Starting phenix.real_space_refine on Thu Mar 13 19:42:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zoa_14845/03_2025/7zoa_14845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zoa_14845/03_2025/7zoa_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_2025/7zoa_14845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2025/7zoa_14845.map" model { file = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2025/7zoa_14845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zoa_14845/03_2025/7zoa_14845.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.073 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.89, per 1000 atoms: 0.65 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: 2.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 0.95 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: 2.71 Time building geometry restraints manager: 3.33 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: 0.010 Normalize map: mean=0, sd=1: 0.930 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.160 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- 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 9190 Z= 0.277 Angle : 0.811 10.411 12448 Z= 0.422 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (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 TRP 0.015 0.002 TRP B 62 HIS 0.006 0.001 HIS B 191 PHE 0.018 0.001 PHE B 421 TYR 0.017 0.001 TYR A 96 ARG 0.018 0.001 ARG A 408 *********************** 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 : 1.067 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: 0.7946 (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: 0.1954 time to fit residues: 65.4010 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 : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.149381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109343 restraints weight = 21870.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112423 restraints weight = 13296.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114509 restraints weight = 9366.996| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9190 Z= 0.392 Angle : 0.887 8.793 12448 Z= 0.424 Chirality : 0.049 0.331 1524 Planarity : 0.006 0.093 1560 Dihedral : 20.869 106.712 1580 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.52 % Favored : 96.13 % Rotamer: Outliers : 2.35 % Allowed : 15.88 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1136 helix: 1.28 (0.19), residues: 730 sheet: 0.44 (0.63), residues: 78 loop : -2.23 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 238 HIS 0.011 0.002 HIS A 197 PHE 0.029 0.003 PHE B 133 TYR 0.024 0.003 TYR A 461 ARG 0.016 0.001 ARG B 408 *********************** 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 190 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8312 (ppp) cc_final: 0.7830 (ppp) REVERT: A 71 MET cc_start: 0.8213 (mmm) cc_final: 0.7900 (tpt) REVERT: A 92 MET cc_start: 0.8752 (tpp) cc_final: 0.8515 (tpp) REVERT: A 236 LEU cc_start: 0.9133 (mt) cc_final: 0.8559 (pt) REVERT: A 243 SER cc_start: 0.9147 (p) cc_final: 0.8930 (p) REVERT: B 61 MET cc_start: 0.7965 (ppp) cc_final: 0.7707 (ppp) REVERT: B 68 PHE cc_start: 0.8713 (t80) cc_final: 0.8199 (t80) REVERT: B 130 TRP cc_start: 0.9157 (m-10) cc_final: 0.8628 (m-90) REVERT: B 152 MET cc_start: 0.8240 (ttp) cc_final: 0.7465 (tpt) REVERT: B 156 MET cc_start: 0.6266 (pmm) cc_final: 0.5701 (pmm) REVERT: B 171 MET cc_start: 0.8498 (mtp) cc_final: 0.7993 (ttp) REVERT: B 223 ASP cc_start: 0.8473 (m-30) cc_final: 0.8112 (t0) REVERT: B 477 ARG cc_start: 0.8932 (ptp90) cc_final: 0.8643 (ptp-170) REVERT: B 496 ASP cc_start: 0.8321 (p0) cc_final: 0.8069 (p0) REVERT: B 542 MET cc_start: 0.5563 (tmm) cc_final: 0.5207 (tmm) REVERT: B 543 ASP cc_start: 0.7990 (p0) cc_final: 0.7419 (p0) outliers start: 22 outliers final: 17 residues processed: 185 average time/residue: 0.2240 time to fit residues: 61.3433 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 13 TYR 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 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 93 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.149201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109954 restraints weight = 22186.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113146 restraints weight = 13039.