Starting phenix.real_space_refine on Tue Mar 3 23:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zoa_14845/03_2026/7zoa_14845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zoa_14845/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2026/7zoa_14845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2026/7zoa_14845.map" model { file = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2026/7zoa_14845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2026/7zoa_14845.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-5986/lib/python3.9/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 dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 2.12, per 1000 atoms: 0.23 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: 0.88 Conformation dependent library (CDL) restraints added in 351.7 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: 0.25 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: 1.38 Time building geometry restraints manager: 1.17 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 - 24.70: 5201 24.70 - 49.41: 337 49.41 - 74.11: 69 74.11 - 98.81: 68 98.81 - 123.52: 55 Dihedral angle restraints: 5730 sinusoidal: 2440 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=" C3 BGC D 18 " pdb=" C1 BGC D 18 " pdb=" C2 BGC D 18 " pdb=" O5 BGC D 18 " ideal model delta sinusoidal sigma weight residual -58.08 65.44 -123.52 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 5727 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: 1.370 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 24.010 123.517 3598 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 covalent geometry : bond 0.00427 ( 9190) covalent geometry : angle 0.81078 (12448) hydrogen bonds : bond 0.12502 ( 588) hydrogen bonds : angle 4.67881 ( 1728) link_BETA1-2 : bond 0.02483 ( 18) link_BETA1-2 : angle 6.77600 ( 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 : 0.349 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: 0.0828 time to fit residues: 28.2560 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 : 0.256 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4065 r_free = 0.4065 target = 0.141267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101713 restraints weight = 22046.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104548 restraints weight = 13667.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106470 restraints weight = 9830.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107800 restraints weight = 7819.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108571 restraints weight = 6668.043| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9208 Z= 0.299 Angle : 0.972 11.428 12502 Z= 0.458 Chirality : 0.051 0.384 1524 Planarity : 0.006 0.106 1560 Dihedral : 20.699 106.276 1580 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.87 % Favored : 95.69 % Rotamer: Outliers : 2.99 % Allowed : 16.84 % Favored : 80.17 % 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: 0.14 (0.25), residues: 1136 helix: 1.10 (0.19), residues: 728 sheet: 0.41 (0.63), residues: 78 loop : -2.30 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 408 TYR 0.030 0.003 TYR A 461 PHE 0.029 0.003 PHE B 133 TRP 0.023 0.003 TRP A 130 HIS 0.012 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00668 ( 9190) covalent geometry : angle 0.93678 (12448) hydrogen bonds : bond 0.05599 ( 588) hydrogen bonds : angle 4.50424 ( 1728) link_BETA1-2 : bond 0.01232 ( 18) link_BETA1-2 : angle 4.04214 ( 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 199 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8291 (ppp) cc_final: 0.7808 (ppp) REVERT: A 71 MET cc_start: 0.8227 (mmm) cc_final: 0.7850 (tpt) REVERT: A 160 LEU cc_start: 0.8556 (pp) cc_final: 0.8352 (mp) REVERT: A 201 THR cc_start: 0.9410 (t) cc_final: 0.8734 (t) REVERT: B 68 PHE cc_start: 0.8731 (t80) cc_final: 0.8232 (t80) REVERT: B 130 TRP cc_start: 0.9233 (m-10) cc_final: 0.8751 (m-90) REVERT: B 171 MET cc_start: 0.8452 (mtp) cc_final: 0.8036 (ttp) REVERT: B 223 ASP cc_start: 0.8400 (m-30) cc_final: 0.8107 (t0) REVERT: B 477 ARG cc_start: 0.8930 (ptp90) cc_final: 0.8670 (ptp-170) REVERT: B 496 ASP cc_start: 0.8389 (p0) cc_final: 0.8056 (p0) REVERT: B 542 MET cc_start: 0.5595 (tmm) cc_final: 0.5218 (tmm) REVERT: B 543 ASP cc_start: 0.7907 (p0) cc_final: 0.7292 (p0) outliers start: 28 outliers final: 20 residues processed: 193 average time/residue: 0.0778 time to fit residues: 22.0066 Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 16 VAL Chi-restraints excluded: chain B residue 95 SER 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: 8.9990 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4079 r_free = 0.4079 target = 0.142377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103397 restraints weight = 21965.