Starting phenix.real_space_refine on Thu Jul 2 15:51:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zoa_14845/07_2026/7zoa_14845.map" } 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= 0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5708 2.51 5 N 1570 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 9042 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Chain: "B" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 198 Unusual residues: {'BGC': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 1.45, per 1000 atoms: 0.16 Number of scatterers: 9042 At special positions: 0 Unit cell: (72.775, 111.725, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1720 8.00 N 1570 7.00 C 5708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BGC D 1 " - " BGC D 2 " " BGC D 1 " - " BGC D 18 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " " BGC D 5 " - " BGC D 6 " " BGC D 6 " - " BGC D 7 " " BGC D 7 " - " BGC D 8 " " BGC D 8 " - " BGC D 9 " " BGC D 9 " - " BGC D 10 " " BGC D 10 " - " BGC D 11 " " BGC D 11 " - " BGC D 12 " " BGC D 12 " - " BGC D 13 " " BGC D 13 " - " BGC D 14 " " BGC D 14 " - " BGC D 15 " " BGC D 15 " - " BGC D 16 " " BGC D 16 " - " BGC D 17 " " BGC D 17 " - " BGC D 18 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 197.8 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 68.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 3.660A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 47 removed outlier: 3.571A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 101 removed outlier: 3.808A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.701A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 136 removed outlier: 3.830A pdb=" N MET A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 204 removed outlier: 3.747A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 8.465A pdb=" N ARG A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 236 through 268 removed outlier: 6.143A pdb=" N ASN A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 318 removed outlier: 4.738A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.625A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.513A pdb=" N ALA A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.609A pdb=" N LYS A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.567A pdb=" N SER A 535 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.522A pdb=" N GLY A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 47 removed outlier: 3.572A pdb=" N THR B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 55 through 101 removed outlier: 3.809A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.701A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 136 removed outlier: 3.830A pdb=" N MET B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 204 removed outlier: 3.747A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 8.464A pdb=" N ARG B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 244 through 268 removed outlier: 3.852A pdb=" N LYS B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 318 removed outlier: 4.739A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 424 through 431 Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.625A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.513A pdb=" N ALA B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 503 through 517 removed outlier: 3.608A pdb=" N LYS B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.566A pdb=" N SER B 535 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.521A pdb=" N GLY B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 6.137A pdb=" N PHE A 337 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N MET A 393 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN A 339 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A 391 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 389 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 494 removed outlier: 7.165A pdb=" N LEU A 493 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 367 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 355 through 358 removed outlier: 6.137A pdb=" N PHE B 337 " --> pdb=" O MET B 393 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET B 393 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN B 339 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG B 391 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 389 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 492 through 494 removed outlier: 7.165A pdb=" N LEU B 493 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE B 526 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 367 " --> pdb=" O LEU B 540 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1728 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: 1.03 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1466 1.30 - 1.43: 2382 1.43 - 1.56: 5256 1.56 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 9190 Sorted by residual: bond pdb=" C GLN A 184 " pdb=" O GLN A 184 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.72e+01 bond pdb=" C2 BGC D 9 " pdb=" O2 BGC D 9 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C2 BGC D 10 " pdb=" O2 BGC D 10 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" C2 BGC D 5 " pdb=" O2 BGC D 5 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" C2 BGC D 6 " pdb=" O2 BGC D 6 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.98e+00 ... (remaining 9185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 12097 2.08 - 4.16: 264 4.16 - 6.25: 60 6.25 - 8.33: 18 8.33 - 10.41: 9 Bond angle restraints: 12448 Sorted by residual: angle pdb=" N SER B 243 " pdb=" CA SER B 243 " pdb=" CB SER B 243 " ideal model delta sigma weight residual 110.56 120.60 -10.04 1.38e+00 5.25e-01 5.29e+01 angle pdb=" C LEU B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta sigma weight residual 120.29 111.86 8.43 1.42e+00 4.96e-01 3.53e+01 angle pdb=" CA ARG B 408 " pdb=" CB ARG B 408 " pdb=" CG ARG B 408 " ideal model delta sigma weight residual 114.10 103.69 10.41 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CA ARG A 408 " pdb=" CB ARG A 408 " pdb=" CG ARG A 408 " ideal model delta sigma weight residual 114.10 103.70 10.40 2.00e+00 2.50e-01 2.71e+01 angle pdb=" C ALA B 242 " pdb=" N SER B 243 " pdb=" CA SER B 243 " ideal model delta sigma weight residual 122.65 114.37 8.28 1.66e+00 3.63e-01 2.49e+01 ... (remaining 12443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4832 17.35 - 34.70: 444 34.70 - 52.04: 90 52.04 - 69.39: 14 69.39 - 86.74: 8 Dihedral angle restraints: 5388 sinusoidal: 2098 harmonic: 3290 Sorted by residual: dihedral pdb=" N SER B 243 " pdb=" C SER B 243 " pdb=" CA SER B 243 " pdb=" CB SER B 243 " ideal model delta harmonic sigma weight residual 122.80 148.62 -25.82 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" C SER B 243 " pdb=" N SER B 243 " pdb=" CA SER B 243 " pdb=" CB SER B 243 " ideal model delta harmonic sigma weight residual -122.60 -147.84 25.24 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" CA HIS A 438 " pdb=" C HIS A 438 " pdb=" N GLU A 439 " pdb=" CA GLU A 439 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 1516 0.302 - 0.605: 5 0.605 - 0.907: 1 0.907 - 1.210: 1 1.210 - 1.512: 1 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C1 BGC D 7 " pdb=" O2 BGC D 6 " pdb=" C2 BGC D 7 " pdb=" O5 BGC D 7 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.72e+03 chirality pdb=" C1 BGC D 3 " pdb=" O2 BGC D 2 " pdb=" C2 BGC D 3 " pdb=" O5 BGC D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.68e+03 chirality pdb=" C1 BGC D 1 " pdb=" C2 BGC D 1 " pdb=" O5 BGC D 1 " pdb=" O2 BGC D 18 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.70e+02 ... (remaining 1521 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 241 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C LEU B 241 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU B 241 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 242 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 187 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C VAL A 187 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 187 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 188 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " -0.134 9.50e-02 1.11e+02 6.06e-02 3.32e+00 pdb=" NE ARG A 408 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " -0.011 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 399 2.72 - 3.27: 9600 3.27 - 3.81: 14913 3.81 - 4.36: 15850 4.36 - 4.90: 27760 Nonbonded interactions: 68522 Sorted by model distance: nonbonded pdb=" ND2 ASN A 422 " pdb=" OE2 GLU B 196 " model vdw 2.176 3.120 nonbonded