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115303 restraints weight = 9042.858| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9190 Z= 0.232 Angle : 0.735 9.535 12448 Z= 0.337 Chirality : 0.044 0.247 1524 Planarity : 0.004 0.062 1560 Dihedral : 17.575 106.122 1580 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 3.94 % Allowed : 19.51 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1136 helix: 1.67 (0.19), residues: 730 sheet: 0.31 (0.60), residues: 80 loop : -2.15 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 238 HIS 0.014 0.001 HIS B 451 PHE 0.017 0.002 PHE B 264 TYR 0.021 0.002 TYR B 342 ARG 0.006 0.001 ARG A 408 *********************** 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 200 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9141 (mt) cc_final: 0.8536 (mt) REVERT: A 61 MET cc_start: 0.8326 (ppp) cc_final: 0.7918 (ppp) REVERT: A 71 MET cc_start: 0.8310 (mmm) cc_final: 0.7936 (tpt) REVERT: A 92 MET cc_start: 0.8744 (tpp) cc_final: 0.8312 (tpp) REVERT: A 155 ASP cc_start: 0.7138 (t70) cc_final: 0.5571 (m-30) REVERT: A 236 LEU cc_start: 0.9227 (mt) cc_final: 0.8678 (pt) REVERT: A 271 ARG cc_start: 0.7379 (ptp90) cc_final: 0.7173 (mtm180) REVERT: B 61 MET cc_start: 0.7813 (ppp) cc_final: 0.7518 (ppp) REVERT: B 71 MET cc_start: 0.7713 (mmp) cc_final: 0.6949 (mtt) REVERT: B 130 TRP cc_start: 0.9139 (m-10) cc_final: 0.8694 (m-90) REVERT: B 152 MET cc_start: 0.8298 (ttp) cc_final: 0.7506 (tpp) REVERT: B 171 MET cc_start: 0.8476 (mtp) cc_final: 0.8004 (ttp) REVERT: B 223 ASP cc_start: 0.8404 (m-30) cc_final: 0.8067 (t0) REVERT: B 342 TYR cc_start: 0.7766 (t80) cc_final: 0.7337 (t80) outliers start: 37 outliers final: 24 residues processed: 186 average time/residue: 0.1945 time to fit residues: 52.2051 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 478 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 30.0000 chunk 47 optimal weight: 0.0670 chunk 103 optimal weight: 0.0470 chunk 111 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 overall best weight: 0.3734 ------------------------------------------------------------------------------- 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 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.152181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.113345 restraints weight = 22259.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116628 restraints weight = 13015.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118813 restraints weight = 8967.058| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.003 0.036 9190 Z= 0.189 Angle : 0.714 10.032 12448 Z= 0.322 Chirality : 0.043 0.246 1524 Planarity : 0.003 0.026 1560 Dihedral : 15.824 105.116 1580 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 3.62 % Allowed : 20.68 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1136 helix: 1.85 (0.19), residues: 726 sheet: 0.38 (0.60), residues: 80 loop : -1.99 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 238 HIS 0.006 0.001 HIS B 451 PHE 0.014 0.001 PHE B 264 TYR 0.011 0.001 TYR B 342 ARG 0.016 0.001 ARG B 408 *********************** 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 187 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8201 (ppp) cc_final: 0.7860 (ppp) REVERT: A 71 MET cc_start: 0.8244 (mmm) cc_final: 0.7779 (tpt) REVERT: A 102 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5445 (ttt) REVERT: A 155 ASP cc_start: 0.6880 (t70) cc_final: 0.5414 (m-30) REVERT: A 160 LEU cc_start: 0.8783 (mp) cc_final: 0.8570 (mm) REVERT: A 314 ASP cc_start: 0.8109 (m-30) cc_final: 0.7558 (t0) REVERT: B 68 PHE cc_start: 0.8584 (t80) cc_final: 0.8144 (t80) REVERT: B 130 TRP cc_start: 0.9092 (m-10) cc_final: 0.8649 (m-90) REVERT: B 152 MET cc_start: 0.8274 (ttp) cc_final: 0.7620 (tpp) REVERT: B 171 MET cc_start: 0.8397 (mtp) cc_final: 0.7936 (ttp) REVERT: B 223 ASP cc_start: 0.8340 (m-30) cc_final: 0.8044 (t0) REVERT: B 311 GLN cc_start: 0.8651 (tp40) cc_final: 0.8398 (tm-30) REVERT: B 342 TYR cc_start: 0.7790 (t80) cc_final: 0.7328 (t80) outliers start: 34 outliers final: 26 residues processed: 173 average time/residue: 0.1789 time to fit residues: 44.8710 Evaluate side-chains 171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 408 ARG 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 25 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG 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 84 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108182 restraints weight = 21816.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111271 restraints weight = 12817.