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.106289 restraints weight = 13283.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.108297 restraints weight = 9415.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109647 restraints weight = 7412.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110459 restraints weight = 6284.411| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9208 Z= 0.176 Angle : 0.791 10.976 12502 Z= 0.356 Chirality : 0.044 0.241 1524 Planarity : 0.004 0.071 1560 Dihedral : 17.864 106.544 1580 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 3.52 % Allowed : 21.11 % Favored : 75.37 % 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: 0.66 (0.25), residues: 1136 helix: 1.52 (0.19), residues: 734 sheet: 0.23 (0.60), residues: 80 loop : -2.12 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 408 TYR 0.021 0.002 TYR B 342 PHE 0.018 0.002 PHE A 233 TRP 0.012 0.001 TRP A 238 HIS 0.013 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9190) covalent geometry : angle 0.75098 (12448) hydrogen bonds : bond 0.04988 ( 588) hydrogen bonds : angle 4.11252 ( 1728) link_BETA1-2 : bond 0.01270 ( 18) link_BETA1-2 : angle 3.86304 ( 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 190 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9143 (mt) cc_final: 0.8536 (mt) REVERT: A 61 MET cc_start: 0.8257 (ppp) cc_final: 0.7916 (ppp) REVERT: A 71 MET cc_start: 0.8289 (mmm) cc_final: 0.7943 (tpt) REVERT: A 248 MET cc_start: 0.8190 (mtp) cc_final: 0.7846 (mtp) REVERT: A 314 ASP cc_start: 0.8159 (m-30) cc_final: 0.7633 (t0) REVERT: B 61 MET cc_start: 0.7946 (ppp) cc_final: 0.7675 (ppp) REVERT: B 71 MET cc_start: 0.7756 (mmp) cc_final: 0.7046 (mtt) REVERT: B 130 TRP cc_start: 0.9154 (m-10) cc_final: 0.8736 (m-90) REVERT: B 171 MET cc_start: 0.8397 (mtp) cc_final: 0.8019 (ttp) REVERT: B 223 ASP cc_start: 0.8365 (m-30) cc_final: 0.8072 (t0) REVERT: B 342 TYR cc_start: 0.7718 (t80) cc_final: 0.7302 (t80) outliers start: 33 outliers final: 23 residues processed: 178 average time/residue: 0.0704 time to fit residues: 19.0796 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU 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 161 VAL 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 25 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 94 ASP 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 328 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 283 GLN B 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.148230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108287 restraints weight = 22286.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111452 restraints weight = 13164.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113553 restraints weight = 9179.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115097 restraints weight = 7140.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115813 restraints weight = 5993.947| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9208 Z= 0.150 Angle : 0.748 10.148 12502 Z= 0.333 Chirality : 0.043 0.253 1524 Planarity : 0.003 0.026 1560 Dihedral : 15.995 105.353 1580 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 4.69 % Allowed : 21.11 % Favored : 74.20 % 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: 1.75 (0.19), residues: 734 sheet: 0.39 (0.60), residues: 80 loop : -1.85 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 408 TYR 0.012 0.001 TYR B 342 PHE 0.013 0.001 PHE A 233 TRP 0.011 0.001 TRP A 238 HIS 0.007 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9190) covalent geometry : angle 0.70944 (12448) hydrogen