Starting phenix.real_space_refine on Sat Aug 23 09:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqe_38574/08_2025/8xqe_38574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqe_38574/08_2025/8xqe_38574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqe_38574/08_2025/8xqe_38574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqe_38574/08_2025/8xqe_38574.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqe_38574/08_2025/8xqe_38574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqe_38574/08_2025/8xqe_38574.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.041 sd= 1.339 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 88 5.16 5 C 7290 2.51 5 N 1889 2.21 5 O 2081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11348 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 447 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "R" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2372 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 109 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 9} Chain: "Q" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2206 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 3.20, per 1000 atoms: 0.28 Number of scatterers: 11348 At special positions: 0 Unit cell: (111.28, 115.44, 128.96, 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 88 16.00 O 2081 8.00 N 1889 7.00 C 7290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.04 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 102 " - pdb=" SG CYS Q 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 632.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2708 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 16 sheets defined 48.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.540A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.411A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.589A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.559A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 35 through 56 Processing helix chain 'C' and resid 60 through 75 Processing helix chain 'R' and resid 26 through 55 removed outlier: 3.680A pdb=" N LEU R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) Proline residue: R 32 - end of helix removed outlier: 3.577A pdb=" N LEU R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 100 through 133 Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.565A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 172 through 176 Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.616A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 236 through 278 Proline residue: R 263 - end of helix removed outlier: 3.514A pdb=" N HIS R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 310 removed outlier: 3.767A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Proline residue: R 292 - end of helix Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 321 Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'Q' and resid 30 through 56 removed outlier: 3.565A pdb=" N THR Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU Q 48 " --> pdb=" O THR Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 80 removed outlier: 3.671A pdb=" N PHE Q 78 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 89 Processing helix chain 'Q' and resid 98 through 133 removed outlier: 4.215A pdb=" N MET Q 113 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 144 removed outlier: 3.800A pdb=" N ALA Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG Q 139 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU Q 140 " --> pdb=" O ALA Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 168 Proline residue: Q 163 - end of helix removed outlier: 4.191A pdb=" N ARG Q 168 " --> pdb=" O VAL Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 176 Processing helix chain 'Q' and resid 184 through 188 removed outlier: 3.906A pdb=" N MET Q 187 " --> pdb=" O ASP Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 231 removed outlier: 5.914A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) Proline residue: Q 213 - end of helix Processing helix chain 'Q' and resid 237 through 239 No H-bonds generated for 'chain 'Q' and resid 237 through 239' Processing helix chain 'Q' and resid 240 through 277 removed outlier: 3.788A pdb=" N LEU Q 246 " --> pdb=" O LYS Q 242 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 3.806A pdb=" N MET Q 272 " --> pdb=" O LYS Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 299 removed outlier: 3.655A pdb=" N PHE Q 286 " --> pdb=" O ASP Q 282 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU Q 287 " --> pdb=" O PHE Q 283 " (cutoff:3.500A) Proline residue: Q 292 - end of helix Processing helix chain 'Q' and resid 300 through 310 Proline residue: Q 306 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.707A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.568A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.258A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.636A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.468A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.343A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 7.522A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.071A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N CYS B 294 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY B 306 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL B 296 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG B 304 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 168 through 170 Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.404A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 93 through 94 Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'S' and resid 159 through 160 Processing sheet with id=AB7, first strand: chain 'S' and resid 186 through 189 removed outlier: 5.760A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1677 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: 2.11 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3579 1.35 - 1.47: 3000 1.47 - 1.59: 4901 1.59 - 1.71: 0 1.71 - 1.83: 130 Bond restraints: 11610 Sorted by residual: bond pdb=" C THR S 150 " pdb=" N PRO S 151 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.25e-02 6.40e+03 4.74e+00 bond pdb=" C SER A 281 " pdb=" N PRO A 282 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.22e-02 6.72e+03 4.55e+00 bond pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.18e+00 bond pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 1.465 1.449 0.017 1.19e-02 7.06e+03 1.93e+00 bond pdb=" CA ALA A 203 " pdb=" C ALA A 203 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.14e-02 7.69e+03 1.86e+00 ... (remaining 11605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 15441 2.28 - 4.56: 255 4.56 - 6.83: 51 6.83 - 9.11: 6 9.11 - 11.39: 6 Bond angle restraints: 15759 Sorted by residual: angle pdb=" N PRO R 32 " pdb=" CA PRO R 32 " pdb=" C PRO R 32 " ideal model delta sigma weight residual 113.53 107.45 6.08 1.39e+00 5.18e-01 1.92e+01 angle pdb=" CB MET Q 36 " pdb=" CG MET Q 36 " pdb=" SD MET Q 36 " ideal model delta sigma weight residual 112.70 124.09 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 128.63 -7.09 1.91e+00 2.74e-01 1.38e+01 angle pdb=" CA MET Q 272 " pdb=" CB MET Q 272 " pdb=" CG MET Q 272 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA PRO Q 213 " pdb=" N PRO Q 213 " pdb=" CD PRO Q 213 " ideal model delta sigma weight residual 112.00 107.22 4.78 1.40e+00 5.10e-01 1.17e+01 ... (remaining 15754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5951 17.98 - 35.95: 683 35.95 - 53.93: 152 53.93 - 71.91: 36 71.91 - 89.89: 7 Dihedral angle restraints: 6829 sinusoidal: 2630 harmonic: 4199 Sorted by residual: dihedral pdb=" CB CYS Q 102 " pdb=" SG CYS Q 102 " pdb=" SG CYS Q 181 " pdb=" CB CYS Q 181 " ideal model delta sinusoidal sigma weight residual 93.00 171.75 -78.75 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 281 " pdb=" CB CYS R 281 " ideal model delta sinusoidal sigma weight residual 93.00 21.13 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CA HIS Q 278 " pdb=" C HIS Q 278 " pdb=" N TRP Q 279 " pdb=" CA TRP Q 279 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 6826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1282 0.041 - 0.082: 383 0.082 - 0.123: 111 0.123 - 0.164: 16 0.164 - 0.205: 5 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CB ILE S 51 " pdb=" CA ILE S 51 " pdb=" CG1 ILE S 51 " pdb=" CG2 ILE S 51 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE R 109 " pdb=" CA ILE R 109 " pdb=" CG1 ILE R 109 " pdb=" CG2 ILE R 109 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU Q 276 " pdb=" CB LEU Q 276 " pdb=" CD1 LEU Q 276 " pdb=" CD2 LEU Q 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 1794 not shown) Planarity restraints: 1968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 95 " -0.033 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP Q 95 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 95 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 95 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 95 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 95 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 95 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 95 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 95 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 95 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL Q 212 " 0.051 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO Q 213 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO Q 213 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO Q 213 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 262 " 0.047 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO R 263 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO R 263 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 263 " 0.040 5.00e-02 4.00e+02 ... (remaining 1965 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 296 2.68 - 3.24: 11998 3.24 - 3.79: 19320 3.79 - 4.35: 25701 4.35 - 4.90: 40754 Nonbonded interactions: 98069 Sorted by model distance: nonbonded pdb=" OH TYR R 221 " pdb=" OH TYR R 309 " model vdw 2.128 3.040 nonbonded pdb=" O ALA Q 74 " pdb=" OG1 THR Q 77 " model vdw 2.143 3.040 nonbonded pdb=" O LEU Q 120 " pdb=" OG SER Q 124 " model vdw 2.164 3.040 nonbonded pdb=" O VAL R 203 " pdb=" OG1 THR R 206 " model vdw 2.197 3.040 nonbonded pdb=" O PHE Q 39 " pdb=" OG1 THR Q 43 " model vdw 2.225 3.040 ... (remaining 98064 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 'Q' and (resid 29 through 56 or resid 64 through 310)) selection = (chain 'R' and resid 29 through 310) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11614 Z= 0.165 Angle : 0.755 11.392 15767 Z= 0.397 Chirality : 0.044 0.205 1797 Planarity : 0.005 0.075 1968 Dihedral : 16.122 89.885 4109 