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113360 restraints weight = 8904.721| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9190 Z= 0.243 Angle : 0.732 9.639 12448 Z= 0.334 Chirality : 0.043 0.214 1524 Planarity : 0.003 0.031 1560 Dihedral : 15.008 104.329 1580 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 4.48 % Allowed : 22.17 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1136 helix: 1.79 (0.19), residues: 736 sheet: 0.44 (0.60), residues: 80 loop : -1.80 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 238 HIS 0.006 0.001 HIS B 191 PHE 0.009 0.001 PHE B 563 TYR 0.012 0.002 TYR B 96 ARG 0.018 0.001 ARG B 408 *********************** 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 193 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5680 (ttt) REVERT: A 314 ASP cc_start: 0.8273 (m-30) cc_final: 0.7732 (t0) REVERT: A 467 GLU cc_start: 0.8514 (pm20) cc_final: 0.8061 (pp20) REVERT: B 24 MET cc_start: 0.8405 (tpp) cc_final: 0.8139 (tpp) REVERT: B 97 GLU cc_start: 0.8498 (tp30) cc_final: 0.8274 (pt0) REVERT: B 130 TRP cc_start: 0.9263 (m-10) cc_final: 0.9005 (m-10) REVERT: B 152 MET cc_start: 0.8328 (ttp) cc_final: 0.7466 (tpt) REVERT: B 171 MET cc_start: 0.8528 (mtp) cc_final: 0.8032 (ttp) REVERT: B 223 ASP cc_start: 0.8451 (m-30) cc_final: 0.8101 (t0) REVERT: B 311 GLN cc_start: 0.8684 (tp40) cc_final: 0.8411 (tm-30) REVERT: B 342 TYR cc_start: 0.7957 (t80) cc_final: 0.7433 (t80) REVERT: B 393 MET cc_start: 0.7907 (mmm) cc_final: 0.6756 (tmm) outliers start: 42 outliers final: 27 residues processed: 178 average time/residue: 0.1839 time to fit residues: 47.3415 Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 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 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 463 THR Chi-restraints excluded: chain B residue 465 VAL 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 39 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109416 restraints weight = 21774.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112580 restraints weight = 12779.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.114689 restraints weight = 8839.432| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9190 Z= 0.197 Angle : 0.718 11.080 12448 Z= 0.326 Chirality : 0.042 0.204 1524 Planarity : 0.003 0.047 1560 Dihedral : 14.684 103.639 1580 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 4.16 % Allowed : 23.67 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1136 helix: 1.89 (0.19), residues: 736 sheet: 0.49 (0.60), residues: 80 loop : -1.86 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 238 HIS 0.004 0.001 HIS A 409 PHE 0.011 0.001 PHE A 421 TYR 0.008 0.001 TYR A 96 ARG 0.024 0.001 ARG A 408 *********************** 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 188 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8594 (tt0) REVERT: A 92 MET cc_start: 0.8612 (tpp) cc_final: 0.8291 (tpp) REVERT: A 102 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5446 (ttt) REVERT: A 314 ASP cc_start: 0.8291 (m-30) cc_final: 0.7747 (t0) REVERT: B 11 MET cc_start: 0.8576 (tpp) cc_final: 0.8336 (mmp) REVERT: B 24 MET cc_start: 0.8236 (tpp) cc_final: 0.8020 (tpp) REVERT: B 68 PHE cc_start: 0.8651 (t80) cc_final: 0.8131 (t80) REVERT: B 71 MET cc_start: 0.7896 (mmp) cc_final: 0.7057 (mtt) REVERT: B 97 GLU cc_start: 0.8480 (tp30) cc_final: 0.8269 (pt0) REVERT: B 130 TRP cc_start: 0.9204 (m-10) cc_final: 0.8955 (m-10) REVERT: B 152 MET cc_start: 0.8306 (ttp) cc_final: 0.7490 (tpt) REVERT: B 171 MET cc_start: 0.8450 (mtp) cc_final: 0.8028 (ttp) REVERT: B 223 ASP cc_start: 0.8409 (m-30) cc_final: 0.8115 (t0) REVERT: B 311 GLN cc_start: 0.8659 (tp40) cc_final: 0.8399 (tm-30) REVERT: B 342 TYR cc_start: 0.7774 (t80) cc_final: 0.7240 (t80) REVERT: B 393 MET cc_start: 0.7927 (mmm) cc_final: 0.6924 (tmm) outliers start: 39 outliers final: 27 residues processed: 174 average time/residue: 0.1795 time to fit residues: 45.4014 Evaluate side-chains 169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 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 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 62 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109886 restraints weight = 22172.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113103 restraints weight = 12939.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115231 restraints weight = 8980.706| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9190 Z= 0.201 Angle : 0.742 10.948 12448 Z= 0.332 Chirality : 0.042 0.224 1524 Planarity : 0.003 0.053 1560 Dihedral : 14.464 102.707 1580 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer: Outliers : 3.84 % Allowed : 24.