bonds : bond 0.04585 ( 588) hydrogen bonds : angle 3.96558 ( 1728) link_BETA1-2 : bond 0.01143 ( 18) link_BETA1-2 : angle 3.66178 ( 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 189 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9103 (mt) cc_final: 0.8451 (mt) REVERT: A 61 MET cc_start: 0.8239 (ppp) cc_final: 0.7872 (ppp) REVERT: A 71 MET cc_start: 0.8238 (mmm) cc_final: 0.7774 (tpt) REVERT: A 102 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5531 (ttt) REVERT: A 155 ASP cc_start: 0.7149 (t70) cc_final: 0.5375 (m-30) REVERT: A 156 MET cc_start: 0.5931 (pmm) cc_final: 0.4942 (ptt) REVERT: A 160 LEU cc_start: 0.8794 (mp) cc_final: 0.8590 (mm) REVERT: A 248 MET cc_start: 0.8272 (mtp) cc_final: 0.8010 (mtp) REVERT: A 314 ASP cc_start: 0.8177 (m-30) cc_final: 0.7681 (t0) REVERT: B 61 MET cc_start: 0.7808 (ppp) cc_final: 0.7542 (ppp) REVERT: B 71 MET cc_start: 0.7807 (mmp) cc_final: 0.6943 (mtt) REVERT: B 130 TRP cc_start: 0.9173 (m-10) cc_final: 0.8768 (m-90) REVERT: B 152 MET cc_start: 0.8288 (ttp) cc_final: 0.7245 (tpp) REVERT: B 171 MET cc_start: 0.8445 (mtp) cc_final: 0.7907 (tmm) REVERT: B 223 ASP cc_start: 0.8411 (m-30) cc_final: 0.8076 (t0) REVERT: B 342 TYR cc_start: 0.7901 (t80) cc_final: 0.7409 (t80) REVERT: B 420 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7635 (mm) REVERT: B 542 MET cc_start: 0.5860 (tmm) cc_final: 0.5485 (tmm) outliers start: 44 outliers final: 29 residues processed: 176 average time/residue: 0.0711 time to fit residues: 18.6686 Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 284 LEU 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 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 59 LEU 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 272 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 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 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 137 HIS ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 512 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095377 restraints weight = 22105.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097930 restraints weight = 13437.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099717 restraints weight = 9052.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099993 restraints weight = 7766.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.100187 restraints weight = 7088.120| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9208 Z= 0.273 Angle : 0.884 14.287 12502 Z= 0.412 Chirality : 0.046 0.221 1524 Planarity : 0.005 0.091 1560 Dihedral : 15.361 104.415 1580 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % Rotamer: Outliers : 5.65 % Allowed : 22.71 % 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: 0.63 (0.25), residues: 1136 helix: 1.36 (0.19), residues: 736 sheet: 0.49 (0.59), residues: 80 loop : -1.84 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 408 TYR 0.016 0.002 TYR A 169 PHE 0.015 0.002 PHE A 233 TRP 0.015 0.002 TRP A 130 HIS 0.010 0.002 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 9190) covalent geometry : angle 0.85393 (12448) hydrogen bonds : bond 0.05572 ( 588) hydrogen bonds : angle 4.30533 ( 1728) link_BETA1-2 : bond 0.01225 ( 18) link_BETA1-2 : angle 3.56382 ( 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 200 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6202 (ttt) REVERT: A 156 MET cc_start: 0.6586 (pmm) cc_final: 0.5827 (ptt) REVERT: A 248 MET cc_start: 0.8374 (mtp) cc_final: 0.8114 (mtp) REVERT: A 314 ASP cc_start: 0.8486 (m-30) cc_final: 0.8065 (t0) REVERT: B 61 MET cc_start: 0.8071 (ppp) cc_final: 0.7816 (ppp) REVERT: B 152 MET cc_start: 0.8330 (ttp) cc_final: 0.7763 (tpt) REVERT: B 171 MET cc_start: 0.8609 (mtp) cc_final: 0.8260 (ttp) REVERT: B 223 ASP cc_start: 0.8462 (m-30) cc_final: 0.8231 (t0) REVERT: B 263 TYR cc_start: 0.8711 (t80) cc_final: 0.8510 (t80) REVERT: B 285 MET cc_start: 0.8459 (ppp) cc_final: 0.7676 (tmm) REVERT: B 342 TYR cc_start: 0.7854 (t80) cc_final: 0.7252 (t80) REVERT: B 393 MET cc_start: 0.8042 (mmm) cc_final: 0.6972 (tmm) REVERT: B 420 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8016 (mm) outliers start: 53 outliers final: 36 residues