pdb=" NE2 GLN A 478 " pdb=" O ALA A 498 " model vdw 2.181 3.120 nonbonded pdb=" NE2 GLN B 478 " pdb=" O ALA B 498 " model vdw 2.181 3.120 nonbonded pdb=" O VAL A 431 " pdb=" NH1 ARG B 213 " model vdw 2.194 3.120 nonbonded pdb=" O ARG A 433 " pdb=" NH2 ARG B 213 " model vdw 2.209 3.120 ... (remaining 68517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.980 Find NCS groups from input model: 0.090 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.004 0.065 9208 Z= 0.230 Angle : 0.923 19.191 12502 Z= 0.446 Chirality : 0.073 1.512 1524 Planarity : 0.004 0.061 1560 Dihedral : 13.969 86.738 3256 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.26 % Favored : 96.39 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.09 % 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: 0.93 (0.26), residues: 1136 helix: 1.98 (0.20), residues: 708 sheet: 0.38 (0.66), residues: 78 loop : -2.35 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 408 TYR 0.017 0.001 TYR A 96 PHE 0.018 0.001 PHE B 421 TRP 0.015 0.002 TRP B 62 HIS 0.006 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.22 ( 9190) covalent geometry : angle 0.81078 / 0.42 (12448) hydrogen bonds : bond 0.12502 / 7.88 ( 588) hydrogen bonds : angle 4.67881 / 3.39 ( 1728) link_BETA1-2 : bond 0.02483 / 1.69 ( 18) link_BETA1-2 : angle 6.77600 / 4.10 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.7015 (ptpp) cc_final: 0.6551 (mmtt) REVERT: A 61 MET cc_start: 0.7945 (ppp) cc_final: 0.7279 (ppp) REVERT: A 201 THR cc_start: 0.8335 (t) cc_final: 0.7995 (t) REVERT: B 12 GLN cc_start: 0.8581 (tt0) cc_final: 0.8381 (tp40) REVERT: B 171 MET cc_start: 0.8132 (mtp) cc_final: 0.7474 (ttp) REVERT: B 248 MET cc_start: 0.8838 (mmm) cc_final: 0.8602 (mmm) REVERT: B 298 GLN cc_start: 0.8743 (tt0) cc_final: 0.8496 (mm-40) REVERT: B 394 ILE cc_start: 0.7766 (tp) cc_final: 0.7361 (mm) REVERT: B 546 HIS cc_start: 0.7192 (m-70) cc_final: 0.6914 (m-70) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0844 time to fit residues: 28.9593 Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 108 GLN B 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.141687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101452 restraints weight = 22120.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104335 restraints weight = 13745.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106270 restraints weight = 9918.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.107595 restraints weight = 7903.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108513 restraints weight = 6770.451| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9208 Z= 0.289 Angle : 0.897 10.810 12502 Z= 0.439 Chirality : 0.048 0.234 1524 Planarity : 0.006 0.100 1560 Dihedral : 4.158 19.822 1238 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.87 % Favored : 95.77 % Rotamer: Outliers : 2.67 % Allowed : 16.84 % Favored : 80.49 % 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: 0.18 (0.25), residues: 1136 helix: 1.13 (0.19), residues: 728 sheet: 0.43 (0.63), residues: 78 loop : -2.29 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 408 TYR 0.016 0.002 TYR B 461 PHE 0.026 0.003 PHE B 133 TRP 0.024 0.002 TRP A 130 HIS 0.012 0.002 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.29 ( 9190) covalent geometry : angle 0.87791 / 0.44 (12448) hydrogen bonds : bond 0.05575 / 3.79 ( 588) hydrogen bonds : angle 4.47049 / 3.36 ( 1728) link_BETA1-2 : bond 0.01220 / 0.82 ( 18) link_BETA1-2 : angle 2.95073 / 1.94 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8289 (ppp) cc_final: 0.7798 (ppp) REVERT: A 71 MET cc_start: 0.8231 (mmm) cc_final: 0.7801 (tpt) REVERT: A 160 LEU cc_start: 0.8554 (pp) cc_final: 0.8343 (mp) REVERT: A 201 THR cc_start: 0.9393 (t) cc_final: 0.8725 (t) REVERT: B 68 PHE cc_start: 0.8726 (t80) cc_final: 0.8233 (t80) REVERT: B 130 TRP cc_start: 0.9222 (m-10) cc_final: 0.8726 (m-90) REVERT: B 152 MET cc_start: 0.8125 (ttp) cc_final: 0.7531 (tpt) REVERT: B 156 MET cc_start: 0.6220 (pmm) cc_final: 0.5653 (pmm) REVERT: B 171 MET cc_start: 0.8439 (mtp) cc_final: 0.8034 (ttp) REVERT: B 223 ASP cc_start: 0.8401 (m-30) cc_final: 0.8103 (t0) REVERT: B 477 ARG cc_start: 0.8927 (ptp90) cc_final: 0.8656 (ptp-170) REVERT: B 496 ASP cc_start: 0.8396 (p0) cc_final: 0.8056 (p0) REVERT: B 542 MET cc_start: 0.5609 (tmm) cc_final: 0.5231 (tmm) REVERT: B 543 ASP cc_start: 0.7986 (p0) cc_final: 0.7395 (p0) outliers start: 25 outliers final: 18 residues processed: 190 average time/residue: 0.0804 time to fit residues: 22.4088 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN B 438 HIS B 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.149485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110458 restraints weight = 21872.