Starting phenix.real_space_refine on Wed May 14 02:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqe_38574/05_2025/8xqe_38574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqe_38574/05_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_38574/05_2025/8xqe_38574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqe_38574/05_2025/8xqe_38574.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqe_38574/05_2025/8xqe_38574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqe_38574/05_2025/8xqe_38574.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.041 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.50, per 1000 atoms: 0.57 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: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.18 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: 3.10 Time building geometry restraints manager: 3.23 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.100 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- 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 : 20.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (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 TRP 0.063 0.002 TRP Q 95 HIS 0.005 0.001 HIS R 265 PHE 0.030 0.002 PHE Q 118 TYR 0.020 0.002 TYR R 264 ARG 0.008 0.001 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.18600 ( 585) hydrogen bonds : angle 6.81240 ( 1677) SS BOND : bond 0.00302 ( 4) SS BOND : angle 2.53275 ( 8) covalent geometry : bond 0.00342 (11610) covalent geometry : angle 0.75255 (15759) *********************** 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 : 1.186 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 94 ASP cc_start: 0.6848 (m-30) cc_final: 0.6635 (m-30) 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: 0.7717 (mp) REVERT: Q 294 CYS cc_start: 0.6499 (m) cc_final: 0.6129 (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: 0.2531 time to fit residues: 109.1736 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 : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.145498 restraints weight = 21580.171| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.19 r_work: 0.3882 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11614 Z= 0.195 Angle : 0.703 9.947 15767 Z= 0.366 Chirality : 0.044 0.178 1797 Planarity : 0.005 0.048 1968 Dihedral : 4.658 21.274 1568 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.04 % Allowed : 25.42 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.22), residues: 1420 helix: 0.52 (0.20), residues: 639 sheet: -1.82 (0.31), residues: 246 loop : -2.34 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP Q 95 HIS 0.008 0.001 HIS R 265 PHE 0.023 0.002 PHE R 311 TYR 0.015 0.002 TYR S 190 ARG 0.005 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 585) hydrogen bonds : angle 5.44449 ( 1677) SS BOND : bond 0.00583 ( 4) SS BOND : angle 2.73526 ( 8) covalent geometry : bond 0.00416 (11610) covalent geometry : angle 0.70065 (15759) *********************** 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 384 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.6059 (tp30) cc_final: 0.5625 (tp30) REVERT: A 229 ASP cc_start: 0.5014 (p0) cc_final: 0.4791 (p0) REVERT: A 242 ARG cc_start: 0.7033 (mpt-90) cc_final: 0.6325 (mpt-90) REVERT: A 243 MET cc_start: 0.6984 (mmt) cc_final: 0.6509 (mtm) REVERT: A 256 ASN cc_start: 0.6808 (t0) cc_final: 0.6526 (t0) REVERT: A 287 TYR cc_start: 0.4547 (OUTLIER) cc_final: 0.4319 (p90) REVERT: A 305 CYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7407 (p) REVERT: A 308 GLU cc_start: 0.7276 (pp20) cc_final: 0.6961 (pp20) REVERT: A 313 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6616 (ptp90) REVERT: A 333 GLN cc_start: 0.7886 (pp30) cc_final: 0.7369 (pp30) REVERT: A 341 ASP cc_start: 0.8178 (t0) cc_final: 0.7802 (t0) REVERT: A 345 LYS cc_start: 0.6949 (mptp) cc_final: 0.6715 (mttp) REVERT: A 349 LYS cc_start: 0.6566 (mmtt) cc_final: 0.6335 (mmtt) REVERT: B 339 TRP cc_start: 0.6847 (m100) cc_final: 0.6509 (m100) REVERT: C 60 LYS cc_start: 0.5630 (tptp) cc_final: 0.4997 (mmmm) REVERT: C 71 TYR cc_start: 0.7376 (t80) cc_final: 0.7112 (t80) REVERT: R 91 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.6985 (mtm110) REVERT: R 94 ASP cc_start: 0.7240 (m-30) cc_final: 0.6919 (m-30) REVERT: R 133 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6849 (mtp85) REVERT: R 245 ARG cc_start: 0.7111 (ttm170) cc_final: 0.6705 (ttm170) REVERT: S 95 TYR cc_start: 0.7846 (m-80) cc_final: 0.7635 (m-80) REVERT: S 105 SER cc_start: 0.8240 (p) cc_final: 0.8015 (m) REVERT: S 172 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7842 (p) REVERT: S 175 TYR cc_start: 0.7639 (m-80) cc_final: 0.7389 (m-80) REVERT: S 179 GLN cc_start: 0.7642 (pp30) cc_final: 0.7135 (pp30) REVERT: S 186 GLN cc_start: 0.7921 (mt0) cc_final: 0.7662 (mt0) REVERT: Q 36 MET cc_start: 0.5897 (tmm) cc_final: 0.5663 (tmm) REVERT: Q 114 TYR cc_start: 0.7818 (m-80) cc_final: 0.7607 (m-80) REVERT: Q 118 PHE cc_start: 0.7574 (m-80) cc_final: 0.7277 (m-80) REVERT: Q 294 CYS cc_start: 0.7059 (m) cc_final: 0.6789 (m) REVERT: Q 304 LEU cc_start: 0.7943 (mt) cc_final: 0.7621 (mt) outliers start: 50 outliers final: 33 residues processed: 365 average time/residue: 0.2718 time to fit residues: 135.0141 Evaluate side-chains 361 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 324 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 49 VAL 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 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 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 83 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 132 ASN B 176 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 305 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.167661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145440 restraints weight = 21805.685| |-----------------------------------------------------------------------------| r_work (start): 0.4004 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: 0.6660 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11614 Z= 0.152 Angle : 0.656 10.302 15767 Z= 0.339 Chirality : 0.043 0.167 1797 Planarity : 0.004 0.042 1968 Dihedral : 4.518 20.717 1568 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.28 % Allowed : 25.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1420 helix: 0.67 (0.20), residues: 637 sheet: -1.66 (0.31), residues: 254 loop : -2.36 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Q 95 HIS 0.009 0.001 HIS R 265 PHE 0.024 0.001 PHE R 311 TYR 0.014 0.001 TYR R 264 ARG 0.005 0.000 ARG R 91 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 585) hydrogen bonds : angle 5.19763 ( 1677) SS BOND : bond 0.00670 ( 4) SS BOND : angle 2.34383 ( 8) covalent geometry : bond 0.00327 (11610) covalent geometry : angle 0.65379 (15759) *********************** 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 374 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7447 (mm110) cc_final: 0.6955 (mm-40) REVERT: A 229 ASP cc_start: 0.5167 (p0) cc_final: 0.4506 (m-30) REVERT: A 242 ARG cc_start: 0.7229 (mpt-90) cc_final: 0.6624 (mpt-90) REVERT: A 256 ASN cc_start: 0.6897 (t0) cc_final: 0.6597 (t0) REVERT: A 274 PHE cc_start: 0.7083 (t80) cc_final: 0.6741 (t80) REVERT: A 311 ASN cc_start: 0.6882 (p0) cc_final: 0.6484 (p0) REVERT: A 313 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6567 (ptp90) REVERT: A 333 GLN cc_start: 0.7841 (pp30) cc_final: 0.7342 (pp30) REVERT: A 341 ASP cc_start: 0.8257 (t70) cc_final: 0.7989 (t0) REVERT: A 347 ASN cc_start: 0.5824 (m-40) cc_final: 0.5557 (t0) REVERT: A 348 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6296 (mm) REVERT: B 129 ARG cc_start: 0.7125 (tmt170) cc_final: 0.6896 (tmt170) REVERT: B 188 MET cc_start: 0.7114 (mmp) cc_final: 0.6872 (mmm) REVERT: B 209 LYS cc_start: 0.7601 (mtpt) cc_final: 0.7080 (mtpt) REVERT: B 260 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5482 (tp30) REVERT: B 339 TRP cc_start: 0.6817 (m100) cc_final: 0.6499 (m100) REVERT: C 71 TYR cc_start: 0.7380 (t80) cc_final: 0.7098 (t80) REVERT: R 94 ASP cc_start: 0.7158 (m-30) cc_final: 0.6902 (m-30) REVERT: R 133 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7224 (mtp85) REVERT: R 245 ARG cc_start: 0.7108 (ttm170) cc_final: 0.6691 (ttm170) REVERT: S 105 SER cc_start: 0.8281 (p) cc_final: 0.8056 (m) REVERT: S 172 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7858 (p) REVERT: S 179 GLN cc_start: 0.7558 (pp30) cc_final: 0.6966 (pp30) REVERT: S 186 GLN cc_start: 0.7855 (mt0) cc_final: 0.7568 (mt0) REVERT: Q 36 MET cc_start: 0.6060 (tmm) cc_final: 0.5782 (tmm) REVERT: Q 118 PHE cc_start: 0.7616 (m-80) cc_final: 0.7251 (m-80) REVERT: Q 294 CYS cc_start: 0.6956 (m) cc_final: 0.6685 (m) REVERT: Q 304 LEU cc_start: 0.7926 (mt) cc_final: 0.7569 (mt) outliers start: 53 outliers final: 35 residues processed: 353 average time/residue: 0.2631 time to fit residues: 126.9711 Evaluate side-chains 351 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 39 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 348 LEU Chi-restraints excluded: chain B residue 15 LYS 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 271 CYS 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 R residue 99 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 247 LEU 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 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 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 215 THR 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 19 optimal weight: 2.9990 chunk 123 optimal weight: 0.0770 chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN A 347 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 = 0.4290 r_free = 0.4290 target = 0.167660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.144941 restraints weight = 21883.197| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.23 r_work: 0.3863 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11614 Z= 0.158 Angle : 0.652 9.811 15767 Z= 0.338 Chirality : 0.042 0.169 1797 Planarity : 0.004 0.044 1968 Dihedral : 4.517 20.472 1568 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.05 % Allowed : 24.54 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1420 