processed: 179 average time/residue: 0.0696 time to fit residues: 18.9392 Evaluate side-chains 171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 LEU 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 161 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 276 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 25 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 74 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 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 420 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 136 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.138866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099699 restraints weight = 22287.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102674 restraints weight = 13241.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104703 restraints weight = 9286.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106101 restraints weight = 7289.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.107014 restraints weight = 6174.244| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9208 Z= 0.148 Angle : 0.786 10.421 12502 Z= 0.351 Chirality : 0.044 0.322 1524 Planarity : 0.004 0.058 1560 Dihedral : 14.792 104.048 1580 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 3.94 % Allowed : 24.52 % Favored : 71.54 % 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: 1.05 (0.26), residues: 1136 helix: 1.63 (0.19), residues: 744 sheet: 0.53 (0.62), residues: 80 loop : -1.59 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 408 TYR 0.011 0.001 TYR A 96 PHE 0.010 0.001 PHE A 421 TRP 0.012 0.001 TRP B 130 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9190) covalent geometry : angle 0.75375 (12448) hydrogen bonds : bond 0.04814 ( 588) hydrogen bonds : angle 3.84954 ( 1728) link_BETA1-2 : bond 0.01118 ( 18) link_BETA1-2 : angle 3.47703 ( 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 193 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9070 (mt) cc_final: 0.8865 (mt) REVERT: A 61 MET cc_start: 0.8183 (tmm) cc_final: 0.7588 (tpt) REVERT: A 102 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5987 (ttt) REVERT: A 155 ASP cc_start: 0.7413 (t70) cc_final: 0.5565 (m-30) REVERT: A 156 MET cc_start: 0.6219 (pmm) cc_final: 0.5304 (ptt) REVERT: A 248 MET cc_start: 0.8316 (mtp) cc_final: 0.8025 (mtp) REVERT: A 314 ASP cc_start: 0.8372 (m-30) cc_final: 0.7917 (t0) REVERT: B 71 MET cc_start: 0.8101 (mmp) cc_final: 0.7319 (mtt) REVERT: B 130 TRP cc_start: 0.9207 (m-10) cc_final: 0.8922 (m-10) REVERT: B 152 MET cc_start: 0.8199 (ttp) cc_final: 0.7641 (tpt) REVERT: B 171 MET cc_start: 0.8529 (mtp) cc_final: 0.8036 (tmm) REVERT: B 223 ASP cc_start: 0.8374 (m-30) cc_final: 0.8167 (t0) REVERT: B 285 MET cc_start: 0.8135 (ppp) cc_final: 0.7353 (tmm) REVERT: B 311 GLN cc_start: 0.8561 (tp40) cc_final: 0.8225 (tm-30) REVERT: B 342 TYR cc_start: 0.7902 (t80) cc_final: 0.7346 (t80) REVERT: B 393 MET cc_start: 0.7976 (mmm) cc_final: 0.6990 (tmm) outliers start: 37 outliers final: 25 residues processed: 178 average time/residue: 0.0705 time to fit residues: 18.7506 Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 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 208 VAL 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 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 33 LEU Chi-restraints excluded: chain B residue 59 LEU 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 243 SER 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 525 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 0.0040 chunk 41 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 62 optimal weight: 0.0970 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 85 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.140006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.102064 restraints weight = 22274.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104700 restraints weight = 12414.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.106522 restraints weight = 8155.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.106828 restraints weight = 7071.