Starting phenix.real_space_refine on Wed Feb 4 16:53:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efo_28086/02_2026/8efo_28086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efo_28086/02_2026/8efo_28086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8efo_28086/02_2026/8efo_28086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efo_28086/02_2026/8efo_28086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efo_28086/02_2026/8efo_28086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efo_28086/02_2026/8efo_28086.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 100 5.16 5 C 7618 2.51 5 N 1900 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 156 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {'8QY': 1, 'CLR': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 137 Unusual residues: {'8QY': 1, 'CLR': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11708 At special positions: 0 Unit cell: (104, 110.24, 149.76, 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 100 16.00 O 2090 8.00 N 1900 7.00 C 7618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 0.88 Conformation dependent library (CDL) restraints added in 426.1 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 49.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 67 through 98 removed outlier: 3.503A pdb=" N VAL R 96 " --> pdb=" O MET R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.613A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.509A pdb=" N ILE R 144 " --> pdb=" O ILE R 140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.514A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.166A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 243 Processing helix chain 'R' and resid 243 through 264 Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.574A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.528A pdb=" N CYS R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.754A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.811A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.576A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.713A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.608A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.946A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'M' and resid 67 through 98 removed outlier: 3.503A pdb=" N VAL M 96 " --> pdb=" O MET M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 133 removed outlier: 3.613A pdb=" N TYR M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Proline residue: M 124 - end of helix Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.510A pdb=" N ILE M 144 " --> pdb=" O ILE M 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.513A pdb=" N LEU M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 4.166A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 243 Processing helix chain 'M' and resid 243 through 264 Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 339 removed outlier: 3.573A pdb=" N HIS M 321 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 removed outlier: 3.528A pdb=" N CYS M 348 " --> pdb=" O ASN M 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.039A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.508A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.861A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.782A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.247A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.524A 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: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.629A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.535A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.492A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.902A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AB7, first strand: chain 'M' and resid 208 through 213 667 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2738 1.33 - 1.46: 2741 1.46 - 1.58: 6358 1.58 - 1.70: 0 1.70 - 1.83: 149 Bond restraints: 11986 Sorted by residual: bond pdb=" C19 8QY M 401 " pdb=" O20 8QY M 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" C19 8QY R 401 " pdb=" O20 8QY R 401 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C02 8QY M 401 " pdb=" N12 8QY M 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C02 8QY R 401 " pdb=" N12 8QY R 401 " ideal model delta sigma weight residual 1.360 1.407 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.94e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15623 1.92 - 3.84: 580 3.84 - 5.76: 84 5.76 - 7.68: 22 7.68 - 9.60: 1 Bond angle restraints: 16310 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 120.63 126.54 -5.91 1.61e+00 