helix: 0.65 (0.20), residues: 643 sheet: -1.53 (0.31), residues: 256 loop : -2.30 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 95 HIS 0.010 0.001 HIS R 265 PHE 0.023 0.001 PHE R 311 TYR 0.027 0.002 TYR S 103 ARG 0.007 0.000 ARG R 91 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 585) hydrogen bonds : angle 5.10555 ( 1677) SS BOND : bond 0.00611 ( 4) SS BOND : angle 2.44154 ( 8) covalent geometry : bond 0.00349 (11610) covalent geometry : angle 0.64988 (15759) *********************** 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 398 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 323 time to evaluate : 1.399 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: symmetry clash REVERT: A 229 ASP cc_start: 0.5891 (p0) cc_final: 0.4715 (m-30) REVERT: A 240 MET cc_start: 0.4619 (mpp) cc_final: 0.4319 (mpp) REVERT: A 242 ARG cc_start: 0.7498 (mpt-90) cc_final: 0.6842 (mpt-90) REVERT: A 256 ASN cc_start: 0.6992 (t0) cc_final: 0.6700 (t0) REVERT: A 274 PHE cc_start: 0.7160 (t80) cc_final: 0.6824 (t80) REVERT: A 302 TYR cc_start: 0.6101 (t80) cc_final: 0.5740 (t80) REVERT: A 311 ASN cc_start: 0.6578 (p0) cc_final: 0.6337 (p0) REVERT: A 313 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6644 (ptp90) REVERT: A 341 ASP cc_start: 0.8378 (t70) cc_final: 0.7570 (t0) REVERT: A 345 LYS cc_start: 0.7166 (mttp) cc_final: 0.6707 (mptp) REVERT: A 349 LYS cc_start: 0.6477 (mmtt) cc_final: 0.6243 (mmtt) REVERT: B 188 MET cc_start: 0.7089 (mmp) cc_final: 0.6885 (mmm) REVERT: B 209 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7046 (mtpt) REVERT: B 260 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5373 (tp30) REVERT: C 71 TYR cc_start: 0.7370 (t80) cc_final: 0.7155 (t80) REVERT: R 91 ARG cc_start: 0.7406 (mtp-110) cc_final: 0.6804 (mtm110) REVERT: R 94 ASP cc_start: 0.7236 (m-30) cc_final: 0.6739 (m-30) REVERT: R 133 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7202 (mtp85) REVERT: R 215 THR cc_start: 0.4824 (OUTLIER) cc_final: 0.4233 (m) REVERT: R 245 ARG cc_start: 0.7127 (ttm170) cc_final: 0.6719 (ttm170) REVERT: S 95 TYR cc_start: 0.7900 (m-80) cc_final: 0.7683 (m-80) REVERT: S 172 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7891 (p) REVERT: S 179 GLN cc_start: 0.7536 (pp30) cc_final: 0.6975 (pp30) REVERT: S 186 GLN cc_start: 0.7886 (mt0) cc_final: 0.7617 (mt0) REVERT: Q 36 MET cc_start: 0.6115 (tmm) cc_final: 0.5805 (tmm) REVERT: Q 118 PHE cc_start: 0.7374 (m-80) cc_final: 0.7095 (m-80) REVERT: Q 128 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.4702 (p90) REVERT: Q 167 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.6811 (tp) REVERT: Q 216 ILE cc_start: 0.7464 (tt) cc_final: 0.7255 (tp) REVERT: Q 276 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6845 (mm) REVERT: Q 294 CYS cc_start: 0.7017 (m) cc_final: 0.6765 (m) REVERT: Q 304 LEU cc_start: 0.7942 (mt) cc_final: 0.7583 (mt) outliers start: 75 outliers final: 54 residues processed: 368 average time/residue: 0.2481 time to fit residues: 126.1676 Evaluate side-chains 371 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 310 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 308 GLU 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 335 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 ASN 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 75 GLN 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 271 CYS 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 198 GLU Chi-restraints excluded: chain R residue 215 THR 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 269 THR 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 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 215 THR Chi-restraints excluded: chain Q residue 232 PHE Chi-restraints excluded: chain Q residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4290 r_free = 0.4290 target = 0.167801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145170 restraints weight = 21638.701| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.21 r_work: 0.3864 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11614 Z= 0.152 Angle : 0.660 10.180 15767 Z= 0.339 Chirality : 0.042 0.179 1797 Planarity : 0.004 0.043 1968 Dihedral : 4.464 20.842 1568 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.73 % Allowed : 26.23 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1420 helix: 0.69 (0.20), residues: 643 sheet: -1.43 (0.31), residues: 247 loop : -2.28 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.008 0.001 HIS R 265 PHE 0.029 0.001 PHE R 39 TYR 0.021 0.002 TYR S 103 ARG 0.005 0.000 ARG R 91 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 585) hydrogen bonds : angle 5.05394 ( 1677) SS BOND : bond 0.00642 ( 4) SS BOND : angle 2.37797 ( 8) covalent geometry : bond 0.00341 (11610) covalent geometry : angle 0.65814 (15759) *********************** 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 387 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 316 time to evaluate : 1.137 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: 0.7460 (tt0) cc_final: 0.6884 (mm-30) REVERT: A 229 