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 30.27 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.21), residues: 1420 helix: 0.35 (0.20), residues: 617 sheet: -1.80 (0.32), residues: 243 loop : -2.25 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 242 TYR 0.020 0.002 TYR R 264 PHE 0.030 0.002 PHE Q 118 TRP 0.063 0.002 TRP Q 95 HIS 0.005 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00342 (11610) covalent geometry : angle 0.75255 (15759) SS BOND : bond 0.00302 ( 4) SS BOND : angle 2.53275 ( 8) hydrogen bonds : bond 0.18600 ( 585) hydrogen bonds : angle 6.81240 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.6577 (mpt-90) cc_final: 0.6197 (mpt-90) REVERT: A 333 GLN cc_start: 0.7339 (pp30) cc_final: 0.6847 (pp30) REVERT: B 129 ARG cc_start: 0.6466 (tmt170) cc_final: 0.6159 (tpt90) REVERT: B 175 GLN cc_start: 0.7083 (mm110) cc_final: 0.6863 (mm110) REVERT: B 188 MET cc_start: 0.6774 (mmp) cc_final: 0.6556 (mmm) REVERT: B 339 TRP cc_start: 0.6473 (m100) cc_final: 0.5805 (m100) REVERT: R 91 ARG cc_start: 0.6954 (mtp-110) cc_final: 0.6705 (mtp-110) REVERT: R 133 ARG cc_start: 0.7373 (mtp85) cc_final: 0.7116 (mtp85) REVERT: R 245 ARG cc_start: 0.6716 (ttm170) cc_final: 0.6440 (ttm170) REVERT: S 179 GLN cc_start: 0.7502 (pp30) cc_final: 0.7200 (pp30) REVERT: S 186 GLN cc_start: 0.7304 (mt0) cc_final: 0.7030 (mt0) REVERT: Q 76 LEU cc_start: 0.7997 (mp) cc_final: 0.7716 (mp) REVERT: Q 294 CYS cc_start: 0.6499 (m) cc_final: 0.6130 (m) REVERT: Q 304 LEU cc_start: 0.7863 (mt) cc_final: 0.7624 (mt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1282 time to fit residues: 55.7419 Evaluate side-chains 304 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 305 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.169037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146232 restraints weight = 21609.657| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.25 r_work: 0.3889 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11614 Z= 0.179 Angle : 0.693 9.893 15767 Z= 0.359 Chirality : 0.044 0.178 1797 Planarity : 0.005 0.048 1968 Dihedral : 4.589 20.490 1568 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.79 % Allowed : 25.99 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.22), residues: 1420 helix: 0.56 (0.20), residues: 639 sheet: -1.79 (0.31), residues: 246 loop : -2.33 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.013 0.002 TYR B 264 PHE 0.023 0.002 PHE R 311 TRP 0.049 0.002 TRP Q 95 HIS 0.008 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00384 (11610) covalent geometry : angle 0.69093 (15759) SS BOND : bond 0.00539 ( 4) SS BOND : angle 2.64621 ( 8) hydrogen bonds : bond 0.05042 ( 585) hydrogen bonds : angle 5.41435 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.6026 (tp30) cc_final: 0.5554 (tp30) REVERT: A 242 ARG cc_start: 0.7056 (mpt-90) cc_final: 0.6342 (mpt-90) REVERT: A 243 MET cc_start: 0.6974 (mmt) cc_final: 0.6505 (mtm) REVERT: A 256 ASN cc_start: 0.6889 (t0) cc_final: 0.6592 (t0) REVERT: A 287 TYR cc_start: 0.4537 (OUTLIER) cc_final: 0.4315 (p90) REVERT: A 305 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7393 (p) REVERT: A 308 GLU cc_start: 0.7301 (pp20) cc_final: 0.6982 (pp20) REVERT: A 313 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6631 (ptp90) REVERT: A 331 ASN cc_start: 0.7142 (m-40) cc_final: 0.6856 (m-40) REVERT: A 333 GLN cc_start: 0.7889 (pp30) cc_final: 0.7374 (pp30) REVERT: A 341 ASP cc_start: 0.8179 (t0) cc_final: 0.7825 (t0) REVERT: A 345 LYS cc_start: 0.6849 (mptp) cc_final: 0.6640 (mttp) REVERT: A 349 LYS cc_start: 0.6564 (mmtt) cc_final: 0.6332 (mmtt) REVERT: B 339 TRP cc_start: 0.6790 (m100) cc_final: 0.6486 (m100) REVERT: C 60 LYS cc_start: 0.5625 (tptp) cc_final: 0.4977 (mmmm) REVERT: C 71 TYR cc_start: 0.7373 (t80) cc_final: 0.7149 (t80) REVERT: R 133 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6990 (mtp85) REVERT: R 245 ARG cc_start: 0.7135 (ttm170) cc_final: 0.6725 (ttm170) REVERT: S 105 SER cc_start: 0.8238 (p) cc_final: 0.7982 (m) REVERT: S 172 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7844 (p) REVERT: S 175 TYR cc_start: 0.7606 (m-80) cc_final: 0.7335 (m-80) REVERT: S 179 GLN cc_start: 0.7608 (pp30) cc_final: 0.7105 (pp30) REVERT: S 186 GLN cc_start: 0.7962 (mt0) cc_final: 0.7686 (mt0) REVERT: Q 36 MET cc_start: 0.5924 (tmm) cc_final: 0.5698 (tmm) REVERT: Q 114 TYR cc_start: 0.7772 (m-80) cc_final: 0.7547 (m-80) REVERT: Q 118 PHE cc_start: 0.7566 (m-80) cc_final: 0.7249 (m-80) REVERT: Q 304 LEU cc_start: 0.7947 (mt) cc_final: 0.7638 (mt) outliers start: 47 outliers final: 31 residues processed: 363 average time/residue: 0.1111 time to fit residues: 55.0895 Evaluate side-chains 352 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 38 optimal weight: 0.0020 chunk 22 optimal weight: 4.