3.86e-01 1.35e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.47 128.08 -4.61 1.53e+00 4.27e-01 9.08e+00 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 110.23 114.59 -4.36 1.45e+00 4.76e-01 9.03e+00 ... (remaining 16305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 7045 11.90 - 23.80: 405 23.80 - 35.71: 74 35.71 - 47.61: 34 47.61 - 59.51: 23 Dihedral angle restraints: 7581 sinusoidal: 3368 harmonic: 4213 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 57.75 35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS R 142 " pdb=" SG CYS R 142 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual 93.00 124.29 -31.29 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 7578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1695 0.086 - 0.172: 169 0.172 - 0.259: 24 0.259 - 0.345: 10 0.345 - 0.431: 10 Chirality restraints: 1908 Sorted by residual: chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1905 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " -0.008 2.00e-02 2.50e+03 1.37e-02 4.71e+00 pdb=" CG TRP E 111 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ILE B 232 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 232 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 233 " 0.011 2.00e-02 2.50e+03 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1734 2.77 - 3.30: 11006 3.30 - 3.84: 19649 3.84 - 4.37: 23130 4.37 - 4.90: 40050 Nonbonded interactions: 95569 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.241 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.323 3.040 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.331 3.040 nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.331 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.336 3.040 ... (remaining 95564 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 'M' selection = (chain 'R' and resid 66 through 405) } 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: 2.520 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11989 Z= 0.224 Angle : 0.852 9.597 16316 Z= 0.452 Chirality : 0.065 0.431 1908 Planarity : 0.005 0.053 1965 Dihedral : 9.172 59.509 4848 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1423 helix: -0.48 (0.16), residues: 629 sheet: 0.09 (0.30), residues: 263 loop : -0.95 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.022 0.002 TYR M 254 PHE 0.020 0.002 PHE B 234 TRP 0.034 0.002 TRP E 111 HIS 0.010 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00436 (11986) covalent geometry : angle 0.85155 (16310) SS BOND : bond 0.00244 ( 3) SS BOND : angle 1.18907 ( 6) hydrogen bonds : bond 0.25504 ( 667) hydrogen bonds : angle 8.36308 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 231 GLU cc_start: 0.7684 (tt0) cc_final: 0.7461 (tt0) REVERT: A 272 ASP cc_start: 0.7709 (p0) cc_final: 0.7439 (p0) REVERT: A 290 TYR cc_start: 0.6417 (t80) cc_final: 0.6062 (t80) REVERT: B 44 GLN cc_start: 0.6884 (mt0) cc_final: 0.6420 (pp30) REVERT: B 188 MET cc_start: 0.7762 (mmm) cc_final: 0.7537 (mmm) outliers start: 0 outliers final: 1 residues processed: 371 average time/residue: 0.5212 time to fit residues: 208.7784 Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN C 18 GLN E 77 ASN M 106 ASN M 126 GLN M 173 HIS M 185 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.160554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132790 restraints weight = 15604.936| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.83 r_work: 0.3506 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11989 Z= 0.153 Angle : 0.579 8.556 16316 Z= 0.308 Chirality : 0.042 0.204 1908 Planarity : 0.004 0.041 1965 Dihedral : 8.043 53.846 2249 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.46 % Allowed : 13.73 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1423 helix: 1.61 (0.18), residues: 669 sheet: 0.23 (0.29), residues: 283 loop : -0.69 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.022 0.002 TYR E 191 PHE 0.016 0.001 PHE A 189 TRP 0.022 0.002 TRP B 169 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00323 (11986) covalent geometry : angle 0.57910 (16310) SS BOND : bond 0.00585 ( 3) SS BOND : angle 0.63735 ( 6) hydrogen bonds : bond 0.04618 ( 667) hydrogen bonds : angle 5.18181 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 68 ILE cc_start: 0.7532 (mp) cc_final: 0.7287 (mm) REVERT: R 97 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6773 (ttm-80) REVERT: R 140 ILE cc_start: 0.8066 (tp) cc_final: 0.7688 (tt) REVERT: R 231 GLU cc_start: 0.8424 (tt0) cc_final: 0.8150 (tt0) REVERT: A 225 VAL cc_start: 0.7365 (p) cc_final: 0.7104 (m) REVERT: A 269 ASN cc_start: 0.8506 (m110) cc_final: 0.8200 (m110) REVERT: A 276 