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107128 restraints weight = 6330.659| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9208 Z= 0.145 Angle : 0.776 10.637 12502 Z= 0.345 Chirality : 0.043 0.270 1524 Planarity : 0.003 0.037 1560 Dihedral : 14.498 103.035 1580 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % Rotamer: Outliers : 3.41 % Allowed : 24.95 % 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: 1.13 (0.26), residues: 1136 helix: 1.66 (0.19), residues: 752 sheet: 0.47 (0.62), residues: 80 loop : -1.50 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 408 TYR 0.022 0.001 TYR B 263 PHE 0.009 0.001 PHE A 233 TRP 0.009 0.001 TRP A 238 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9190) covalent geometry : angle 0.74622 (12448) hydrogen bonds : bond 0.04521 ( 588) hydrogen bonds : angle 3.82310 ( 1728) link_BETA1-2 : bond 0.01061 ( 18) link_BETA1-2 : angle 3.32972 ( 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 178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9040 (mt) cc_final: 0.8791 (mt) REVERT: A 61 MET cc_start: 0.8124 (tmm) cc_final: 0.7487 (tpt) REVERT: A 102 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.5960 (ttt) REVERT: A 155 ASP cc_start: 0.7216 (t70) cc_final: 0.5521 (m-30) REVERT: A 248 MET cc_start: 0.8294 (mtp) cc_final: 0.8059 (mtp) REVERT: A 314 ASP cc_start: 0.8344 (m-30) cc_final: 0.7905 (t0) REVERT: A 542 MET cc_start: 0.3169 (tpt) cc_final: 0.2633 (tpt) REVERT: B 71 MET cc_start: 0.8025 (mmp) cc_final: 0.7175 (mtt) REVERT: B 130 TRP cc_start: 0.9183 (m-10) cc_final: 0.8906 (m-10) REVERT: B 152 MET cc_start: 0.8295 (ttp) cc_final: 0.7655 (tpt) REVERT: B 171 MET cc_start: 0.8490 (mtp) cc_final: 0.7977 (tmm) REVERT: B 223 ASP cc_start: 0.8428 (m-30) cc_final: 0.8213 (t0) REVERT: B 311 GLN cc_start: 0.8556 (tp40) cc_final: 0.8227 (tm-30) REVERT: B 342 TYR cc_start: 0.7958 (t80) cc_final: 0.7349 (t80) REVERT: B 393 MET cc_start: 0.8053 (mmm) cc_final: 0.7101 (tmm) outliers start: 32 outliers final: 24 residues processed: 166 average time/residue: 0.0688 time to fit residues: 17.3866 Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 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 208 VAL Chi-restraints excluded: chain A residue 284 LEU 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 290 ASP 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 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: 10.0000 chunk 23 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN B 451 HIS B 512 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.145316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106580 restraints weight = 22397.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109750 restraints weight = 12909.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111868 restraints weight = 8882.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113312 restraints weight = 6869.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114042 restraints weight = 5753.454| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9208 Z= 0.143 Angle : 0.773 12.676 12502 Z= 0.343 Chirality : 0.043 0.244 1524 Planarity : 0.003 0.037 1560 Dihedral : 14.153 101.611 1580 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 3.30 % Allowed : 25.27 % Favored : 71.43 % 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: 1.15 (0.26), residues: 1136 helix: 1.62 (0.19), residues: 764 sheet: 0.37 (0.60), residues: 80 loop : -1.41 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 408 TYR 0.021 0.001 TYR B 263 PHE 0.010 0.001 PHE B 195 TRP 0.008 0.001 TRP A 238 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9190) covalent geometry : angle 0.74469 (12448) hydrogen bonds : bond 0.04370 ( 588) hydrogen bonds : angle 3.80444 ( 1728) link_BETA1-2 : bond 0.01008 ( 18) link_BETA1-2 : angle 3.22800 ( 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 180 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9063 (mt) cc_final: 0.8824 (mt) REVERT: A 61 MET cc_start: 0.8129 (tmm) cc_final: 0.7512 (tpt) REVERT: A 102 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5633 (ttt) REVERT: A 155 ASP cc_start: 0.7293 (t70) cc_final: 0.7081 (t70) REVERT: A 156 MET cc_start: 0.6338 (pmm) cc_final: 0.5456 (ptt) REVERT: A 248 MET