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1136 helix: 1.92 (0.19), residues: 736 sheet: 0.45 (0.60), residues: 80 loop : -1.81 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 238 HIS 0.004 0.000 HIS A 191 PHE 0.010 0.001 PHE B 337 TYR 0.008 0.001 TYR B 211 ARG 0.025 0.001 ARG B 408 *********************** 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 191 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8137 (mmm) cc_final: 0.7857 (mmm) REVERT: A 102 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5568 (ttt) REVERT: A 285 MET cc_start: 0.8662 (ttp) cc_final: 0.8438 (ttm) REVERT: A 314 ASP cc_start: 0.8200 (m-30) cc_final: 0.7655 (t0) REVERT: A 542 MET cc_start: 0.3217 (tpt) cc_final: 0.2648 (tpt) REVERT: B 11 MET cc_start: 0.8552 (tpp) cc_final: 0.8344 (mmp) REVERT: B 24 MET cc_start: 0.8259 (tpp) cc_final: 0.8033 (tpp) REVERT: B 71 MET cc_start: 0.7876 (mmp) cc_final: 0.7004 (mtt) REVERT: B 130 TRP cc_start: 0.9184 (m-10) cc_final: 0.8941 (m-10) REVERT: B 152 MET cc_start: 0.8306 (ttp) cc_final: 0.7420 (tpt) REVERT: B 171 MET cc_start: 0.8504 (mtp) cc_final: 0.7890 (tmm) REVERT: B 223 ASP cc_start: 0.8430 (m-30) cc_final: 0.8116 (t0) REVERT: B 311 GLN cc_start: 0.8648 (tp40) cc_final: 0.8402 (tm-30) REVERT: B 342 TYR cc_start: 0.7847 (t80) cc_final: 0.7228 (t80) REVERT: B 393 MET cc_start: 0.7980 (mmm) cc_final: 0.6935 (tmm) outliers start: 36 outliers final: 28 residues processed: 179 average time/residue: 0.1730 time to fit residues: 45.4679 Evaluate side-chains 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 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 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 208 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 502 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 73 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 chunk 109 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 478 GLN B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.149185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109707 restraints weight = 22388.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112922 restraints weight = 13118.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115076 restraints weight = 9096.403| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9190 Z= 0.201 Angle : 0.748 13.619 12448 Z= 0.336 Chirality : 0.042 0.219 1524 Planarity : 0.003 0.030 1560 Dihedral : 14.166 101.629 1580 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 3.62 % Allowed : 24.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1136 helix: 1.97 (0.19), residues: 732 sheet: 0.36 (0.59), residues: 80 loop : -1.84 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 238 HIS 0.004 0.001 HIS A 191 PHE 0.013 0.001 PHE A 421 TYR 0.019 0.001 TYR B 96 ARG 0.024 0.001 ARG B 408 *********************** 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 181 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5494 (ttt) REVERT: A 314 ASP cc_start: 0.8233 (m-30) cc_final: 0.7697 (t0) REVERT: A 467 GLU cc_start: 0.8419 (pm20) cc_final: 0.8164 (pp20) REVERT: A 542 MET cc_start: 0.3212 (tpt) cc_final: 0.2705 (tpt) REVERT: B 68 PHE cc_start: 0.8610 (t80) cc_final: 0.8110 (t80) REVERT: B 71 MET cc_start: 0.7890 (mmp) cc_final: 0.7044 (mtt) REVERT: B 130 TRP cc_start: 0.9213 (m-10) cc_final: 0.8980 (m-10) REVERT: B 152 MET cc_start: 0.8308 (ttp) cc_final: 0.7463 (tpt) REVERT: B 171 MET cc_start: 0.8548 (mtp) cc_final: 0.8013 (ttp) REVERT: B 177 MET cc_start: 0.8023 (mtm) cc_final: 0.7354 (ttp) REVERT: B 223 ASP cc_start: 0.8426 (m-30) cc_final: 0.8122 (t0) REVERT: B 311 GLN cc_start: 0.8617 (tp40) cc_final: 0.8414 (tm-30) REVERT: B 342 TYR cc_start: 0.7869 (t80) cc_final: 0.7197 (t80) REVERT: B 393 MET cc_start: 0.8057 (mmm) cc_final: 0.7011 (tmm) outliers start: 34 outliers final: 27 residues processed: 171 average time/residue: 0.1684 time to fit residues: 42.7277 Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 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 33 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 208 VAL 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 463 THR Chi-restraints excluded: chain B residue 465 VAL 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 3 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 478 GLN B 85 HIS B 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110314 restraints weight = 22043.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113463 restraints weight = 13005.