: 0.1705 (mtp) cc_final: 0.1424 (mtp) REVERT: A 266 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8406 (m-80) outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 0.0856 time to fit residues: 5.7105 Evaluate side-chains 39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 105 optimal weight: 0.1980 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.075614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049511 restraints weight = 45416.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048647 restraints weight = 33336.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048879 restraints weight = 26025.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049029 restraints weight = 24214.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049144 restraints weight = 21644.828| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10105 Z= 0.108 Angle : 0.484 9.425 13755 Z= 0.241 Chirality : 0.040 0.162 1494 Planarity : 0.003 0.034 1760 Dihedral : 3.870 53.805 1311 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.94 % Allowed : 9.18 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1196 helix: 2.21 (0.27), residues: 391 sheet: 1.16 (0.40), residues: 154 loop : -0.79 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.015 0.001 TYR D 50 PHE 0.006 0.001 PHE D 369 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10083) covalent geometry : angle 0.47693 / 0.24 (13708) SS BOND : bond 0.00136 / 0.09 ( 13) SS BOND : angle 0.46252 / 0.29 ( 26) hydrogen bonds : bond 0.03189 / 2.12 ( 416) hydrogen bonds : angle 4.12339 / 3.05 ( 1146) metal coordination : bond 0.00116 / 0.06 ( 2) link_NAG-ASN : bond 0.00277 / 0.16 ( 7) link_NAG-ASN : angle 2.14236 / 1.35 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8993 (tpp) cc_final: 0.8617 (tpt) REVERT: D 190 MET cc_start: 0.9372 (ttp) cc_final: 0.9134 (tmm) REVERT: D 248 LEU cc_start: 0.9257 (tp) cc_final: 0.8993 (tp) REVERT: D 270 MET cc_start: 0.8429 (tpp) cc_final: 0.7977 (tpp) REVERT: D 332 MET cc_start: 0.8051 (ppp) cc_final: 0.7821 (tmm) REVERT: D 360 MET cc_start: 0.8425 (mtm) cc_final: 0.8050 (ttp) REVERT: D 375 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8279 (mp0) REVERT: A 177 MET cc_start: 0.1412 (mtp) cc_final: 0.1170 (mtp) REVERT: A 266 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8327 (m-80) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 0.0740 time to fit residues: 4.9811 Evaluate side-chains 39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.075517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049018 restraints weight = 44915.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048630 restraints weight = 28722.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048678 restraints weight = 24224.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048934 restraints weight = 22495.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049010 restraints weight = 19914.677| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10105 Z= 0.111 Angle : 0.475 9.386 13755 Z= 0.237 Chirality : 0.040 0.162 1494 Planarity : 0.003 0.034 1760 Dihedral : 3.897 53.785 1311 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.56 % Allowed : 9.55 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1196 helix: 2.20 (0.27), residues: 391 sheet: 1.11 (0.40), residues: 155 loop : -0.78 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.013 0.001 TYR A 612 PHE 0.008 0.001 PHE D 369 TRP 0.008 0.001 TRP D 275 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10083) covalent geometry : angle 0.46779 / 0.24 (13708) SS BOND : bond 0.00133 / 0.09 ( 13) SS BOND : angle 0.46320 / 0.29 ( 26) hydrogen bonds : bond 0.03214 / 2.14 ( 416) hydrogen bonds : angle 4.15324 / 3.09 ( 1146) metal coordination : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : bond 0.00277 / 0.16 ( 7) link_NAG-ASN : angle 2.15351 / 1.36 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.9017 (tpp) cc_final: 0.8642 (tpt) REVERT: D 190 MET cc_start: 0.9379 (ttp) cc_final: 0.9152 (tmm) REVERT: D 270 MET cc_start: 0.8464 (tpp) cc_final: 0.7989 (tpp) REVERT: D 332 MET cc_start: 0.8085 (ppp) cc_final: 0.7871 (tmm) REVERT: D 360 MET cc_start: 0.8426 (mtm) cc_final: 0.8078 (ttp) REVERT: D 375 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8269 (mp0) REVERT: A 177 MET cc_start: 0.1713 (mtp) cc_final: 0.1461 (mtp) REVERT: A 266 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8418 (m-80) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.0792 time to fit residues: 4.8665 Evaluate side-chains 37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 0.0050 chunk 110 optimal weight: 0.9980 chunk 19 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.076167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046319 restraints weight = 45163.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047903 restraints weight = 25685.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048941 restraints weight = 18193.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.049465 restraints weight = 14719.