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: B 33 ILE cc_start: 0.6874 (mt) cc_final: 0.6488 (mt) REVERT: B 217 MET cc_start: 0.7546 (pmm) cc_final: 0.7327 (pmm) REVERT: B 259 GLN cc_start: 0.6464 (mp10) cc_final: 0.6056 (mp10) REVERT: B 325 MET cc_start: 0.8211 (tpp) cc_final: 0.7855 (tpt) REVERT: B 331 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 28 ILE cc_start: 0.7476 (pt) cc_final: 0.7133 (pp) REVERT: E 63 THR cc_start: 0.7844 (t) cc_final: 0.7528 (m) REVERT: M 67 MET cc_start: 0.5478 (tmt) cc_final: 0.4637 (ttm) REVERT: M 86 PHE cc_start: 0.7530 (t80) cc_final: 0.7034 (t80) REVERT: M 97 ARG cc_start: 0.6743 (tpt170) cc_final: 0.6108 (ttt180) REVERT: M 144 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7070 (mp) REVERT: M 278 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6338 (tpt170) REVERT: F 340 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7374 (t) REVERT: F 342 VAL cc_start: 0.8457 (t) cc_final: 0.8219 (p) outliers start: 31 outliers final: 9 residues processed: 252 average time/residue: 0.5781 time to fit residues: 157.3444 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 27 optimal weight: 0.2980 chunk 139 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN E 77 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 225 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129625 restraints weight = 15902.582| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.78 r_work: 0.3464 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11989 Z= 0.125 Angle : 0.531 8.900 16316 Z= 0.278 Chirality : 0.040 0.155 1908 Planarity : 0.004 0.063 1965 Dihedral : 7.621 54.966 2249 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.54 % Allowed : 15.63 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1423 helix: 2.12 (0.19), residues: 677 sheet: 0.14 (0.29), residues: 303 loop : -0.40 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 219 TYR 0.021 0.002 TYR M 130 PHE 0.013 0.001 PHE A 189 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00272 (11986) covalent geometry : angle 0.53099 (16310) SS BOND : bond 0.00363 ( 3) SS BOND : angle 0.68139 ( 6) hydrogen bonds : bond 0.04128 ( 667) hydrogen bonds : angle 4.87171 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 97 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6838 (ttm-80) REVERT: R 231 GLU cc_start: 0.8465 (tt0) cc_final: 0.8208 (tt0) REVERT: R 282 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7477 (ttt-90) REVERT: A 53 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7209 (mtt) REVERT: A 269 ASN cc_start: 0.8495 (m110) cc_final: 0.8190 (m110) REVERT: B 33 ILE cc_start: 0.6957 (mt) cc_final: 0.6651 (mt) REVERT: B 217 MET cc_start: 0.7769 (pmm) cc_final: 0.7560 (pmm) REVERT: B 259 GLN cc_start: 0.6449 (mp-120) cc_final: 0.6058 (mp10) REVERT: B 325 MET cc_start: 0.8171 (tpp) cc_final: 0.7760 (tpt) REVERT: B 331 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8549 (t) REVERT: C 28 ILE cc_start: 0.7550 (pt) cc_final: 0.7207 (pp) REVERT: E 11 LEU cc_start: 0.7249 (mm) cc_final: 0.6915 (mt) REVERT: E 63 THR cc_start: 0.7947 (t) cc_final: 0.7645 (m) REVERT: M 86 PHE cc_start: 0.7573 (t80) cc_final: 0.7108 (t80) REVERT: M 97 ARG cc_start: 0.6824 (tpt170) cc_final: 0.6177 (ttt180) REVERT: M 144 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7123 (mp) REVERT: M 206 PHE cc_start: 0.7323 (m-80) cc_final: 0.7118 (m-10) REVERT: M 278 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6299 (tpt170) REVERT: F 340 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7410 (t) REVERT: F 342 VAL cc_start: 0.8499 (t) cc_final: 0.8264 (p) outliers start: 32 outliers final: 13 residues processed: 225 average time/residue: 0.6125 time to fit residues: 148.8364 Evaluate side-chains 200 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 5 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN A 213 HIS B 340 ASN E 187 GLN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126615 restraints weight = 15630.173| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.79 r_work: 0.3421 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11989 Z= 0.134 Angle : 0.527 10.161 16316 Z= 0.274 Chirality : 0.040 0.155 1908 Planarity : 0.004 0.043 1965 Dihedral : 7.386 56.008 2249 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.81 % Allowed : 15.79 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.22), residues: 1423 helix: 2.28 (0.19), residues: 677 sheet: 0.15 (0.29), residues: 297 loop : -0.27 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.022 0.002 TYR M 130 PHE 0.014 0.001 PHE A 189 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00301 (11986) covalent geometry : angle 0.52741 (16310) SS