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113622 restraints weight = 12781.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115810 restraints weight = 8844.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.117228 restraints weight = 6833.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117842 restraints weight = 5728.051| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9208 Z= 0.151 Angle : 0.720 9.972 12502 Z= 0.334 Chirality : 0.043 0.245 1524 Planarity : 0.004 0.064 1560 Dihedral : 3.850 19.136 1238 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.96 % Favored : 95.69 % Rotamer: Outliers : 3.52 % Allowed : 20.58 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1136 helix: 1.58 (0.19), residues: 734 sheet: 0.33 (0.60), residues: 78 loop : -2.17 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 408 TYR 0.022 0.002 TYR B 342 PHE 0.018 0.002 PHE A 233 TRP 0.013 0.001 TRP A 238 HIS 0.012 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 9190) covalent geometry : angle 0.69918 / 0.33 (12448) hydrogen bonds : bond 0.04850 / 3.27 ( 588) hydrogen bonds : angle 4.05652 / 3.03 ( 1728) link_BETA1-2 : bond 0.01041 / 0.70 ( 18) link_BETA1-2 : angle 2.68096 / 1.72 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9125 (mt) cc_final: 0.8511 (mt) REVERT: A 61 MET cc_start: 0.8263 (ppp) cc_final: 0.7860 (ppp) REVERT: A 71 MET cc_start: 0.8256 (mmm) cc_final: 0.7891 (tpt) REVERT: A 155 ASP cc_start: 0.7108 (t70) cc_final: 0.5528 (m-30) REVERT: A 248 MET cc_start: 0.8138 (mtp) cc_final: 0.7816 (mtp) REVERT: A 314 ASP cc_start: 0.8101 (m-30) cc_final: 0.7568 (t0) REVERT: B 61 MET cc_start: 0.7935 (ppp) cc_final: 0.7618 (ppp) REVERT: B 71 MET cc_start: 0.7749 (mmp) cc_final: 0.6979 (mtt) REVERT: B 130 TRP cc_start: 0.9113 (m-10) cc_final: 0.8554 (m-90) REVERT: B 171 MET cc_start: 0.8428 (mtp) cc_final: 0.7989 (ttp) REVERT: B 223 ASP cc_start: 0.8327 (m-30) cc_final: 0.8027 (t0) REVERT: B 342 TYR cc_start: 0.7712 (t80) cc_final: 0.7316 (t80) REVERT: B 427 ASP cc_start: 0.8112 (m-30) cc_final: 0.7743 (m-30) outliers start: 33 outliers final: 20 residues processed: 182 average time/residue: 0.0759 time to fit residues: 20.6512 Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 112 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 104 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.151765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.112588 restraints weight = 22444.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115759 restraints weight = 13165.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117945 restraints weight = 9120.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.119475 restraints weight = 7051.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.120264 restraints weight = 5911.973| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9208 Z= 0.135 Angle : 0.690 10.047 12502 Z= 0.315 Chirality : 0.043 0.235 1524 Planarity : 0.003 0.029 1560 Dihedral : 3.715 18.034 1238 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.23 % Favored : 95.51 % Rotamer: Outliers : 3.94 % Allowed : 21.11 % Favored : 74.95 % 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: 1.02 (0.26), residues: 1136 helix: 1.79 (0.19), residues: 730 sheet: 0.38 (0.60), residues: 80 loop : -1.92 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 408 TYR 0.012 0.001 TYR B 342 PHE 0.013 0.001 PHE A 233 TRP 0.010 0.001 TRP A 238 HIS 0.006 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9190) covalent geometry : angle 0.67327 / 0.31 (12448) hydrogen bonds : bond 0.04372 / 2.96 ( 588) hydrogen bonds : angle 3.89071 / 2.90 ( 1728) link_BETA1-2 : bond 0.00911 / 0.63 ( 18) link_BETA1-2 : angle 2.38515 / 1.55 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8167 (ppp) cc_final: 0.7815 (ppp) REVERT: A 71 MET cc_start: 0.8205 (mmm) cc_final: 0.7709 (tpt) REVERT: A 102 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5565 (ttt) REVERT: A 155 ASP cc_start: 0.6842 (t70) cc_final: 0.5402 (m-30) REVERT: A 160 LEU cc_start: 0.8703 (mp) cc_final: 0.8480 (mm) REVERT: A 248 MET cc_start: 0.8244 (mtp) cc_final: 0.8038 (mtp) REVERT: A 314 ASP cc_start: 0.8018 (m-30) cc_final: 0.7464 (t0) REVERT: B 24 MET cc_start: 0.8184 (tpp) cc_final: 0.7897 (tpp) REVERT: B 68 PHE cc_start: 0.8562 (t80) cc_final: 0.8046 (t80) REVERT: B 71 MET cc_start: 0.7673 (mmp) cc_final: 0.6842 (mtt) REVERT: B 130 TRP cc_start: 0.9113 (m-10) cc_final: 0.8629 (m-90) REVERT: B 152 MET cc_start: 0.8247 (ttp) cc_final: 0.7248 (tpp) REVERT: B 171 MET cc_start: 0.8406 (mtp) cc_final: 0.7876 (tmm) REVERT: B 223 ASP cc_start: 0.8327 (m-30) cc_final: 0.8037 (t0) REVERT: B 311 GLN cc_start: 0.8567 (tp40) cc_final: 0.8335 (tm-30) REVERT: B 342 TYR cc_start: 0.7767 (t80) cc_final: 0.7335 (t80) outliers start: 37 outliers final: 24 residues processed: 172 average time/residue: 0.0714 time to fit residues: 18.7712 Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 0.0010 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108737 restraints weight = 22168.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.111873 restraints weight = 13122.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.113955 restraints weight = 9136.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115411 restraints weight = 7115.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116254 restraints weight = 6003.314| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9208 Z= 0.154 Angle : 0.703 10.323 12502 Z= 0.323 Chirality : 0.042 0.230 1524 Planarity : 0.003 0.039 1560 Dihedral : 3.723 18.864 1238 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.77 % Rotamer: Outliers : 4.16 % Allowed : 22.49 % Favored : 73.35 % 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: 1.08 (0.26), residues: 1136 helix: 1.79 (0.19), residues: 736 sheet: 0.40 (0.60), residues: 80 loop : -1.81 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 408 TYR 0.010 0.001 TYR B 96 PHE 0.012 0.001 PHE A 233 TRP 0.010 0.001 TRP A 238 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9190) covalent geometry : angle 0.68999 / 0.32 (12448) hydrogen bonds : bond 0.04469 / 3.01 ( 588) hydrogen bonds : angle 3.82839 / 2.85 ( 1728) link_BETA1-2 : bond 0.00861 / 0.60 ( 18) link_BETA1-2 : angle 2.16517 / 1.41 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8646 (tpp) cc_final: 0.8396 (tpp) REVERT: A 102 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5668 (ttt) REVERT: A 248 MET cc_start: 0.8350 (mtp) cc_final: 0.8083 (mtp) REVERT: A 314 ASP cc_start: 0.8176 (m-30) cc_final: 0.7710 (t0) REVERT: A 542 MET cc_start: 0.3201 (tpt) cc_final: 0.2717 (tpt) REVERT: B 24 MET cc_start: 0.8310 (tpp) cc_final: 0.8055 (tpp) REVERT: B 130 TRP cc_start: 0.9217 (m-10) cc_final: 0.8983 (m-10) REVERT: B 152 MET cc_start: 0.8324 (ttp) cc_final: 0.7283 (tpp) REVERT: B 171 MET cc_start: 0.8479 (mtp) cc_final: 0.8019 (ttp) REVERT: B 223 ASP cc_start: 0.8404 (m-30) cc_final: 0.8089 (t0) REVERT: B 311 GLN cc_start: 0.8609 (tp40) cc_final: 0.8374 (tm-30) REVERT: B 342 TYR cc_start: 0.7925 (t80) cc_final: 0.7366 (t80) outliers start: 39 outliers final: 29 residues processed: 174 average time/residue: 0.0726 time to fit residues: 19.2582 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 0.0870 chunk 92 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110228 restraints weight = 22045.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113413 restraints weight = 12939.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115604 restraints weight = 9012.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117038 restraints weight = 7006.