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 347 ASN B 132 ASN B 176 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.168941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146398 restraints weight = 21906.399| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.26 r_work: 0.3889 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11614 Z= 0.140 Angle : 0.640 9.801 15767 Z= 0.331 Chirality : 0.042 0.158 1797 Planarity : 0.004 0.039 1968 Dihedral : 4.422 20.032 1568 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.68 % Allowed : 25.34 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.22), residues: 1420 helix: 0.69 (0.20), residues: 636 sheet: -1.67 (0.31), residues: 254 loop : -2.31 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.012 0.001 TYR Q 264 PHE 0.023 0.001 PHE R 311 TRP 0.056 0.002 TRP Q 95 HIS 0.010 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00303 (11610) covalent geometry : angle 0.63831 (15759) SS BOND : bond 0.00618 ( 4) SS BOND : angle 2.25923 ( 8) hydrogen bonds : bond 0.04396 ( 585) hydrogen bonds : angle 5.14291 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 315 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.5876 (tp30) cc_final: 0.5516 (tp30) REVERT: A 242 ARG cc_start: 0.7070 (mpt-90) cc_final: 0.6524 (mpt-90) REVERT: A 256 ASN cc_start: 0.6967 (t0) cc_final: 0.6640 (t0) REVERT: A 274 PHE cc_start: 0.7065 (t80) cc_final: 0.6722 (t80) REVERT: A 308 GLU cc_start: 0.7246 (pp20) cc_final: 0.7021 (tp30) REVERT: A 311 ASN cc_start: 0.6850 (p0) cc_final: 0.6132 (p0) REVERT: A 313 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6539 (ptp90) REVERT: A 331 ASN cc_start: 0.7094 (m-40) cc_final: 0.6753 (m-40) REVERT: A 333 GLN cc_start: 0.7827 (pp30) cc_final: 0.7321 (pp30) REVERT: A 341 ASP cc_start: 0.8313 (t70) cc_final: 0.8040 (t0) REVERT: A 348 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6246 (mm) REVERT: B 129 ARG cc_start: 0.7110 (tmt170) cc_final: 0.6894 (tmt170) REVERT: B 188 MET cc_start: 0.7052 (mmp) cc_final: 0.6812 (mmm) REVERT: B 209 LYS cc_start: 0.7568 (mtpt) cc_final: 0.6848 (mtpp) REVERT: B 260 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5405 (tp30) REVERT: B 339 TRP cc_start: 0.6738 (m100) cc_final: 0.6484 (m100) REVERT: C 71 TYR cc_start: 0.7376 (t80) cc_final: 0.7130 (t80) REVERT: R 91 ARG cc_start: 0.7325 (mtm110) cc_final: 0.7101 (mtm110) REVERT: R 133 ARG cc_start: 0.7382 (mtp85) cc_final: 0.6934 (mtp85) REVERT: S 105 SER cc_start: 0.8260 (p) cc_final: 0.7991 (m) REVERT: S 172 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7844 (p) REVERT: S 179 GLN cc_start: 0.7538 (pp30) cc_final: 0.6957 (pp30) REVERT: S 186 GLN cc_start: 0.7860 (mt0) cc_final: 0.7576 (mt0) REVERT: Q 36 MET cc_start: 0.6087 (tmm) cc_final: 0.5792 (tmm) REVERT: Q 118 PHE cc_start: 0.7620 (m-80) cc_final: 0.7240 (m-80) REVERT: Q 167 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6351 (tp) REVERT: Q 304 LEU cc_start: 0.7947 (mt) cc_final: 0.7599 (mt) outliers start: 58 outliers final: 37 residues processed: 351 average time/residue: 0.1057 time to fit residues: 51.1330 Evaluate side-chains 346 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 269 ASN B 132 ASN B 176 GLN B 340 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 265 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.167713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145050 restraints weight = 22118.087| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.25 r_work: 0.3863 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11614 Z= 0.165 Angle : 0.655 10.176 15767 Z= 0.339 Chirality : 0.043 0.169 1797 Planarity : 0.004 0.043 1968 Dihedral : 4.488 20.514 1568 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.25 % Allowed : 24.70 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.22), residues: 1420 helix: 0.63 (0.20), residues: 643 sheet: -1.55 (0.31), residues: 256 loop : -2.30 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 91 TYR 0.024 0.002 TYR S 103 PHE 0.025 0.002 PHE R 39 TRP 0.042 0.002 TRP Q 95 HIS 0.010 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00365 (11610) covalent geometry : angle 0.65271 (15759) SS BOND : bond 0.00538 ( 4) SS BOND : angle 2.37780 ( 8) hydrogen bonds : bond 0.04413 ( 585) hydrogen bonds : angle 5.10948 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.6202 (p0) cc_final: 0.5214 (m-30) REVERT: A 240 MET cc_start: 0.4611 (mpp) cc_final: 0.4297 (mpp) REVERT: A 242 ARG cc_start: 0.7431 (mpt-90) cc_final: 0.6830 (mpt-90) REVERT: A 256 ASN cc_start: 0.6989 (t0) cc_final: 0.6673 (t0) REVERT: A 274 PHE cc_start: 0.7128 (t80) cc_final: 0.6849 (t80) REVERT: A 302 TYR cc_start: 0.6068 (t80) cc_final: 0.5732 (t80) REVERT: A 308 GLU cc_start: 0.7321 (pp20) cc_final: 0.7060 (tp30) REVERT: A 311 ASN cc_start: 0.6870 (p0) cc_final: 0.6100 (p0) REVERT: A 313 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6625 (ptp90) REVERT: A 341 ASP cc_start: 0.8392 (t70) cc_final: 0.8029 (t0) REVERT: B 169 TRP cc_start: 0.7519 (m100) cc_final: 0.7312 (m100) REVERT: B 209 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7065 (mtpt) REVERT: B 219 ARG cc_start: 0.7176 (mmp80) cc_final: 0.6726 (mmp-170) REVERT: B 260 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5388 (tp30) REVERT: C 71 TYR cc_start: 0.7379 (t80) cc_final: 0.7119 (t80) REVERT: R 133 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7208 (mtp85) REVERT: R 243 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.7151 (mmt180) REVERT: R 245 ARG cc_start: 0.7164 (ttm170) cc_final: 0.6753 (ttm170) REVERT: S 172 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7898 (p) REVERT: S 179 GLN cc_start: 0.7537 (pp30) cc_final: 0.7022 (pp30) REVERT: S 186 GLN cc_start: 0.7888 (mt0) cc_final: 0.7610 (mt0) REVERT: Q 36 MET cc_start: 0.5928 (tmm) cc_final: 0.5664 (tmm) REVERT: Q 118 PHE cc_start: 0.7360 (m-80) cc_final: 0.7088 (m-80) REVERT: Q 128 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.4628 (p90) REVERT: Q 167 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6642 (tp) REVERT: Q 216 ILE cc_start: 0.7648 (tt) cc_final: 0.7432 (tp) REVERT: Q 304 LEU cc_start: 0.7948 (mt) cc_final: 0.7601 (mt) outliers start: 65 outliers final: 50 residues processed: 355 average time/residue: 0.1094 time to fit residues: 53.7352 Evaluate side-chains 361 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 265 HIS Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 163 LYS Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 232 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 0.0370 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 132 ASN B 176 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.168590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.146007 restraints weight = 21866.931| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.23 r_work: 0.3875 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11614 Z= 0.138 Angle : 0.640 9.948 15767 Z= 0.327 Chirality : 0.042 0.175 1797 Planarity : 0.004 0.043 1968 Dihedral : 4.348 20.477 1568 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.33 % Allowed : 25.99 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.22), residues: 1420 helix: 0.71 (0.20), residues: 643 sheet: -1.45 (0.31), residues: 247 loop : -2.27 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 91 TYR 0.019 0.001 TYR S 103 PHE 0.019 0.001 PHE R 311 TRP 0.029 0.002 TRP Q 95 HIS 0.010 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00300 (11610) covalent geometry : angle 0.63801 (15759) SS BOND : bond 0.00648 ( 4) SS BOND : angle 2.18408 ( 8) hydrogen bonds : bond 0.04107 ( 585) hydrogen bonds : angle 4.99553 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 324 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5695 (p0) cc_final: 0.4908 (m-30) REVERT: A 240 MET cc_start: 0.4702 (mpp) cc_final: 0.4397 (mpp) REVERT: A 242 ARG cc_start: 0.7473 (mpt-90) cc_final: 0.6846 (mpt-90) REVERT: A 256 ASN cc_start: 0.7006 (t0) cc_final: 0.6667 (t0) REVERT: A 274 PHE cc_start: 0.7124 (t80) cc_final: 0.6801 (t80) REVERT: A 302 TYR cc_start: 0.6066 (t80) cc_final: 0.5768 (t80) REVERT: A 308 GLU cc_start: 0.7293 (pp20) cc_final: 0.7085 (tp30) REVERT: A 311 ASN cc_start: 0.6815 (p0) cc_final: 0.6212 (p0) REVERT: A 313 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6640 (ptp90) REVERT: A 318 GLU cc_start: 0.7021 (pm20) cc_final: 0.6781 (pm20) REVERT: A 319 ILE cc_start: 0.8306 (pt) cc_final: 0.8005 (pt) REVERT: A 333 GLN cc_start: 0.7708 (pp30) cc_final: 0.7355 (pp30) REVERT: A 341 ASP cc_start: 0.8368 (t70) cc_final: 0.7854 (t0) REVERT: A 345 LYS cc_start: 0.7197 (mttp) cc_final: 0.6849 (mttp) REVERT: B 45 MET cc_start: 0.6523 (ptp) cc_final: 0.6269 (ptp) REVERT: B 129 ARG cc_start: 0.7215 (tmt170) cc_final: 0.6915 (tmt170) REVERT: B 209 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7151 (mtpt) REVERT: B 219 ARG cc_start: 0.7157 (mmp80) cc_final: 0.6717 (mmp-170) REVERT: B 228 ASP cc_start: 0.7468 (p0) cc_final: 0.7197 (p0) REVERT: B 260 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5419 (tp30) REVERT: R 133 ARG cc_start: 0.7457 (mtp85) cc_final: 0.7120 (mtp85) REVERT: R 215 THR cc_start: 0.4946 (OUTLIER) cc_final: 0.4540 (m) REVERT: R 236 ARG cc_start: 0.5800 (mmp80) cc_final: 0.5517 (mmp80) REVERT: R 245 ARG cc_start: 0.7180 (ttm170) cc_final: 0.6765 (ttm170) REVERT: S 172 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7942 (p) REVERT: S 179 GLN cc_start: 0.7511 (pp30) cc_final: 0.6986 (pp30) REVERT: S 186 GLN cc_start: 0.7842 (mt0) cc_final: 0.7584 (mt0) REVERT: Q 36 MET cc_start: 0.6135 (tmm) cc_final: 0.5877 (tmm) REVERT: Q 128 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.4747 (p90) REVERT: Q 167 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6647 (tp) REVERT: Q 216 ILE cc_start: 0.7646 (tt) cc_final: 0.7423 (tp) REVERT: Q 262 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5850 (tpt) REVERT: Q 304 LEU cc_start: 0.7929 (mt) cc_final: 0.7577 (mt) outliers start: 66 outliers final: 44 residues processed: 368 average time/residue: 0.1017 time to fit residues: 51.1842 Evaluate side-chains 368 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 163 LYS Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 132 ASN B 176 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.169539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146932 restraints weight = 21883.051| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.25 r_work: 0.3892 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11614 Z= 0.127 Angle : 0.636 10.590 15767 Z= 0.322 Chirality : 0.041 0.161 1797 Planarity : 0.004 0.042 1968 Dihedral : 4.242 19.249 1568 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.17 % Allowed : 26.55 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.22), residues: 1420 helix: 0.83 (0.20), residues: 644 sheet: -1.54 (0.32), residues: 240 loop : -2.11 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 127 TYR 0.021 0.001 TYR S 103 PHE 0.020 0.001 PHE A 191 TRP 0.022 0.002 TRP Q 95 HIS 0.007 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00272 (11610) covalent geometry : angle 0.63481 (15759) SS BOND : bond 0.00369 ( 4) SS BOND : angle 1.89269 ( 8) hydrogen bonds : bond 0.03872 ( 585) hydrogen bonds : angle 4.90494 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.5575 (ptpp) cc_final: 0.5218 (ttmt) REVERT: A 198 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7407 (mmm) REVERT: A 229 ASP cc_start: 0.6023 (p0) cc_final: 0.5036 (m-30) REVERT: A 240 MET cc_start: 