BOND : bond 0.00347 ( 3) SS BOND : angle 0.71916 ( 6) hydrogen bonds : bond 0.03933 ( 667) hydrogen bonds : angle 4.82125 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7997 (m-10) cc_final: 0.7554 (m-10) REVERT: R 97 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6824 (ttm-80) REVERT: R 147 SER cc_start: 0.8765 (t) cc_final: 0.8492 (p) REVERT: R 155 THR cc_start: 0.8776 (m) cc_final: 0.8541 (p) REVERT: R 210 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8023 (p) REVERT: R 211 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7581 (mtpp) REVERT: R 231 GLU cc_start: 0.8381 (tt0) cc_final: 0.8091 (tt0) REVERT: A 269 ASN cc_start: 0.8528 (m110) cc_final: 0.8169 (m110) REVERT: A 275 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6431 (tm-30) REVERT: B 146 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 259 GLN cc_start: 0.6750 (mp-120) cc_final: 0.6268 (mp10) REVERT: B 325 MET cc_start: 0.8182 (tpp) cc_final: 0.7771 (tpt) REVERT: B 331 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (t) REVERT: C 28 ILE cc_start: 0.7586 (pt) cc_final: 0.7216 (pp) REVERT: E 11 LEU cc_start: 0.7323 (mm) cc_final: 0.6796 (tp) REVERT: E 63 THR cc_start: 0.8011 (t) cc_final: 0.7684 (m) REVERT: M 67 MET cc_start: 0.5513 (tmt) cc_final: 0.4935 (ttm) REVERT: M 86 PHE cc_start: 0.7688 (t80) cc_final: 0.7124 (t80) REVERT: M 144 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7121 (mp) REVERT: M 218 ASP cc_start: 0.7113 (t70) cc_final: 0.6551 (p0) REVERT: M 278 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6451 (tpt-90) REVERT: F 340 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7417 (t) REVERT: F 341 ASP cc_start: 0.8148 (t0) cc_final: 0.7381 (m-30) REVERT: F 342 VAL cc_start: 0.8585 (t) cc_final: 0.8327 (p) outliers start: 48 outliers final: 16 residues processed: 226 average time/residue: 0.5765 time to fit residues: 140.5595 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 222 THR Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.0770 chunk 132 optimal weight: 5.9990 chunk 35 optimal weight: 0.0040 chunk 120 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** R 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN B 75 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 18 GLN E 77 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124749 restraints weight = 15540.438| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.94 r_work: 0.3380 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11989 Z= 0.133 Angle : 0.527 9.114 16316 Z= 0.273 Chirality : 0.040 0.158 1908 Planarity : 0.004 0.037 1965 Dihedral : 7.086 55.869 2249 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.10 % Allowed : 17.78 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1423 helix: 2.41 (0.19), residues: 677 sheet: 0.10 (0.30), residues: 278 loop : -0.22 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 282 TYR 0.017 0.001 TYR M 130 PHE 0.013 0.001 PHE A 189 TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00301 (11986) covalent geometry : angle 0.52651 (16310) SS BOND : bond 0.00219 ( 3) SS BOND : angle 0.56931 ( 6) hydrogen bonds : bond 0.03805 ( 667) hydrogen bonds : angle 4.78766 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7960 (m-10) cc_final: 0.7623 (m-10) REVERT: R 147 SER cc_start: 0.8713 (t) cc_final: 0.8467 (p) REVERT: R 155 THR cc_start: 0.8798 (m) cc_final: 0.8541 (p) REVERT: R 210 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8146 (p) REVERT: R 211 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7698 (mtpp) REVERT: R 231 GLU cc_start: 0.8447 (tt0) cc_final: 0.8143 (tt0) REVERT: R 282 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7489 (ttt-90) REVERT: A 20 ASP cc_start: 0.8274 (m-30) cc_final: 0.8046 (m-30) REVERT: A 269 ASN cc_start: 0.8568 (m110) cc_final: 0.8172 (m110) REVERT: A 275 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6429 (tm-30) REVERT: B 44 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: B 146 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8601 (tp) REVERT: B 259 GLN cc_start: 0.6759 (mp-120) cc_final: 0.6225 (mp10) REVERT: B 325 MET cc_start: 0.8153 (tpp) cc_final: 0.7726 (tpt) REVERT: B 331 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 28 ILE cc_start: 0.7562 (pt) cc_final: 0.7204 (pp) REVERT: C 47 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7214 (mt-10) REVERT: E 11 LEU cc_start: 0.7402 (mm) cc_final: 0.6864 (tp) REVERT: E 63 THR cc_start: 0.8012 (t) cc_final: 0.7663 (m) REVERT: M 86 PHE cc_start: 0.7745 (t80) cc_final: 0.7211 (t80) REVERT: M 144 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7062 (mp) REVERT: M 218 ASP cc_start: 0.7326 (t70) cc_final: 0.6557 (p0) REVERT: M 278 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6138 (tpp80) REVERT: F 340 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7422 (t) REVERT: F 341 ASP cc_start: 0.8101 (t0) cc_final: 0.7371 (m-30) REVERT: F 342 VAL cc_start: 0.8571 (t) cc_final: 0.8301 (p) outliers start: 39 outliers final: 19 residues processed: 230 average time/residue: 0.5388 time to fit residues: 133.8504 Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 3 optimal weight: 0.0050 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 GLN A 22 ASN B 156 GLN B 340 ASN C 18 GLN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118662 restraints weight = 15589.384| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.93 r_work: 0.3329 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11989 Z= 0.169 Angle : 0.571 9.100 16316 Z= 0.295 Chirality : 0.041 0.158 1908 Planarity : 0.004 0.037 1965 Dihedral : 7.229 57.733 2249 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.57 % Allowed : 18.10 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1423 helix: 2.39 (0.19), residues: 675 sheet: 0.06 (0.30), residues: 292 loop : -0.25 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 184 TYR 0.016 0.002 TYR M 130 PHE 0.017 0.001 PHE A 189 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00392 (11986) covalent geometry : angle 0.57099 (16310) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.55950 ( 6) hydrogen bonds : bond 0.03953 ( 667) hydrogen bonds : angle 4.93675 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7897 (m-10) cc_final: 0.7630 (m-10) REVERT: R 210 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8303 (p) REVERT: R 211 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7699 (mtpp) REVERT: R 231 GLU cc_start: 0.8530 (tt0) cc_final: 0.8190 (tt0) REVERT: R 282 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7396 (ttt-90) REVERT: A 20 ASP cc_start: 0.8298 (m-30) cc_final: 0.8093 (m-30) REVERT: A 225 VAL cc_start: 0.7952 (p) cc_final: 0.7718 (m) REVERT: A 245 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: A 269 ASN cc_start: 0.8547 (m110) cc_final: 0.8226 (m110) REVERT: A 275 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6384 (tm-30) REVERT: B 44 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: B 259 GLN cc_start: 0.6972 (mp-120) cc_final: 0.6418 (mp10) REVERT: B 325 MET cc_start: 0.8065 (tpp) cc_final: 0.7710 (tpt) REVERT: B 331 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8768 (t) REVERT: C 28 ILE cc_start: 0.7567 (pt) cc_final: 0.7223 (pp) REVERT: E 3 GLN cc_start: 0.7777 (mt0) cc_final: 0.7440 (mt0) REVERT: E 63 THR cc_start: 0.8144 (t) cc_final: 0.7784 (m) REVERT: M 144 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7049 (mp) REVERT: M 209 THR cc_start: 0.6461 (m) cc_final: 0.6104 (p) REVERT: M 218 ASP cc_start: 0.7503 (t70) cc_final: 0.7111 (t70) REVERT: M 278 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6187 (tpp80) REVERT: F 340 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7420 (t) REVERT: F 341 ASP cc_start: 0.8033 (t0) cc_final: 0.7398 (m-30) REVERT: F 342 VAL cc_start: 0.8547 (t) cc_final: 0.8279 (p) outliers start: 45 outliers final: 20 residues processed: 228 average time/residue: 0.6237 time to fit residues: 152.7604 Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 222 THR Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 269 ASN B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120643 restraints weight = 15573.230| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.93 r_work: 0.3306 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11989 Z= 0.136 Angle : 0.549 9.789 16316 Z= 0.283 Chirality : 0.040 0.156 1908 Planarity : 0.004 0.040 1965 Dihedral : 6.960 58.214 2249 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.17 % Allowed : 19.21 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1423 helix: 2.46 (0.19), residues: 676 sheet: 0.17 (0.30), residues: 277 loop : -0.36 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 67 TYR 0.015 0.001 TYR M 130 PHE 0.012 0.001 PHE A 189 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00310 (11986) covalent geometry : angle 0.54917 (16310) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.49544 ( 6) hydrogen bonds : bond 0.03760 ( 667) hydrogen bonds : angle 4.81402 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7903 (m-10) cc_final: 0.7662 (m-10) REVERT: R 231 GLU cc_start: 0.8515 (tt0) cc_final: 0.8179 (tt0) REVERT: R 282 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7346 (ttt-90) REVERT: A 20 ASP cc_start: 0.8243 (m-30) cc_final: 0.8019 (m-30) REVERT: A 225 VAL cc_start: 0.7913 (p) cc_final: 0.7695 (m) REVERT: A 