cc_start: 0.8346 (mtp) cc_final: 0.8105 (mtp) REVERT: A 314 ASP cc_start: 0.8266 (m-30) cc_final: 0.7832 (t0) REVERT: B 97 GLU cc_start: 0.8577 (tp30) cc_final: 0.8336 (pt0) REVERT: B 130 TRP cc_start: 0.9198 (m-10) cc_final: 0.8982 (m-10) REVERT: B 152 MET cc_start: 0.8341 (ttp) cc_final: 0.7642 (tpt) REVERT: B 171 MET cc_start: 0.8547 (mtp) cc_final: 0.7900 (tmm) REVERT: B 223 ASP cc_start: 0.8442 (m-30) cc_final: 0.8177 (t0) REVERT: B 285 MET cc_start: 0.8231 (ppp) cc_final: 0.7822 (ppp) REVERT: B 311 GLN cc_start: 0.8550 (tp40) cc_final: 0.8209 (tm-30) REVERT: B 342 TYR cc_start: 0.7889 (t80) cc_final: 0.7276 (t80) REVERT: B 393 MET cc_start: 0.8045 (mmm) cc_final: 0.7026 (tmm) REVERT: B 512 GLN cc_start: 0.9253 (pt0) cc_final: 0.8867 (mm110) outliers start: 31 outliers final: 26 residues processed: 169 average time/residue: 0.0652 time to fit residues: 16.9775 Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 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 208 VAL 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 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 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 243 SER Chi-restraints excluded: chain B residue 290 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 30.0000 chunk 88 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100951 restraints weight = 22132.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.103946 restraints weight = 13131.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105966 restraints weight = 9171.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107349 restraints weight = 7155.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108139 restraints weight = 6032.344| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5103 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= 0.145 Angle : 0.776 14.396 12502 Z= 0.345 Chirality : 0.043 0.302 1524 Planarity : 0.003 0.042 1560 Dihedral : 13.888 100.113 1580 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 2.88 % Allowed : 25.16 % 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: 1.24 (0.26), residues: 1136 helix: 1.69 (0.19), residues: 764 sheet: 0.38 (0.61), residues: 80 loop : -1.40 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 408 TYR 0.021 0.001 TYR B 263 PHE 0.017 0.001 PHE B 68 TRP 0.011 0.001 TRP B 239 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9190) covalent geometry : angle 0.74962 (12448) hydrogen bonds : bond 0.04342 ( 588) hydrogen bonds : angle 3.77906 ( 1728) link_BETA1-2 : bond 0.00971 ( 18) link_BETA1-2 : angle 3.16407 ( 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 175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9054 (mt) cc_final: 0.8815 (mt) REVERT: A 61 MET cc_start: 0.8074 (tmm) cc_final: 0.7536 (tpt) REVERT: A 102 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.5750 (ttt) REVERT: A 248 MET cc_start: 0.8344 (mtp) cc_final: 0.8110 (mtp) REVERT: A 314 ASP cc_start: 0.8274 (m-30) cc_final: 0.7857 (t0) REVERT: B 68 PHE cc_start: 0.8646 (t80) cc_final: 0.8142 (t80) REVERT: B 97 GLU cc_start: 0.8514 (tp30) cc_final: 0.8302 (pt0) REVERT: B 130 TRP cc_start: 0.9266 (m-10) cc_final: 0.9018 (m-10) REVERT: B 152 MET cc_start: 0.8359 (ttp) cc_final: 0.7784 (tpp) REVERT: B 171 MET cc_start: 0.8505 (mtp) cc_final: 0.8106 (ttp) REVERT: B 223 ASP cc_start: 0.8433 (m-30) cc_final: 0.8186 (t0) REVERT: B 285 MET cc_start: 0.8293 (ppp) cc_final: 0.7863 (ppp) REVERT: B 311 GLN cc_start: 0.8532 (tp40) cc_final: 0.8169 (tm-30) REVERT: B 342 TYR cc_start: 0.7759 (t80) cc_final: 0.7176 (t80) REVERT: B 393 MET cc_start: 0.8091 (mmm) cc_final: 0.7030 (tmm) outliers start: 27 outliers final: 25 residues processed: 164 average time/residue: 0.0639 time to fit residues: 16.2621 Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 208 VAL 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 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 290 ASP 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 517 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 58 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.139972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101216 restraints weight = 22214.