ASP cc_start: 0.6041 (p0) cc_final: 0.5000 (m-30) REVERT: A 240 MET cc_start: 0.4699 (mpp) cc_final: 0.4366 (mpp) REVERT: A 242 ARG cc_start: 0.7506 (mpt-90) cc_final: 0.6845 (mpt-90) REVERT: A 256 ASN cc_start: 0.7022 (t0) cc_final: 0.6707 (t0) REVERT: A 274 PHE cc_start: 0.7163 (t80) cc_final: 0.6822 (t80) REVERT: A 302 TYR cc_start: 0.5997 (t80) cc_final: 0.5748 (t80) REVERT: A 311 ASN cc_start: 0.6606 (p0) cc_final: 0.6403 (p0) REVERT: A 313 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6592 (ptp90) REVERT: A 318 GLU cc_start: 0.6985 (pm20) cc_final: 0.6774 (pm20) REVERT: A 333 GLN cc_start: 0.7730 (pp30) cc_final: 0.7371 (pp30) REVERT: A 341 ASP cc_start: 0.8381 (t70) cc_final: 0.8141 (t0) REVERT: B 45 MET cc_start: 0.6527 (ptp) cc_final: 0.6271 (ptp) REVERT: B 129 ARG cc_start: 0.7222 (tmt170) cc_final: 0.6921 (tmt170) REVERT: B 188 MET cc_start: 0.7185 (mmp) cc_final: 0.6935 (mmm) REVERT: B 219 ARG cc_start: 0.7183 (mmp80) cc_final: 0.6667 (mmp-170) REVERT: B 252 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5739 (pp) REVERT: B 260 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5388 (tp30) REVERT: C 71 TYR cc_start: 0.7383 (t80) cc_final: 0.7182 (t80) REVERT: R 91 ARG cc_start: 0.7362 (mtp-110) cc_final: 0.6952 (mtp-110) REVERT: R 94 ASP cc_start: 0.7164 (m-30) cc_final: 0.6784 (m-30) REVERT: R 125 PHE cc_start: 0.7279 (t80) cc_final: 0.6975 (t80) REVERT: R 133 ARG cc_start: 0.7472 (mtp85) cc_final: 0.7196 (mtp85) REVERT: R 215 THR cc_start: 0.4970 (OUTLIER) cc_final: 0.4572 (m) REVERT: R 245 ARG cc_start: 0.7112 (ttm170) cc_final: 0.6709 (ttm170) REVERT: S 172 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7936 (p) REVERT: S 179 GLN cc_start: 0.7549 (pp30) cc_final: 0.7000 (pp30) REVERT: S 186 GLN cc_start: 0.7910 (mt0) cc_final: 0.7631 (mt0) REVERT: Q 36 MET cc_start: 0.6091 (tmm) cc_final: 0.5846 (tmm) REVERT: Q 128 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.4693 (p90) REVERT: Q 167 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6672 (tp) REVERT: Q 216 ILE cc_start: 0.7435 (tt) cc_final: 0.7224 (tp) REVERT: Q 294 CYS cc_start: 0.7055 (m) cc_final: 0.6800 (m) REVERT: Q 304 LEU cc_start: 0.7942 (mt) cc_final: 0.7592 (mt) outliers start: 71 outliers final: 49 residues processed: 358 average time/residue: 0.2535 time to fit residues: 126.2370 Evaluate side-chains 367 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 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 75 GLN 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 252 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 CYS 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 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 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 269 THR 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 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 165 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 63 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 132 ASN B 176 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4289 r_free = 0.4289 target = 0.167663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144618 restraints weight = 21776.629| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.28 r_work: 0.3856 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11614 Z= 0.145 Angle : 0.659 10.439 15767 Z= 0.336 Chirality : 0.042 0.170 1797 Planarity : 0.004 0.044 1968 Dihedral : 4.445 20.293 1568 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.08 % Allowed : 27.04 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1420 helix: 0.70 (0.20), residues: 646 sheet: -1.40 (0.32), residues: 236 loop : -2.30 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 197 HIS 0.008 0.001 HIS R 265 PHE 0.021 0.001 PHE A 191 TYR 0.023 0.001 TYR S 103 ARG 0.006 0.000 ARG Q 127 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 585) hydrogen bonds : angle 4.97705 ( 1677) SS BOND : bond 0.00523 ( 4) SS BOND : angle 2.29381 ( 8) covalent geometry : bond 0.00323 (11610) covalent geometry : angle 0.65671 (15759) *********************** 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 374 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 1.139 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: symmetry clash REVERT: A 198 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7393 (mmm) REVERT: A 229 ASP cc_start: 0.6246 (p0) cc_final: 0.5238 (m-30) REVERT: A 240 MET cc_start: 0.4743 (mpp) cc_final: 0.4412 (mpp) REVERT: A 242 ARG cc_start: 0.7558 (mpt-90) cc_final: 0.6832 (mpt-90) REVERT: A 256 ASN cc_start: 0.7091 (t0) cc_final: 0.6771 (t0) REVERT: A 274 PHE cc_start: 0.7197 (t80) cc_final: 0.6809 (t80) REVERT: A 302 TYR cc_start: 0.6115 (t80) cc_final: 0.5789 (t80) REVERT: A 313 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6616 (ptp90) REVERT: A 318 GLU cc_start: 0.7000 (pm20) cc_final: 0.6752 (pm20) REVERT: A 333 GLN cc_start: 0.7675 (pp30) cc_final: 0.7350 (pp30) REVERT: A 341 ASP cc_start: 0.8386 (t70) cc_final: 0.8117 (t0) REVERT: B 45 MET cc_start: 0.6515 (ptp) cc_final: 0.6281 (ptp) REVERT: B 129 ARG cc_start: 0.7421 (tmt170) cc_final: 0.7119 (tmt170) REVERT: B 209 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7338 (mmmt) REVERT: B 219 ARG cc_start: 0.7144 (mmp80) cc_final: 0.6748 (mmp-170) REVERT: B 228 ASP cc_start: 0.7745 (p0) cc_final: 0.7526 (p0) REVERT: B 252 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5627 (pp) REVERT: B 260 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5423 (tp30) REVERT: C 71 TYR cc_start: 0.7329 (t80) cc_final: 0.7106 (t80) REVERT: R 91 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.7039 (mtp85) REVERT: R 94 ASP cc_start: 0.7078 (m-30) cc_final: 0.6833 (m-30) REVERT: R 125 PHE cc_start: 0.7309 (t80) cc_final: 0.7051 (t80) REVERT: R 133 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7074 (mtp85) REVERT: R 245 ARG cc_start: 0.7158 (ttm170) cc_final: 0.6731 (ttm170) REVERT: S 172 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7898 (p) REVERT: S 179 GLN cc_start: 0.7535 (pp30) cc_final: 0.6933 (pp30) REVERT: S 186 GLN cc_start: 0.7835 (mt0) cc_final: 0.7562 (mt0) REVERT: Q 36 MET cc_start: 0.6156 (tmm) cc_final: 0.5911 (tmm) REVERT: Q 128 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.4855 (p90) REVERT: Q 167 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6683 (tp) REVERT: Q 216 ILE cc_start: 0.7393 (tt) cc_final: 0.7191 (tp) REVERT: Q 217 MET cc_start: 0.5873 (mtm) cc_final: 0.5617 (mtm) REVERT: Q 294 CYS cc_start: 0.7051 (m) cc_final: 0.6800 (m) REVERT: Q 304 LEU cc_start: 0.7941 (mt) cc_final: 0.7595 (mt) outliers start: 63 outliers final: 47 residues processed: 348 average time/residue: 0.2472 time to fit residues: 118.6919 Evaluate side-chains 358 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 75 GLN 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 252 LEU 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 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 261 TRP Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 269 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 156 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.165788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.142580 restraints weight = 21686.592| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.22 r_work: 0.3824 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11614 Z= 0.198 Angle : 0.704 10.874 15767 Z= 0.365 Chirality : 0.045 0.227 1797 Planarity : 0.004 0.052 1968 Dihedral : 4.710 21.447 1568 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.97 % Allowed : 26.47 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1420 helix: 0.58 (0.20), residues: 642 sheet: -1.49 (0.33), residues: 233 loop : -2.25 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Q 95 HIS 0.011 0.001 HIS R 265 PHE 0.021 0.002 PHE Q 118 TYR 0.034 0.002 TYR S 103 ARG 0.008 0.001 ARG Q 127 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 585) hydrogen bonds : angle 5.16552 ( 1677) SS BOND : bond 0.00757 ( 4) SS BOND : angle 2.94038 ( 8) covalent geometry : bond 0.00436 (11610) covalent geometry : angle 0.70154 (15759) *********************** 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 396 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 322 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.6489 (p0) cc_final: 0.5664 (m-30) REVERT: A 240 MET cc_start: 0.4913 (mpp) cc_final: 0.4605 (mpp) REVERT: A 242 ARG cc_start: 0.7678 (mpt-90) cc_final: 0.7046 (mpt-90) REVERT: A 247 MET cc_start: 0.7420 (mtm) cc_final: 0.7065 (mtm) REVERT: A 256 ASN cc_start: 0.7121 (t0) cc_final: 0.6839 (t0) REVERT: A 274 PHE cc_start: 0.7218 (t80) cc_final: 0.6861 (t80) REVERT: A 313 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6672 (ptp90) REVERT: A 317 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7262 (ptpp) REVERT: A 341 ASP cc_start: 0.8415 (t70) cc_final: 0.8113 (t0) REVERT: B 68 ARG cc_start: 0.6687 (ttt180) cc_final: 0.5932 (ttt180) REVERT: B 137 ARG cc_start: 0.8151 (mmt90) cc_final: 0.7860 (mmm-85) REVERT: B 169 TRP cc_start: 0.7642 (m100) cc_final: 0.7431 (m100) REVERT: B 260 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5426 (tp30) REVERT: C 60 LYS cc_start: 0.5681 (tptp) cc_final: 0.5303 (mmmm) REVERT: C 71 TYR cc_start: 0.7371 (t80) cc_final: 0.7169 (t80) REVERT: R 30 LEU cc_start: 0.6857 (mm) cc_final: 0.6641 (mp) REVERT: R 91 ARG cc_start: 0.7396 (mtp-110) cc_final: 0.6996 (mtm110) REVERT: R 94 ASP cc_start: 0.7128 (m-30) cc_final: 0.6650 (m-30) REVERT: R 133 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7085 (mtp85) REVERT: R 215 THR cc_start: 0.4956 (OUTLIER) cc_final: 0.4350 (m) REVERT: R 243 ARG cc_start: 0.7416 (mtt-85) cc_final: 0.7196 (mmt180) REVERT: R 245 ARG cc_start: 0.7228 (ttm170) cc_final: 0.6791 (ttm170) REVERT: S 172 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7899 (p) REVERT: S 179 GLN cc_start: 0.7560 (pp30) cc_final: 0.7029 (pp30) REVERT: S 186 GLN cc_start: 0.7972 (mt0) cc_final: 0.7720 (mt0) REVERT: S 202 ARG cc_start: 0.5809 (mmt90) cc_final: 0.5589 (mtp85) REVERT: Q 128 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5017 (p90) REVERT: Q 167 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6712 (tp) REVERT: Q 216 ILE cc_start: 0.7442 (tt) cc_final: 0.7214 (tp) REVERT: Q 217 MET cc_start: 0.5922 (mtm) cc_final: 0.5680 (mtm) REVERT: Q 294 CYS cc_start: 0.7017 (m) cc_final: 0.6767 (m) REVERT: Q 304 LEU cc_start: 0.8058 (mt) cc_final: 0.7707 (mt) outliers start: 74 outliers final: 52 residues processed: 364 average time/residue: 0.2604 time to fit residues: 131.4567 Evaluate side-chains 372 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 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 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 75 GLN 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 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 49 VAL 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 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 269 THR 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 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR 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 215 THR 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 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 176 GLN B 220 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.167499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144583 restraints weight = 21432.797| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.20 r_work: 0.3852 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11614 Z= 0.158 Angle : 0.712 11.205 15767 Z= 0.362 Chirality : 0.044 0.208 1797 Planarity : 0.004 0.046 1968 Dihedral : 4.626 21.228 1568 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.73 % Allowed : 26.63 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1420 helix: 0.65 (0.20), residues: 646 sheet: -1.47 (0.32), residues: 239 loop : -2.29 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 279 HIS 0.011 0.001 HIS R 265 PHE 0.024 0.001 PHE R 39 TYR 0.040 0.002 TYR S 103 ARG 0.008 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 585) hydrogen bonds : angle 5.06974 ( 1677) SS BOND : bond 0.00523 ( 4) SS BOND : angle 2.29119 ( 8) covalent geometry : bond 0.00355 (11610) covalent geometry : angle 0.71018 (15759) *********************** 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 386 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 315 time to evaluate : 1.265 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 229 ASP cc_start: 0.6115 (p0) cc_final: 0.5357 (m-30) REVERT: A 240 MET cc_start: 0.5100 (mpp) cc_final: 0.4751 (mpp) REVERT: A 242 ARG cc_start: 0.7415 (mpt-90) cc_final: 0.6800 (mpt-90) REVERT: A 243 MET cc_start: 0.7232 (mtt) cc_final: 0.6994 (tmm) REVERT: A 256 ASN cc_start: 0.7111 (t0) cc_final: 0.6820 (t0) REVERT: A 274 PHE cc_start: 0.7166 (t80) cc_final: 0.6789 (t80) REVERT: A 313 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6619 (ptp90) REVERT: A 314 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7664 (mtmm) REVERT: A 333 GLN cc_start: 0.7717 (pp30) cc_final: 0.7224 (tm-30) REVERT: A 341 ASP cc_start: 0.8386 (t70) cc_final: 0.8170 (t0) REVERT: B 252 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.5785 (pp) REVERT: B 260 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5438 (tp30) REVERT: R 30 LEU cc_start: 0.6844 (mm) cc_final: 0.6623 (mp) REVERT: R 91 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.7038 (mtp85) REVERT: R 94 ASP cc_start: 0.7138 (m-30) cc_final: 0.6860 (m-30) REVERT: R 133 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7033 (mtp85) REVERT: R 215 THR cc_start: 0.4988 (OUTLIER) cc_final: 0.4426 (m) REVERT: R 245 ARG cc_start: 0.7148 (ttm170) cc_final: 0.6728 (ttm170) REVERT: S 172 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7870 (p) REVERT: S 175 TYR cc_start: 0.7896 (m-80) cc_final: 0.7682 (m-80) REVERT: S 179 GLN cc_start: 0.7538 (pp30) cc_final: 0.6940 (pp30) REVERT: S 186 GLN cc_start: 0.7977 (mt0) cc_final: 0.7700 (mt0) REVERT: Q 36 MET cc_start: 0.5864 (tmm) cc_final: 0.5638 (tmm) REVERT: Q 128 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5674 (p90) REVERT: Q 140 LEU cc_start: 0.8066 (tp) cc_final: 0.7815 (pp) REVERT: Q 166 VAL cc_start: 0.7603 (p) cc_final: 0.7331 (m) REVERT: Q 167 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6717 (tp) REVERT: Q 216 ILE cc_start: 0.7350 (tt) cc_final: 0.7118 (tp) REVERT: Q 304 LEU cc_start: 0.7910 (mt) cc_final: 0.7548 (mt) outliers start: 71 outliers final: 52 residues processed: 357 average time/residue: 0.2568 time to fit residues: 126.9158 Evaluate side-chains 358 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 324 THR 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 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 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 252 LEU 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 49 VAL 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 135 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 267 VAL Chi-restraints excluded: chain R residue 269 THR 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 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 102 CYS Chi-restraints excluded: chain Q residue 106 SER Chi-restraints excluded: chain Q residue 128 TYR Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain Q residue 165 MET 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 215 THR 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 108 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 0.0010 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 132 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.168575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145398 restraints weight = 21629.441| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.23 r_work: 0.3872 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11614 Z= 0.145 Angle : 0.713 11.554 15767 Z= 0.360 Chirality : 0.044 0.209 1797 Planarity : 0.004 0.047 1968 Dihedral : 4.569 20.890 1568 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.00 % Allowed : 27.44 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1420 helix: 0.75 (0.20), residues: 641 sheet: -1.58 (0.32), residues: 238 loop : -2.25 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 169 HIS 0.009 0.001 HIS R 265 PHE 0.021 0.001 PHE A 191 TYR 0.036 0.002 TYR S 103 ARG 0.010 0.001 ARG Q 127 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 585) hydrogen bonds : angle 5.01485 ( 1677) SS BOND : bond 0.00662 ( 4) SS BOND : angle 2.19663 ( 8) covalent geometry : bond 0.00323 (11610) covalent geometry : angle 0.71157 (15759) *********************** 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 361 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 299 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7446 (tt0) cc_final: 0.6955 (mm-30) REVERT: A 229 ASP cc_start: 0.6069 (p0) cc_final: 0.5436 (m-30) REVERT: A 240 MET cc_start: 0.5234 (mpp) cc_final: 0.4778 (mpp) REVERT: A 242 ARG cc_start: 0.7413 (mpt-90) cc_final: 0.6752 (mpt-90) REVERT: A 243 MET cc_start: 0.7307 (mtt) cc_final: 0.7094 (tmm) REVERT: A 247 MET cc_start: 0.7592 (mtt) cc_final: 0.7148 (mtm) REVERT: A 256 ASN cc_start: 0.7113 (t0) cc_final: 0.6836 (t0) REVERT: A 274 PHE cc_start: 0.7123 (t80) cc_final: 0.6751 (t80) REVERT: A 313 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6596 (ptp90) REVERT: A 314 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: A 333 GLN cc_start: 0.7670 (pp30) cc_final: 0.7151 (tm-30) REVERT: A 341 ASP cc_start: 0.8419 (t70) cc_final: 0.8162 (t0) REVERT: B 127 LYS cc_start: 0.7664 (mtmt) cc_final: 0.7406 (mtmt) REVERT: B 219 ARG cc_start: 0.7126 (mmp80) cc_final: 0.6673 (mmp-170) REVERT: B 252 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5713 (pp) REVERT: B 260 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5417 (tp30) REVERT: B 335 PHE cc_start: 0.7501 (m-80) cc_final: 0.7037 (m-80) REVERT: B 337 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7471 (mtpt) REVERT: R 30 LEU cc_start: 0.6847 (mm) cc_final: 0.6612 (mp) REVERT: R 91 ARG cc_start: 0.7245 (mtp-110) cc_final: 0.7011 (mtp85) REVERT: R 94 ASP cc_start: 0.7113 (m-30) cc_final: 0.6846 (m-30) REVERT: R 125 PHE cc_start: 0.7347 (t80) cc_final: 0.6846 (t80) REVERT: R 133 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7383 (mmm160) REVERT: R 135 VAL cc_start: 0.4531 (OUTLIER) cc_final: 0.3960 (t) REVERT: R 215 THR cc_start: 0.4952 (OUTLIER) cc_final: 0.4543 (m) REVERT: R 245 ARG cc_start: 0.7169 (ttm170) cc_final: 0.6728 (ttm170) REVERT: S 102 TYR cc_start: 0.8144 (p90) cc_final: 0.7816 (p90) REVERT: S 179 GLN cc_start: 0.7429 (pp30) cc_final: 0.7125 (pp30) REVERT: S 186 GLN cc_start: 0.7962 (mt0) cc_final: 0.7679 (mt0) REVERT: Q 36 MET cc_start: 0.5847 (tmm) cc_final: 0.5581 (tmm) REVERT: Q 128 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.4843 (p90) REVERT: Q 166 VAL cc_start: 0.7552 (p) cc_final: 0.7330 (m) REVERT: Q 216 ILE cc_start: 0.7352 (tt) cc_final: 0.7125 (tp) REVERT: Q 304 LEU cc_start: 0.7815 (mt) cc_final: 0.7447 (mt) outliers start: 62 outliers final: 45 residues processed: 338 average time/residue: 0.2401 time to fit residues: 113.0686 Evaluate side-chains 347 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 314 LYS 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 29 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 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 252 LEU 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 49 VAL 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 135 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 267 VAL Chi-restraints excluded: chain R residue 269 THR 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 164 VAL 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 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 58 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** 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 = 0.4299 r_free = 0.4299 target = 0.168802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145779 restraints weight = 21449.588| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.22 r_work: 0.3878 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3482 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= 0.148 Angle : 0.728 14.739 15767 Z= 0.367 Chirality : 0.044 0.217 1797 Planarity : 