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049886 restraints weight = 12908.109| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10105 Z= 0.081 Angle : 0.474 10.459 13755 Z= 0.233 Chirality : 0.040 0.163 1494 Planarity : 0.003 0.033 1760 Dihedral : 3.844 53.318 1311 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.75 % Allowed : 9.55 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1196 helix: 2.21 (0.27), residues: 388 sheet: 1.12 (0.40), residues: 154 loop : -0.75 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.016 0.001 TYR A 612 PHE 0.008 0.001 PHE D 504 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.08 (10083) covalent geometry : angle 0.46672 / 0.23 (13708) SS BOND : bond 0.00121 / 0.07 ( 13) SS BOND : angle 0.37640 / 0.24 ( 26) hydrogen bonds : bond 0.02968 / 1.96 ( 416) hydrogen bonds : angle 4.13868 / 3.11 ( 1146) metal coordination : bond 0.00037 / 0.02 ( 2) link_NAG-ASN : bond 0.00321 / 0.19 ( 7) link_NAG-ASN : angle 2.13800 / 1.36 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8999 (tpp) cc_final: 0.8684 (tpt) REVERT: D 190 MET cc_start: 0.9158 (ttp) cc_final: 0.8941 (tmm) REVERT: D 270 MET cc_start: 0.8416 (tpp) cc_final: 0.7925 (tpp) REVERT: D 360 MET cc_start: 0.8190 (mtm) cc_final: 0.7964 (ttp) REVERT: D 375 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8214 (mp0) REVERT: A 177 MET cc_start: 0.3620 (mtp) cc_final: 0.3171 (mtp) REVERT: A 266 TYR cc_start: 0.9501 (OUTLIER) cc_final: 0.8745 (m-80) outliers start: 8 outliers final: 3 residues processed: 41 average time/residue: 0.0714 time to fit residues: 4.7328 Evaluate side-chains 37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.075430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.045534 restraints weight = 45191.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047017 restraints weight = 25949.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.048019 restraints weight = 18620.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048637 restraints weight = 15134.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048966 restraints weight = 13325.096| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10105 Z= 0.115 Angle : 0.490 10.315 13755 Z= 0.243 Chirality : 0.040 0.168 1494 Planarity : 0.003 0.033 1760 Dihedral : 3.878 53.333 1311 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.56 % Allowed : 9.93 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1196 helix: 2.15 (0.27), residues: 391 sheet: 1.05 (0.40), residues: 155 loop : -0.78 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.015 0.001 TYR A 612 PHE 0.009 0.001 PHE D 369 TRP 0.008 0.001 TRP A 258 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10083) covalent geometry : angle 0.48275 / 0.24 (13708) SS BOND : bond 0.00134 / 0.09 ( 13) SS BOND : angle 0.45636 / 0.29 ( 26) hydrogen bonds : bond 0.03227 / 2.16 ( 416) hydrogen bonds : angle 4.22118 / 3.18 ( 1146) metal coordination : bond 0.00152 / 0.07 ( 2) link_NAG-ASN : bond 0.00263 / 0.15 ( 7) link_NAG-ASN : angle 2.16262 / 1.37 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.9012 (tpp) cc_final: 0.8700 (tpt) REVERT: D 190 MET cc_start: 0.9212 (ttp) cc_final: 0.8974 (tmm) REVERT: D 270 MET cc_start: 0.8469 (tpp) cc_final: 0.7983 (tpp) REVERT: D 375 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8257 (mp0) REVERT: A 177 MET cc_start: 0.3354 (mtp) cc_final: 0.2907 (mtp) REVERT: A 266 TYR cc_start: 0.9507 (OUTLIER) cc_final: 0.8762 (m-80) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.0878 time to fit residues: 5.2793 Evaluate side-chains 37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 HIS D 340 GLN A 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.073767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043595 restraints weight = 46132.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045065 restraints weight = 26869.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046009 restraints weight = 19318.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046462 restraints weight = 15897.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046923 restraints weight = 14077.072| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10105 Z= 0.249 Angle : 0.598 11.195 13755 Z= 0.305 Chirality : 0.042 0.175 1494 Planarity : 0.003 0.032 1760 Dihedral : 4.313 54.488 1311 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.84 % Allowed : 9.74 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1196 helix: 1.68 (0.27), residues: 389 sheet: 0.96 (0.39), residues: 167 loop : -0.81 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 357 TYR 0.028 0.002 TYR D 207 PHE 0.016 0.002 PHE D 452 TRP 0.011 0.001 TRP D 459 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (10083) covalent geometry : angle 0.59014 / 0.30 (13708) SS BOND : bond 0.00253 / 0.16 ( 13) SS BOND : angle 0.92715 / 0.58 ( 26) hydrogen bonds : bond 0.04304 / 2.88 ( 416) hydrogen bonds : angle 4.62726 / 3.46 ( 1146) metal coordination : bond 0.00453 / 0.22 ( 2) link_NAG-ASN : bond 0.00214 / 0.11 ( 7) link_NAG-ASN : angle 2.34779 / 1.46 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.65 seconds wall clock time: 28 minutes 5.82 seconds (1685.82 seconds total)