0.4729 (mpp) cc_final: 0.4421 (mpp) REVERT: A 242 ARG cc_start: 0.7494 (mpt-90) cc_final: 0.6790 (mpt-90) REVERT: A 256 ASN cc_start: 0.7060 (t0) cc_final: 0.6717 (t0) REVERT: A 274 PHE cc_start: 0.7155 (t80) cc_final: 0.6769 (t80) REVERT: A 302 TYR cc_start: 0.6185 (t80) cc_final: 0.5943 (t80) REVERT: A 311 ASN cc_start: 0.6762 (p0) cc_final: 0.6306 (p0) REVERT: A 313 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6558 (ptp90) REVERT: A 333 GLN cc_start: 0.7601 (pp30) cc_final: 0.7282 (pp30) REVERT: A 341 ASP cc_start: 0.8395 (t70) cc_final: 0.8153 (t0) REVERT: A 349 LYS cc_start: 0.6551 (mmtt) cc_final: 0.6318 (mmtt) REVERT: B 45 MET cc_start: 0.6448 (ptp) cc_final: 0.6222 (ptp) REVERT: B 129 ARG cc_start: 0.7341 (tmt170) cc_final: 0.7114 (tmt170) REVERT: B 175 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6663 (mm110) REVERT: B 228 ASP cc_start: 0.7550 (p0) cc_final: 0.7322 (p0) REVERT: B 260 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5365 (tp30) REVERT: R 133 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7055 (mtp85) REVERT: R 236 ARG cc_start: 0.5781 (mmp80) cc_final: 0.5486 (mmp80) REVERT: R 291 PHE cc_start: 0.8184 (t80) cc_final: 0.7844 (t80) REVERT: S 179 GLN cc_start: 0.7509 (pp30) cc_final: 0.6955 (pp30) REVERT: S 186 GLN cc_start: 0.7807 (mt0) cc_final: 0.7551 (mt0) REVERT: Q 36 MET cc_start: 0.6115 (tmm) cc_final: 0.5652 (tmm) REVERT: Q 128 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.4762 (p90) REVERT: Q 167 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6555 (tp) REVERT: Q 216 ILE cc_start: 0.7599 (tt) cc_final: 0.7389 (tp) REVERT: Q 217 MET cc_start: 0.5812 (mtm) cc_final: 0.5575 (mtm) REVERT: Q 304 LEU cc_start: 0.7927 (mt) cc_final: 0.7585 (mt) outliers start: 64 outliers final: 43 residues processed: 357 average time/residue: 0.1041 time to fit residues: 51.6721 Evaluate side-chains 364 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 232 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 43 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 109 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.170367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.147838 restraints weight = 21824.138| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.23 r_work: 0.3903 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11614 Z= 0.122 Angle : 0.643 10.879 15767 Z= 0.325 Chirality : 0.041 0.182 1797 Planarity : 0.004 0.038 1968 Dihedral : 4.185 18.286 1568 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.00 % Allowed : 26.80 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.22), residues: 1420 helix: 0.95 (0.20), residues: 639 sheet: -1.55 (0.32), residues: 243 loop : -2.14 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 127 TYR 0.027 0.001 TYR S 103 PHE 0.028 0.001 PHE Q 118 TRP 0.019 0.002 TRP Q 197 HIS 0.006 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00271 (11610) covalent geometry : angle 0.64160 (15759) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.71989 ( 8) hydrogen bonds : bond 0.03790 ( 585) hydrogen bonds : angle 4.81092 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 0.466 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 54 LYS cc_start: 0.5521 (ptpp) cc_final: 0.5225 (ttmt) REVERT: A 229 ASP cc_start: 0.5954 (p0) cc_final: 0.4994 (m-30) REVERT: A 242 ARG cc_start: 0.7543 (mpt-90) cc_final: 0.6850 (mpt-90) REVERT: A 256 ASN cc_start: 0.6985 (t0) cc_final: 0.6647 (t0) REVERT: A 274 PHE cc_start: 0.7129 (t80) cc_final: 0.6824 (t80) REVERT: A 302 TYR cc_start: 0.6047 (t80) cc_final: 0.5792 (t80) REVERT: A 313 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6588 (ptp90) REVERT: A 333 GLN cc_start: 0.7489 (pp30) cc_final: 0.7196 (pp30) REVERT: A 341 ASP cc_start: 0.8360 (t70) cc_final: 0.7910 (t0) REVERT: A 349 LYS cc_start: 0.6474 (mmtt) cc_final: 0.6272 (mmtt) REVERT: B 45 MET cc_start: 0.6492 (ptp) cc_final: 0.6273 (ptp) REVERT: B 137 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7794 (mmm-85) REVERT: B 175 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6712 (mm110) REVERT: B 219 ARG cc_start: 0.7258 (mmp80) cc_final: 0.6783 (mmp-170) REVERT: R 133 ARG cc_start: 0.7420 (mtp85) cc_final: 0.6866 (mtp85) REVERT: R 236 ARG cc_start: 0.5758 (mmp80) cc_final: 0.5462 (mmp80) REVERT: R 243 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7151 (mmt180) REVERT: R 245 ARG cc_start: 0.7121 (ttm170) cc_final: 0.6711 (ttm170) REVERT: S 35 HIS cc_start: 0.7968 (m-70) cc_final: 0.7743 (m-70) REVERT: S 179 GLN cc_start: 0.7520 (pp30) cc_final: 0.6966 (pp30) REVERT: S 186 GLN cc_start: 0.7795 (mt0) cc_final: 0.7552 (mt0) REVERT: Q 36 MET cc_start: 0.6088 (tmm) cc_final: 0.5659 (tmm) REVERT: Q 121 THR cc_start: 0.7430 (m) cc_final: 0.7165 (p) REVERT: Q 128 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.4793 (p90) REVERT: Q 216 ILE cc_start: 0.7607 (tt) cc_final: 0.7385 (tp) REVERT: Q 217 MET cc_start: 0.5841 (mtm) cc_final: 0.5622 (mtm) REVERT: Q 262 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5796 (tpt) REVERT: Q 304 LEU cc_start: 0.7948 (mt) cc_final: 0.7605 (mt) outliers start: 62 outliers final: 44 residues processed: 352 average time/residue: 0.1154 time to fit residues: 56.3584 Evaluate side-chains 349 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 163 LYS Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 214 PHE Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 311 ASN B 156 