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117920 restraints weight = 5889.456| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9208 Z= 0.130 Angle : 0.689 10.700 12502 Z= 0.314 Chirality : 0.042 0.220 1524 Planarity : 0.003 0.022 1560 Dihedral : 3.669 18.460 1238 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.58 % Favored : 95.16 % Rotamer: Outliers : 3.84 % Allowed : 23.45 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.24 (0.26), residues: 1136 helix: 1.92 (0.19), residues: 736 sheet: 0.50 (0.61), residues: 80 loop : -1.77 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.008 0.001 TYR A 96 PHE 0.009 0.001 PHE A 233 TRP 0.009 0.001 TRP A 238 HIS 0.003 0.000 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9190) covalent geometry : angle 0.67734 / 0.31 (12448) hydrogen bonds : bond 0.04238 / 2.85 ( 588) hydrogen bonds : angle 3.70976 / 2.75 ( 1728) link_BETA1-2 : bond 0.00826 / 0.57 ( 18) link_BETA1-2 : angle 2.05875 / 1.35 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8595 (tpp) cc_final: 0.8336 (tpp) REVERT: A 102 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5607 (ttt) REVERT: A 248 MET cc_start: 0.8289 (mtp) cc_final: 0.8037 (mtp) REVERT: A 314 ASP cc_start: 0.8138 (m-30) cc_final: 0.7627 (t0) REVERT: B 11 MET cc_start: 0.8517 (tpp) cc_final: 0.8273 (mmp) REVERT: B 24 MET cc_start: 0.8154 (tpp) cc_final: 0.7916 (tpp) REVERT: B 71 MET cc_start: 0.7832 (mmp) cc_final: 0.7050 (mtt) REVERT: B 130 TRP cc_start: 0.9194 (m-10) cc_final: 0.8960 (m-10) REVERT: B 152 MET cc_start: 0.8253 (ttp) cc_final: 0.7405 (tpt) REVERT: B 156 MET cc_start: 0.6361 (pmm) cc_final: 0.5784 (pmm) REVERT: B 171 MET cc_start: 0.8444 (mtp) cc_final: 0.7888 (tmm) REVERT: B 223 ASP cc_start: 0.8347 (m-30) cc_final: 0.8075 (t0) REVERT: B 311 GLN cc_start: 0.8561 (tp40) cc_final: 0.8337 (tm-30) REVERT: B 342 TYR cc_start: 0.7844 (t80) cc_final: 0.7311 (t80) REVERT: B 393 MET cc_start: 0.7870 (mmm) cc_final: 0.6675 (tmm) outliers start: 36 outliers final: 24 residues processed: 170 average time/residue: 0.0708 time to fit residues: 18.5797 Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 0.0040 chunk 73 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.149590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111220 restraints weight = 22457.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.114498 restraints weight = 13116.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.116689 restraints weight = 9010.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118168 restraints weight = 6932.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.119039 restraints weight = 5811.267| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9208 Z= 0.129 Angle : 0.704 11.078 12502 Z= 0.318 Chirality : 0.042 0.221 1524 Planarity : 0.003 0.026 1560 Dihedral : 3.640 17.786 1238 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 3.62 % Allowed : 24.09 % Favored : 72.28 % 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: 1.22 (0.26), residues: 1136 helix: 1.87 (0.19), residues: 742 sheet: 0.41 (0.60), residues: 80 loop : -1.74 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 408 TYR 0.007 0.001 TYR A 96 PHE 0.008 0.001 PHE A 233 TRP 0.008 0.001 TRP A 238 HIS 0.004 0.000 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 9190) covalent geometry : angle 0.69369 / 0.32 (12448) hydrogen bonds : bond 0.04136 / 2.79 ( 588) hydrogen bonds : angle 3.68340 / 2.73 ( 1728) link_BETA1-2 : bond 0.00778 / 0.54 ( 18) link_BETA1-2 : angle 1.99489 / 1.30 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8583 (tpp) cc_final: 0.8316 (tpp) REVERT: A 102 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.5645 (ttt) REVERT: A 248 MET cc_start: 0.8266 (mtp) cc_final: 0.8037 (mtp) REVERT: A 314 ASP cc_start: 0.8063 (m-30) cc_final: 0.7561 (t0) REVERT: A 542 MET cc_start: 0.3111 (tpt) cc_final: 0.2553 (tpt) REVERT: B 11 MET cc_start: 0.8508 (tpp) cc_final: 0.8293 (mmp) REVERT: B 24 MET cc_start: 0.8186 (tpp) cc_final: 0.7945 (tpp) REVERT: B 71 MET cc_start: 0.7824 (mmp) cc_final: 0.7009 (mtt) REVERT: B 130 TRP cc_start: 0.9185 (m-10) cc_final: 0.8947 (m-10) REVERT: B 152 MET cc_start: 0.8289 (ttp) cc_final: 0.7396 (tpt) REVERT: B 156 MET cc_start: 0.6366 (pmm) cc_final: 0.5772 (pmm) REVERT: B 171 MET cc_start: 0.8455 (mtp) cc_final: 0.7971 (ttp) REVERT: B 223 ASP cc_start: 0.8363 (m-30) cc_final: 0.8072 (t0) REVERT: B 311 GLN cc_start: 0.8574 (tp40) cc_final: 0.8358 (tm-30) REVERT: B 342 TYR cc_start: 0.7808 (t80) cc_final: 0.7281 (t80) REVERT: B 393 MET cc_start: 0.7874 (mmm) cc_final: 0.6733 (tmm) REVERT: B 427 ASP cc_start: 0.7993 (m-30) cc_final: 0.7702 (m-30) outliers start: 34 outliers final: 27 residues processed: 172 average time/residue: 0.0682 time to fit residues: 18.3113 Evaluate side-chains 173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS A 478 GLN B 85 HIS B 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.137239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097668 restraints weight = 22294.