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104372 restraints weight = 12739.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.106497 restraints weight = 8739.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107927 restraints weight = 6745.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.108860 restraints weight = 5659.609| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9208 Z= 0.143 Angle : 0.794 14.132 12502 Z= 0.353 Chirality : 0.044 0.402 1524 Planarity : 0.003 0.037 1560 Dihedral : 13.622 99.040 1580 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.67 % Favored : 95.07 % Rotamer: Outliers : 2.77 % Allowed : 25.80 % Favored : 71.43 % 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: 1.25 (0.26), residues: 1136 helix: 1.70 (0.19), residues: 764 sheet: 0.39 (0.61), residues: 80 loop : -1.42 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 408 TYR 0.022 0.001 TYR B 263 PHE 0.014 0.001 PHE B 68 TRP 0.009 0.001 TRP A 62 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9190) covalent geometry : angle 0.76840 (12448) hydrogen bonds : bond 0.04285 ( 588) hydrogen bonds : angle 3.77253 ( 1728) link_BETA1-2 : bond 0.00955 ( 18) link_BETA1-2 : angle 3.12140 ( 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 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8124 (tmm) cc_final: 0.7617 (tpt) REVERT: A 102 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5635 (ttt) REVERT: A 248 MET cc_start: 0.8347 (mtp) cc_final: 0.8079 (mtp) REVERT: A 314 ASP cc_start: 0.8295 (m-30) cc_final: 0.7809 (t0) REVERT: B 68 PHE cc_start: 0.8648 (t80) cc_final: 0.8154 (t80) REVERT: B 92 MET cc_start: 0.8941 (tpp) cc_final: 0.8531 (tpp) REVERT: B 97 GLU cc_start: 0.8454 (tp30) cc_final: 0.8216 (pt0) REVERT: B 130 TRP cc_start: 0.9264 (m-10) cc_final: 0.9029 (m-10) REVERT: B 152 MET cc_start: 0.8383 (ttp) cc_final: 0.8119 (tpp) REVERT: B 171 MET cc_start: 0.8531 (mtp) cc_final: 0.7950 (tmm) REVERT: B 223 ASP cc_start: 0.8453 (m-30) cc_final: 0.8192 (t0) REVERT: B 285 MET cc_start: 0.8255 (ppp) cc_final: 0.7823 (ppp) REVERT: B 311 GLN cc_start: 0.8536 (tp40) cc_final: 0.8187 (tm-30) REVERT: B 342 TYR cc_start: 0.7677 (t80) cc_final: 0.7084 (t80) REVERT: B 393 MET cc_start: 0.8124 (mmm) cc_final: 0.7009 (tmm) outliers start: 26 outliers final: 22 residues processed: 165 average time/residue: 0.0672 time to fit residues: 17.1760 Evaluate side-chains 171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 172 ILE Chi-restraints excluded: chain A residue 208 VAL 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 382 GLN 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 463 THR 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: 0.0970 chunk 70 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.145849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106768 restraints weight = 22008.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109865 restraints weight = 12895.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112054 restraints weight = 8967.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113449 restraints weight = 6956.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114311 restraints weight = 5849.909| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 9208 Z= 0.229 Angle : 1.044 59.107 12502 Z= 0.560 Chirality : 0.044 0.355 1524 Planarity : 0.003 0.034 1560 Dihedral : 13.629 99.371 1580 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.67 % Favored : 95.07 % Rotamer: Outliers : 2.77 % Allowed : 25.80 % Favored : 71.43 % 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: 1.24 (0.26), residues: 1136 helix: 1.69 (0.19), residues: 764 sheet: 0.39 (0.61), residues: 80 loop : -1.41 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 408 TYR 0.021 0.001 TYR B 263 PHE 0.014 0.001 PHE B 68 TRP 0.008 0.001 TRP A 62 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9190) covalent geometry : angle 1.02560 (12448) hydrogen bonds : bond 0.04305 ( 588) hydrogen bonds : angle 3.77725 ( 1728) link_BETA1-2 : bond 0.01032 ( 18) link_BETA1-2 : angle 3.17025 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.74 seconds wall clock time: 24 minutes 24.72 seconds (1464.72 seconds total)