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146507 restraints weight = 21695.746| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.19 r_work: 0.3882 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11614 Z= 0.139 Angle : 0.666 11.201 15767 Z= 0.337 Chirality : 0.042 0.189 1797 Planarity : 0.004 0.050 1968 Dihedral : 4.264 19.676 1568 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.68 % Allowed : 27.20 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.22), residues: 1420 helix: 0.89 (0.20), residues: 645 sheet: -1.39 (0.32), residues: 246 loop : -2.18 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 129 TYR 0.027 0.001 TYR S 103 PHE 0.022 0.001 PHE R 39 TRP 0.026 0.002 TRP Q 95 HIS 0.008 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00307 (11610) covalent geometry : angle 0.66432 (15759) SS BOND : bond 0.00400 ( 4) SS BOND : angle 2.02569 ( 8) hydrogen bonds : bond 0.03895 ( 585) hydrogen bonds : angle 4.86310 ( 1677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 302 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.5571 (ptpp) cc_final: 0.5316 (ttmt) REVERT: A 229 ASP cc_start: 0.6063 (p0) cc_final: 0.4776 (m-30) REVERT: A 241 ASN cc_start: 0.6585 (m-40) cc_final: 0.6138 (m-40) REVERT: A 242 ARG cc_start: 0.7552 (mpt-90) cc_final: 0.7028 (mtt-85) REVERT: A 256 ASN cc_start: 0.7033 (t0) cc_final: 0.6804 (m-40) REVERT: A 302 TYR cc_start: 0.6023 (t80) cc_final: 0.5767 (t80) REVERT: A 313 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6635 (ptp90) REVERT: A 341 ASP cc_start: 0.8281 (t70) cc_final: 0.7940 (t0) REVERT: B 137 ARG cc_start: 0.8006 (mmt90) cc_final: 0.7784 (mmm-85) REVERT: R 125 PHE cc_start: 0.7371 (t80) cc_final: 0.6998 (t80) REVERT: R 133 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7203 (mtp85) REVERT: R 243 ARG cc_start: 0.7385 (mtt180) cc_final: 0.7135 (mmt180) REVERT: R 245 ARG cc_start: 0.7116 (ttm170) cc_final: 0.6693 (ttm170) REVERT: R 291 PHE cc_start: 0.8135 (t80) cc_final: 0.7889 (t80) REVERT: S 18 ARG cc_start: 0.6635 (mmm160) cc_final: 0.6257 (mmm160) REVERT: S 179 GLN cc_start: 0.7543 (pp30) cc_final: 0.6954 (pp30) REVERT: S 186 GLN cc_start: 0.7795 (mt0) cc_final: 0.7546 (mt0) REVERT: Q 36 MET cc_start: 0.5954 (tmm) cc_final: 0.5579 (tmm) REVERT: Q 128 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.4831 (p90) REVERT: Q 167 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6511 (tp) REVERT: Q 216 ILE cc_start: 0.7620 (tt) cc_final: 0.7410 (tp) REVERT: Q 217 MET cc_start: 0.5793 (mtm) cc_final: 0.5439 (mtm) REVERT: Q 262 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5864 (tpt) REVERT: Q 304 LEU cc_start: 0.7972 (mt) cc_final: 0.7644 (mt) outliers start: 58 outliers final: 46 residues processed: 337 average time/residue: 0.1121 time to fit residues: 52.5974 Evaluate side-chains 352 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 302 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 214 PHE Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.168546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145566 restraints weight = 21370.482| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.18 r_work: 0.3874 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11614 Z= 0.170 Angle : 0.697 11.446 15767 Z= 0.358 Chirality : 0.044 0.221 1797 Planarity : 0.004 0.064 1968 Dihedral : 4.418 20.119 1568 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.36 % Allowed : 27.52 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.22), residues: 1420 helix: 0.75 (0.20), residues: 646 sheet: -1.43 (0.32), residues: 243 loop : -2.20 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 68 TYR 0.034 0.002 TYR S 103 PHE 0.024 0.001 PHE R 39 TRP 0.034 0.002 TRP Q 95 HIS 0.010 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00375 (11610) covalent geometry : angle 0.69490 (15759) SS BOND : bond 0.00592 ( 4) SS BOND : angle 2.37162 ( 8) hydrogen bonds : bond 0.04162 ( 585) hydrogen bonds : angle 4.95532 ( 1677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.6511 (OUTLIER) cc_final: 0.5991 (p) REVERT: A 186 GLU cc_start: 0.7449 (tt0) cc_final: 0.6916 (mm-30) REVERT: A 229 ASP cc_start: 0.5921 (p0) cc_final: 0.5291 (m-30) REVERT: A 242 ARG cc_start: 0.7240 (mpt-90) cc_final: 0.6712 (mpt-90) REVERT: A 302 TYR cc_start: 0.6012 (t80) cc_final: 0.5751 (t80) REVERT: A 333 GLN cc_start: 0.7668 (pp30) cc_final: 0.7249 (tm-30) REVERT: A 341 ASP cc_start: 0.8398 (t70) cc_final: 0.8058 (t0) REVERT: B 137 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7837 (mmm-85) REVERT: B 155 ASN cc_start: 0.7471 (t0) cc_final: 0.7135 (t0) REVERT: B 210 LEU cc_start: 0.7956 (tp) cc_final: 0.7735 (tp) REVERT: B 219 ARG cc_start: 0.7495 (mmt180) cc_final: 0.7210 (mmm160) REVERT: R 30 LEU cc_start: 0.6543 (mm) cc_final: 0.6250 (mp) REVERT: R 123 LEU cc_start: 0.7023 (tp) cc_final: 0.6635 (tp) REVERT: R 133 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7087 (mtp85) REVERT: R 167 LEU cc_start: 0.7259 (mp) cc_final: 0.7039 (tp) REVERT: R 243 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7241 (mmt180) REVERT: R 245 ARG cc_start: 0.7143 (ttm170) cc_final: 0.6727 (ttm170) REVERT: S 160 ARG cc_start: 0.6118 (mmm-85) cc_final: 0.5813 (mmm-85) REVERT: S 179 GLN cc_start: 0.7565 (pp30) cc_final: 0.6968 (pp30) REVERT: S 186 GLN cc_start: 0.7856 (mt0) cc_final: 0.7624 (mt0) REVERT: Q 36 MET cc_start: 0.6068 (tmm) cc_final: 0.5705 (tmm) REVERT: Q 128 