0.004 0.064 1968 Dihedral : 4.602 25.426 1568 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.44 % Allowed : 27.93 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1420 helix: 0.66 (0.20), residues: 648 sheet: -1.51 (0.32), residues: 238 loop : -2.31 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.008 0.001 HIS R 265 PHE 0.030 0.001 PHE Q 118 TYR 0.037 0.002 TYR S 103 ARG 0.010 0.001 ARG Q 127 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 585) hydrogen bonds : angle 5.03752 ( 1677) SS BOND : bond 0.00599 ( 4) SS BOND : angle 2.16390 ( 8) covalent geometry : bond 0.00332 (11610) covalent geometry : angle 0.72679 (15759) ********************** 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 350 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7463 (tt0) cc_final: 0.6973 (mm-30) REVERT: A 229 ASP cc_start: 0.6261 (p0) cc_final: 0.5581 (m-30) REVERT: A 240 MET cc_start: 0.5089 (mpp) cc_final: 0.4649 (mpp) REVERT: A 242 ARG cc_start: 0.7402 (mpt-90) cc_final: 0.6731 (mpt-90) REVERT: A 247 MET cc_start: 0.7557 (mtt) cc_final: 0.7106 (mtm) REVERT: A 256 ASN cc_start: 0.7100 (t0) cc_final: 0.6812 (m-40) REVERT: A 274 PHE cc_start: 0.7110 (t80) cc_final: 0.6751 (t80) REVERT: A 308 GLU cc_start: 0.7822 (tp30) cc_final: 0.7408 (mm-30) REVERT: A 313 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6679 (ptp90) REVERT: A 333 GLN cc_start: 0.7596 (pp30) cc_final: 0.7121 (tm-30) REVERT: A 341 ASP cc_start: 0.8406 (t70) cc_final: 0.8100 (t0) REVERT: B 110 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7898 (m110) REVERT: B 127 LYS cc_start: 0.7555 (mtmt) cc_final: 0.7271 (mtmm) REVERT: B 189 SER cc_start: 0.7843 (p) cc_final: 0.7559 (t) REVERT: B 219 ARG cc_start: 0.7114 (mmp80) cc_final: 0.6640 (mmp-170) REVERT: B 252 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5621 (pp) REVERT: B 260 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5433 (tp30) REVERT: B 335 PHE cc_start: 0.7484 (m-80) cc_final: 0.7003 (m-80) REVERT: R 30 LEU cc_start: 0.6842 (mm) cc_final: 0.6551 (mp) REVERT: R 91 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.7011 (mtp85) REVERT: R 94 ASP cc_start: 0.7256 (m-30) cc_final: 0.6963 (m-30) REVERT: R 133 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7368 (mmm160) REVERT: R 215 THR cc_start: 0.4960 (OUTLIER) cc_final: 0.4542 (m) REVERT: R 245 ARG cc_start: 0.7185 (ttm170) cc_final: 0.6742 (ttm170) REVERT: S 102 TYR cc_start: 0.8011 (p90) cc_final: 0.7705 (p90) REVERT: S 179 GLN cc_start: 0.7501 (pp30) cc_final: 0.6981 (pp30) REVERT: S 186 GLN cc_start: 0.7968 (mt0) cc_final: 0.7690 (mt0) REVERT: Q 36 MET cc_start: 0.5857 (tmm) cc_final: 0.5601 (tmm) REVERT: Q 127 ARG cc_start: 0.5295 (ttm110) cc_final: 0.3781 (ttm170) REVERT: Q 128 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5198 (p90) REVERT: Q 166 VAL cc_start: 0.7583 (p) cc_final: 0.7358 (m) REVERT: Q 216 ILE cc_start: 0.7364 (tt) cc_final: 0.7134 (tp) REVERT: Q 304 LEU cc_start: 0.7773 (mt) cc_final: 0.7379 (mt) outliers start: 55 outliers final: 46 residues processed: 331 average time/residue: 0.2454 time to fit residues: 112.6908 Evaluate side-chains 353 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 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 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 51 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 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 252 LEU 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 49 VAL 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 135 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 267 VAL Chi-restraints excluded: chain R residue 269 THR 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 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 78 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 126 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 127 optimal weight: 0.5980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 ASN Q 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.168650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.145560 restraints weight = 21536.809| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.21 r_work: 0.3877 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 11614 Z= 0.212 Angle : 0.952 59.172 15767 Z= 0.533 Chirality : 0.045 0.525 1797 Planarity : 0.005 0.063 1968 Dihedral : 4.640 26.119 1568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.20 % Allowed : 27.44 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1420 helix: 0.65 (0.20), residues: 649 sheet: -1.51 (0.32), residues: 238 loop : -2.28 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.007 0.001 HIS R 265 PHE 0.031 0.001 PHE Q 118 TYR 0.033 0.002 TYR S 103 ARG 0.008 0.001 ARG Q 127 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 585) hydrogen bonds : angle 5.03989 ( 1677) SS BOND : bond 0.00494 ( 4) SS BOND : angle 2.16529 ( 8) covalent geometry : bond 0.00418 (11610) covalent geometry : angle 0.95121 (15759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.14 seconds wall clock time: 99 minutes 24.80 seconds (5964.80 seconds total)