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115650 restraints weight = 9060.501| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9190 Z= 0.200 Angle : 0.762 13.565 12448 Z= 0.341 Chirality : 0.043 0.278 1524 Planarity : 0.003 0.025 1560 Dihedral : 13.900 100.463 1580 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 3.52 % Allowed : 25.69 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1136 helix: 1.99 (0.19), residues: 734 sheet: 0.31 (0.59), residues: 80 loop : -1.78 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 239 HIS 0.004 0.001 HIS A 191 PHE 0.012 0.001 PHE A 421 TYR 0.007 0.001 TYR A 96 ARG 0.022 0.001 ARG B 408 *********************** 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 179 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5462 (ttt) REVERT: A 314 ASP cc_start: 0.8233 (m-30) cc_final: 0.7690 (t0) REVERT: B 68 PHE cc_start: 0.8690 (t80) cc_final: 0.8193 (t80) REVERT: B 71 MET cc_start: 0.7967 (mmp) cc_final: 0.7078 (mtt) REVERT: B 96 TYR cc_start: 0.8775 (t80) cc_final: 0.8493 (t80) REVERT: B 130 TRP cc_start: 0.9246 (m-10) cc_final: 0.9016 (m-10) REVERT: B 152 MET cc_start: 0.8306 (ttp) cc_final: 0.7475 (tpt) REVERT: B 171 MET cc_start: 0.8552 (mtp) cc_final: 0.7982 (ttp) REVERT: B 223 ASP cc_start: 0.8435 (m-30) cc_final: 0.8128 (t0) REVERT: B 311 GLN cc_start: 0.8630 (tp40) cc_final: 0.8381 (tm-30) REVERT: B 342 TYR cc_start: 0.7824 (t80) cc_final: 0.7233 (t80) REVERT: B 393 MET cc_start: 0.8083 (mmm) cc_final: 0.6812 (tmm) outliers start: 33 outliers final: 26 residues processed: 168 average time/residue: 0.1662 time to fit residues: 42.0632 Evaluate side-chains 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 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 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 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 1 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.149577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110260 restraints weight = 22404.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113525 restraints weight = 13216.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115709 restraints weight = 9140.030| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9190 Z= 0.198 Angle : 0.767 14.886 12448 Z= 0.342 Chirality : 0.042 0.295 1524 Planarity : 0.003 0.031 1560 Dihedral : 13.606 99.157 1580 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 2.99 % Allowed : 25.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1136 helix: 1.89 (0.19), residues: 746 sheet: 0.39 (0.60), residues: 80 loop : -1.76 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 62 HIS 0.004 0.000 HIS A 191 PHE 0.011 0.001 PHE A 421 TYR 0.010 0.001 TYR A 211 ARG 0.022 0.001 ARG B 408 ********************** 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 173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5412 (ttt) REVERT: A 314 ASP cc_start: 0.8251 (m-30) cc_final: 0.7705 (t0) REVERT: B 68 PHE cc_start: 0.8688 (t80) cc_final: 0.8195 (t80) REVERT: B 71 MET cc_start: 0.7978 (mmp) cc_final: 0.7050 (mtt) REVERT: B 96 TYR cc_start: 0.8698 (t80) cc_final: 0.8460 (t80) REVERT: B 130 TRP cc_start: 0.9267 (m-10) cc_final: 0.9007 (m-10) REVERT: B 152 MET cc_start: 0.8296 (ttp) cc_final: 0.7441 (tpt) REVERT: B 171 MET cc_start: 0.8516 (mtp) cc_final: 0.7952 (ttp) REVERT: B 223 ASP cc_start: 0.8442 (m-30) cc_final: 0.8133 (t0) REVERT: B 311 GLN cc_start: 0.8627 (tp40) cc_final: 0.8427 (tm-30) REVERT: B 342 TYR cc_start: 0.7840 (t80) cc_final: 0.7236 (t80) REVERT: B 393 MET cc_start: 0.8023 (mmm) cc_final: 0.6817 (tmm) outliers start: 28 outliers final: 23 residues processed: 165 average time/residue: 0.1664 time to fit residues: 40.9625 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 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 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 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 59 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 0.0040 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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** B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.149456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110925 restraints weight = 22066.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114138 restraints weight = 12954.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116286 restraints weight = 8934.336| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9190 Z= 0.191 Angle : 0.769 14.103 12448 Z= 0.342 Chirality : 0.042 0.293 1524 Planarity : 0.003 0.023 1560 Dihedral : 13.399 98.089 1580 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 2.45 % Allowed : 26.55 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1136 helix: 1.97 (0.19), residues: 746 sheet: 0.42 (0.61), residues: 80 loop : -1.77 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 62 HIS 0.004 0.000 HIS A 191 PHE 0.012 0.001 PHE A 421 TYR 0.008 0.001 TYR A 211 ARG 0.019 0.001 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.85 seconds wall clock time: 48 minutes 15.13 seconds (2895.13 seconds total)