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.4913 (p90) REVERT: Q 167 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6611 (tp) REVERT: Q 216 ILE cc_start: 0.7607 (tt) cc_final: 0.7394 (tp) REVERT: Q 217 MET cc_start: 0.5824 (mtm) cc_final: 0.5600 (mtm) REVERT: Q 262 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.6047 (tpt) REVERT: Q 304 LEU cc_start: 0.7970 (mt) cc_final: 0.7639 (mt) outliers start: 54 outliers final: 47 residues processed: 343 average time/residue: 0.1116 time to fit residues: 52.6153 Evaluate side-chains 353 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 302 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 214 PHE Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 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 256 ASN A 306 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 305 ASN Q 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.169549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.146856 restraints weight = 21645.618| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.19 r_work: 0.3891 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11614 Z= 0.147 Angle : 0.705 10.189 15767 Z= 0.359 Chirality : 0.044 0.209 1797 Planarity : 0.004 0.048 1968 Dihedral : 4.402 19.473 1568 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.44 % Allowed : 28.17 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.22), residues: 1420 helix: 0.78 (0.20), residues: 643 sheet: -1.48 (0.33), residues: 237 loop : -2.15 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 68 TYR 0.039 0.002 TYR R 264 PHE 0.037 0.002 PHE R 39 TRP 0.031 0.002 TRP Q 197 HIS 0.010 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00330 (11610) covalent geometry : angle 0.70352 (15759) SS BOND : bond 0.00471 ( 4) SS BOND : angle 2.14082 ( 8) hydrogen bonds : bond 0.04049 ( 585) hydrogen bonds : angle 4.95623 ( 1677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 305 time to evaluate : 0.398 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 186 GLU cc_start: 0.7494 (tt0) cc_final: 0.6963 (mm-30) REVERT: A 229 ASP cc_start: 0.6007 (p0) cc_final: 0.5094 (m-30) REVERT: A 242 ARG cc_start: 0.7454 (mpt-90) cc_final: 0.6769 (mpt-90) REVERT: A 302 TYR cc_start: 0.5937 (t80) cc_final: 0.5677 (t80) REVERT: A 333 GLN cc_start: 0.7652 (pp30) cc_final: 0.7160 (tm-30) REVERT: A 341 ASP cc_start: 0.8393 (t70) cc_final: 0.8102 (t0) REVERT: B 14 LEU cc_start: 0.8116 (mm) cc_final: 0.7700 (pt) REVERT: B 137 ARG cc_start: 0.8049 (mmt90) cc_final: 0.7829 (mmm-85) REVERT: B 155 ASN cc_start: 0.7505 (t0) cc_final: 0.7142 (t0) REVERT: B 210 LEU cc_start: 0.7905 (tp) cc_final: 0.7703 (tp) REVERT: B 219 ARG cc_start: 0.7535 (mmt180) cc_final: 0.7275 (mmm160) REVERT: R 30 LEU cc_start: 0.6599 (mm) cc_final: 0.6294 (mp) REVERT: R 50 LEU cc_start: 0.7455 (mt) cc_final: 0.7217 (mp) REVERT: R 133 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7015 (mtp85) REVERT: R 167 LEU cc_start: 0.7221 (mp) cc_final: 0.7009 (tp) REVERT: R 215 THR cc_start: 0.4965 (OUTLIER) cc_final: 0.4559 (m) REVERT: R 243 ARG cc_start: 0.7415 (mtt180) cc_final: 0.7194 (mmt180) REVERT: R 245 ARG cc_start: 0.7156 (ttm170) cc_final: 0.6712 (ttm170) REVERT: S 6 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: S 102 TYR cc_start: 0.8069 (p90) cc_final: 0.7675 (p90) REVERT: S 160 ARG cc_start: 0.6214 (mmm-85) cc_final: 0.6007 (mmm-85) REVERT: S 179 GLN cc_start: 0.7549 (pp30) cc_final: 0.6941 (pp30) REVERT: S 186 GLN cc_start: 0.7814 (mt0) cc_final: 0.7557 (mt0) REVERT: Q 36 MET cc_start: 0.6039 (tmm) cc_final: 0.5696 (tmm) REVERT: Q 128 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5038 (p90) REVERT: Q 166 VAL cc_start: 0.7688 (p) cc_final: 0.7442 (m) REVERT: Q 167 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6655 (tp) REVERT: Q 262 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6032 (tpt) REVERT: Q 304 LEU cc_start: 0.7981 (mt) cc_final: 0.7612 (mt) outliers start: 55 outliers final: 46 residues processed: 338 average time/residue: 0.0995 time to fit residues: 47.1409 Evaluate side-chains 352 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 261 TRP Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 214 PHE Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 31 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.169458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.146852 restraints weight = 21603.455| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 3.20 r_work: 0.3893 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.254 11614 Z= 0.244 Angle : 0.968 59.198 15767 Z= 0.551 Chirality : 0.047 0.694 1797 Planarity : 0.004 0.050 1968 Dihedral : 4.426 21.759 1568 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.28 % Allowed : 28.33 % Favored : 67.39 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.22), residues: 1420 helix: 0.77 (0.20), residues: 644 sheet: -1.49 (0.33), residues: 237 loop : -2.17 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 197 TYR 0.036 0.002 TYR R 264 PHE 0.041 0.002 PHE S 212 TRP 0.026 0.002 TRP Q 197 HIS 0.006 0.001 HIS R 265 Details of bonding type rmsd covalent geometry : bond 0.00563 (11610) covalent geometry : angle 0.96707 (15759) SS BOND : bond 0.00487 ( 4) SS BOND : angle 2.11921 ( 8) hydrogen bonds : bond 0.04102 ( 585) hydrogen bonds : angle 4.95817 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.35 seconds wall clock time: 45 minutes 26.53 seconds (2726.53 seconds total)