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.100554 restraints weight = 13393.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102498 restraints weight = 9468.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103818 restraints weight = 7502.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104627 restraints weight = 6387.951| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9208 Z= 0.198 Angle : 0.781 13.157 12502 Z= 0.366 Chirality : 0.045 0.229 1524 Planarity : 0.004 0.030 1560 Dihedral : 3.873 21.208 1238 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 4.26 % Allowed : 23.88 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.26), residues: 1136 helix: 1.47 (0.19), residues: 764 sheet: 0.50 (0.60), residues: 80 loop : -1.54 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.012 0.002 TYR A 169 PHE 0.012 0.001 PHE A 421 TRP 0.014 0.002 TRP A 130 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 9190) covalent geometry : angle 0.77189 / 0.36 (12448) hydrogen bonds : bond 0.04938 / 3.37 ( 588) hydrogen bonds : angle 4.00349 / 2.99 ( 1728) link_BETA1-2 : bond 0.00839 / 0.59 ( 18) link_BETA1-2 : angle 1.92466 / 1.26 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.5753 (ttt) REVERT: A 156 MET cc_start: 0.6432 (pmm) cc_final: 0.5541 (ptt) REVERT: A 248 MET cc_start: 0.8289 (mtp) cc_final: 0.8042 (mtp) REVERT: A 314 ASP cc_start: 0.8296 (m-30) cc_final: 0.7882 (t0) REVERT: B 152 MET cc_start: 0.8273 (ttp) cc_final: 0.7951 (tpp) REVERT: B 171 MET cc_start: 0.8492 (mtp) cc_final: 0.8073 (ttp) REVERT: B 177 MET cc_start: 0.8063 (mtm) cc_final: 0.7385 (ttp) REVERT: B 297 ASN cc_start: 0.8652 (t0) cc_final: 0.8442 (t0) REVERT: B 311 GLN cc_start: 0.8549 (tp40) cc_final: 0.8188 (tm-30) REVERT: B 342 TYR cc_start: 0.7812 (t80) cc_final: 0.7187 (t80) REVERT: B 393 MET cc_start: 0.7832 (mmm) cc_final: 0.6847 (tmm) outliers start: 40 outliers final: 31 residues processed: 178 average time/residue: 0.0677 time to fit residues: 18.7465 Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 30.0000 chunk 88 optimal weight: 0.5980 chunk 110 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.0010 chunk 113 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.139603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100661 restraints weight = 22642.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103662 restraints weight = 13509.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105714 restraints weight = 9482.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107160 restraints weight = 7437.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.108085 restraints weight = 6291.776| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9208 Z= 0.144 Angle : 0.755 13.933 12502 Z= 0.346 Chirality : 0.044 0.287 1524 Planarity : 0.003 0.023 1560 Dihedral : 3.806 20.499 1238 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 3.41 % Allowed : 24.63 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.14 (0.26), residues: 1136 helix: 1.68 (0.19), residues: 752 sheet: 0.45 (0.60), residues: 80 loop : -1.55 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 408 TYR 0.011 0.001 TYR A 342 PHE 0.016 0.001 PHE B 68 TRP 0.010 0.001 TRP A 62 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9190) covalent geometry : angle 0.74676 / 0.34 (12448) hydrogen bonds : bond 0.04610 / 3.10 ( 588) hydrogen bonds : angle 3.82693 / 2.85 ( 1728) link_BETA1-2 : bond 0.00789 / 0.55 ( 18) link_BETA1-2 : angle 1.86820 / 1.22 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7451 (tpt) REVERT: A 102 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.5646 (ttt) REVERT: A 156 MET cc_start: 0.6248 (pmm) cc_final: 0.5408 (ptt) REVERT: A 248 MET cc_start: 0.8329 (mtp) cc_final: 0.8066 (mtp) REVERT: A 314 ASP cc_start: 0.8326 (m-30) cc_final: 0.7832 (t0) REVERT: B 130 TRP cc_start: 0.9265 (m-10) cc_final: 0.8953 (m-10) REVERT: B 152 MET cc_start: 0.8348 (ttp) cc_final: 0.7486 (tpt) REVERT: B 171 MET cc_start: 0.8462 (mtp) cc_final: 0.7935 (tmm) REVERT: B 177 MET cc_start: 0.7989 (mtm) cc_final: 0.7366 (ttp) REVERT: B 285 MET cc_start: 0.8091 (ppp) cc_final: 0.7250 (tmm) REVERT: B 297 ASN cc_start: 0.8688 (t0) cc_final: 0.8452 (t0) REVERT: B 311 GLN cc_start: 0.8551 (tp40) cc_final: 0.8240 (tm-30) REVERT: B 342 TYR cc_start: 0.7750 (t80) cc_final: 0.7191 (t80) REVERT: B 393 MET cc_start: 0.7892 (mmm) cc_final: 0.6864 (tmm) outliers start: 32 outliers final: 25 residues processed: 166 average time/residue: 0.0697 time to fit residues: 17.7975 Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.146315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107417 restraints weight = 22306.