269 ASN cc_start: 0.8731 (m-40) cc_final: 0.8338 (m110) REVERT: B 44 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: B 259 GLN cc_start: 0.6889 (mp-120) cc_final: 0.6331 (mp10) REVERT: B 325 MET cc_start: 0.8039 (tpp) cc_final: 0.7773 (tpt) REVERT: B 331 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8733 (t) REVERT: C 28 ILE cc_start: 0.7562 (pt) cc_final: 0.7188 (pp) REVERT: E 63 THR cc_start: 0.8090 (t) cc_final: 0.7704 (m) REVERT: M 86 PHE cc_start: 0.7765 (t80) cc_final: 0.7238 (t80) REVERT: M 144 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.6986 (mp) REVERT: M 209 THR cc_start: 0.6368 (m) cc_final: 0.6019 (p) REVERT: M 218 ASP cc_start: 0.7447 (t70) cc_final: 0.7061 (t70) REVERT: M 278 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6166 (tpp80) REVERT: F 340 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7360 (t) REVERT: F 341 ASP cc_start: 0.7929 (t0) cc_final: 0.7336 (m-30) REVERT: F 342 VAL cc_start: 0.8527 (t) cc_final: 0.8255 (p) outliers start: 40 outliers final: 20 residues processed: 216 average time/residue: 0.5962 time to fit residues: 138.7339 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 188 HIS B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120835 restraints weight = 15512.710| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.95 r_work: 0.3308 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11989 Z= 0.155 Angle : 0.578 10.438 16316 Z= 0.295 Chirality : 0.041 0.156 1908 Planarity : 0.004 0.060 1965 Dihedral : 7.042 56.226 2249 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.65 % Allowed : 19.21 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1423 helix: 2.44 (0.19), residues: 676 sheet: 0.12 (0.31), residues: 269 loop : -0.42 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 184 TYR 0.015 0.002 TYR M 130 PHE 0.014 0.001 PHE A 189 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00362 (11986) covalent geometry : angle 0.57792 (16310) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.72513 ( 6) hydrogen bonds : bond 0.03839 ( 667) hydrogen bonds : angle 4.85735 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7916 (m-10) cc_final: 0.7696 (m-10) REVERT: R 231 GLU cc_start: 0.8505 (tt0) cc_final: 0.8163 (tt0) REVERT: R 282 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7250 (ttt-90) REVERT: A 20 ASP cc_start: 0.8300 (m-30) cc_final: 0.8073 (m-30) REVERT: A 225 VAL cc_start: 0.7946 (p) cc_final: 0.7723 (m) REVERT: A 269 ASN cc_start: 0.8663 (m-40) cc_final: 0.8277 (m110) REVERT: B 44 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: B 212 ASP cc_start: 0.7923 (t70) cc_final: 0.7637 (t0) REVERT: B 325 MET cc_start: 0.8186 (tpp) cc_final: 0.7898 (tpt) REVERT: B 331 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8802 (t) REVERT: C 28 ILE cc_start: 0.7652 (pt) cc_final: 0.7289 (pp) REVERT: C 47 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7328 (mt-10) REVERT: E 3 GLN cc_start: 0.7769 (mt0) cc_final: 0.7424 (mt0) REVERT: E 63 THR cc_start: 0.8037 (t) cc_final: 0.7700 (m) REVERT: M 144 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7039 (mp) REVERT: M 209 THR cc_start: 0.6374 (m) cc_final: 0.6015 (p) REVERT: M 218 ASP cc_start: 0.7464 (t70) cc_final: 0.7086 (t70) REVERT: M 278 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6202 (tpp80) REVERT: F 340 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7355 (t) REVERT: F 341 ASP cc_start: 0.7971 (t0) cc_final: 0.7351 (m-30) REVERT: F 342 VAL cc_start: 0.8545 (t) cc_final: 0.8277 (p) outliers start: 46 outliers final: 26 residues processed: 224 average time/residue: 0.6244 time to fit residues: 150.9972 Evaluate side-chains 215 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 282 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 59 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 255 ASN B 259 GLN B 340 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123507 restraints weight = 15354.986| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.90 r_work: 0.3336 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11989 Z= 0.130 Angle : 0.563 12.094 16316 Z= 0.287 Chirality : 0.040 0.152 1908 Planarity : 0.004 0.037 1965 Dihedral : 6.770 55.055 2249 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.62 % Allowed : 20.16 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1423 helix: 2.49 (0.19), residues: 676 sheet: 0.09 (0.31), residues: 265 loop : -0.41 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 67 TYR 0.015 0.001 TYR M 130 PHE 0.012 0.001 PHE A 189 TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00296 (11986) covalent geometry : angle 0.56345 (16310) SS BOND : bond 0.00081 ( 3) SS BOND : angle 0.59718 ( 6) hydrogen bonds : bond 0.03672 ( 667) hydrogen bonds : angle 4.75648 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7926 (m-10) cc_final: 0.7715 (m-10) REVERT: R 231 GLU cc_start: 0.8509 (tt0) cc_final: 0.8182 (tt0) REVERT: A 20 ASP cc_start: 0.8282 (m-30) cc_final: 0.8065 (m-30) REVERT: A 269 ASN cc_start: 0.8715 (m-40) cc_final: 0.8331 (m110) REVERT: B 325 MET cc_start: 0.8093 (tpp) cc_final: 0.7461 (tpt) REVERT: B 331 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8771 (t) REVERT: C 28 ILE cc_start: 0.7650 (pt) cc_final: 0.7362 (pp) REVERT: C 47 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7312 (mt-10) REVERT: E 3 GLN cc_start: 0.7757 (mt0) cc_final: 0.7410 (mt0) REVERT: M 144 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7098 (mp) REVERT: M 209 THR cc_start: 0.6531 (m) cc_final: 0.6256 (p) REVERT: M 218 ASP cc_start: 0.7506 (t70) cc_final: 0.7131 (t70) REVERT: M 278 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6267 (tpp80) REVERT: F 340 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7367 (t) REVERT: F 341 ASP cc_start: 0.8035 (t0) cc_final: 0.7322 (m-30) REVERT: F 342 VAL cc_start: 0.8545 (t) cc_final: 0.8269 (p) outliers start: 33 outliers final: 18 residues processed: 211 average time/residue: 0.6035 time to fit residues: 137.4748 Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123051 restraints weight = 15473.595| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.89 r_work: 0.3333 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11989 Z= 0.137 Angle : 0.575 11.089 16316 Z= 0.295 Chirality : 0.040 0.152 1908 Planarity : 0.004 0.067 1965 Dihedral : 6.729 54.273 2249 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.06 % Allowed : 20.63 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1423 helix: 2.54 (0.19), residues: 670 sheet: -0.08 (0.31), residues: 272 loop : -0.40 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 184 TYR 0.015 0.001 TYR M 130 PHE 0.012 0.001 PHE R 340 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00315 (11986) covalent geometry : angle 0.57498 (16310) SS BOND : bond 0.00028 ( 3) SS BOND : angle 0.74863 ( 6) hydrogen bonds : bond 0.03742 ( 667) hydrogen bonds : angle 4.78203 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7913 (m-10) cc_final: 0.7699 (m-10) REVERT: R 231 GLU cc_start: 0.8514 (tt0) cc_final: 0.8188 (tt0) REVERT: A 20 ASP cc_start: 0.8298 (m-30) cc_final: 0.8088 (m-30) REVERT: A 269 ASN cc_start: 0.8659 (m-40) cc_final: 0.8247 (m110) REVERT: B 331 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8785 (t) REVERT: C 28 ILE cc_start: 0.7658 (pt) cc_final: 0.7377 (pp) REVERT: C 47 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7449 (mt-10) REVERT: E 3 GLN cc_start: 0.7723 (mt0) cc_final: 0.7376 (mt0) REVERT: M 144 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7072 (mp) REVERT: M 209 THR cc_start: 0.6548 (m) cc_final: 0.6261 (p) REVERT: M 218 ASP cc_start: 0.7507 (t70) cc_final: 0.7128 (t70) REVERT: M 278 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6255 (tpp80) REVERT: F 340 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7374 (t) REVERT: F 341 ASP cc_start: 0.8105 (t0) cc_final: 0.7381 (m-30) REVERT: F 342 VAL cc_start: 0.8598 (t) cc_final: 0.8328 (p) outliers start: 26 outliers final: 21 residues processed: 200 average time/residue: 0.5981 time to fit residues: 129.2699 Evaluate side-chains 198 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 146 ILE Chi-restraints excluded: chain M residue 153 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 176 LYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 57 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120451 restraints weight = 15568.923| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.90 r_work: 0.3278 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11989 Z= 0.170 Angle : 0.607 10.162 16316 Z= 0.310 Chirality : 0.041 0.155 1908 Planarity : 0.004 0.037 1965 Dihedral : 7.004 56.237 2249 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.62 % Allowed : 20.63 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1423 helix: 2.41 (0.19), residues: 670 sheet: -0.21 (0.31), residues: 272 loop : -0.44 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.015 0.002 TYR M 130 PHE 0.012 0.001 PHE A 189 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00395 (11986) covalent geometry : angle 0.60740 (16310) SS BOND : bond 0.00055 ( 3) SS BOND : angle 0.84149 ( 6) hydrogen bonds : bond 0.03962 ( 667) hydrogen bonds : angle 4.91191 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4753.35 seconds wall clock time: 81 minutes 45.32 seconds (4905.32 seconds total)