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110568 restraints weight = 12978.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112713 restraints weight = 9001.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114038 restraints weight = 6991.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115085 restraints weight = 5926.052| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9208 Z= 0.137 Angle : 0.752 15.115 12502 Z= 0.341 Chirality : 0.043 0.311 1524 Planarity : 0.003 0.023 1560 Dihedral : 3.734 19.046 1238 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % Rotamer: Outliers : 3.09 % Allowed : 25.05 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.26), residues: 1136 helix: 1.66 (0.19), residues: 764 sheet: 0.52 (0.61), residues: 80 loop : -1.50 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 408 TYR 0.009 0.001 TYR A 342 PHE 0.009 0.001 PHE A 541 TRP 0.008 0.001 TRP A 62 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 9190) covalent geometry : angle 0.74406 / 0.34 (12448) hydrogen bonds : bond 0.04297 / 2.87 ( 588) hydrogen bonds : angle 3.77187 / 2.81 ( 1728) link_BETA1-2 : bond 0.00743 / 0.52 ( 18) link_BETA1-2 : angle 1.78560 / 1.17 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8158 (ppp) cc_final: 0.7894 (tpt) REVERT: A 102 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.5511 (ttt) REVERT: A 156 MET cc_start: 0.6243 (pmm) cc_final: 0.5328 (ptt) REVERT: A 248 MET cc_start: 0.8313 (mtp) cc_final: 0.8082 (mtp) REVERT: A 314 ASP cc_start: 0.8320 (m-30) cc_final: 0.7771 (t0) REVERT: B 68 PHE cc_start: 0.8622 (t80) cc_final: 0.8172 (t80) REVERT: B 130 TRP cc_start: 0.9260 (m-10) cc_final: 0.9009 (m-10) REVERT: B 152 MET cc_start: 0.8328 (ttp) cc_final: 0.8079 (tpp) REVERT: B 171 MET cc_start: 0.8582 (mtp) cc_final: 0.7937 (tmm) REVERT: B 177 MET cc_start: 0.7995 (mtm) cc_final: 0.7287 (ttp) REVERT: B 285 MET cc_start: 0.8055 (ppp) cc_final: 0.7218 (tmm) REVERT: B 297 ASN cc_start: 0.8680 (t0) cc_final: 0.8432 (m-40) REVERT: B 311 GLN cc_start: 0.8557 (tp40) cc_final: 0.8235 (tm-30) REVERT: B 342 TYR cc_start: 0.7669 (t80) cc_final: 0.7075 (t80) REVERT: B 393 MET cc_start: 0.7839 (mmm) cc_final: 0.6756 (tmm) outliers start: 29 outliers final: 26 residues processed: 165 average time/residue: 0.0677 time to fit residues: 17.3009 Evaluate side-chains 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 0.0570 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.145801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107044 restraints weight = 22377.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110182 restraints weight = 13097.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112317 restraints weight = 9104.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113724 restraints weight = 7093.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.114597 restraints weight = 5975.928| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9208 Z= 0.138 Angle : 0.739 14.668 12502 Z= 0.337 Chirality : 0.043 0.313 1524 Planarity : 0.003 0.023 1560 Dihedral : 3.714 19.147 1238 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.75 % Favored : 94.98 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.64 % 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: 1.24 (0.26), residues: 1136 helix: 1.71 (0.19), residues: 764 sheet: 0.52 (0.61), residues: 80 loop : -1.50 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.021 0.001 TYR B 96 PHE 0.009 0.001 PHE B 195 TRP 0.008 0.001 TRP A 62 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9190) covalent geometry : angle 0.73158 / 0.34 (12448) hydrogen bonds : bond 0.04276 / 2.85 ( 588) hydrogen bonds : angle 3.76607 / 2.81 ( 1728) link_BETA1-2 : bond 0.00731 / 0.52 ( 18) link_BETA1-2 : angle 1.74285 / 1.14 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1536.84 seconds wall clock time: 27 minutes 26.92 seconds (1646.92 seconds total)