c65ef3b3cdca8ea9c5d18bb5ca7b1b22c346d6fe
examples/1I2T.tar.bz2
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examples/phenix.rosetta_refine.log
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| 1 | + |
|
| 2 | +============================== Collecting inputs ============================== |
|
| 3 | + |
|
| 4 | + |
|
| 5 | + ----------Processing X-ray data---------- |
|
| 6 | + |
|
| 7 | +I-obs: |
|
| 8 | + /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:IOBS,SIGIOBS |
|
| 9 | +Miller array info: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:IOBS,SIGIOBS |
|
| 10 | +Observation type: xray.intensity |
|
| 11 | +Type of data: double, size=31449 |
|
| 12 | +Type of sigmas: double, size=31449 |
|
| 13 | +Number of Miller indices: 31449 |
|
| 14 | +Anomalous flag: False |
|
| 15 | +Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) |
|
| 16 | +Space group: P 21 21 21 (No. 19) |
|
| 17 | +Systematic absences: 0 |
|
| 18 | +Centric reflections: 3439 |
|
| 19 | +Resolution range: 19.083 1.04105 |
|
| 20 | +Completeness in resolution range: 0.996609 |
|
| 21 | +Completeness with d_max=infinity: 0.996388 |
|
| 22 | +Wavelength: 1.1000 |
|
| 23 | + |
|
| 24 | + |
|
| 25 | + ----------Scaling input intensities via French-Wilson Method---------- |
|
| 26 | + |
|
| 27 | +Trying 60 bins... |
|
| 28 | +Number of bins = 60 |
|
| 29 | +** Calculating bin mean intensity values for each intensity ** |
|
| 30 | +** Total # rejected intensities: 0 ** |
|
| 31 | +Intensities converted to amplitudes for use in refinement. |
|
| 32 | + |
|
| 33 | +Number of F-obs in resolution range: 31449 |
|
| 34 | +Number of F-obs<0 (these reflections will be rejected): 0 |
|
| 35 | +Number of F-obs=0 (these reflections will be used in refinement): 0 |
|
| 36 | +Refinement resolution range: d_max = 19.0830 |
|
| 37 | + d_min = 1.0411 |
|
| 38 | + |
|
| 39 | +R-free flags: |
|
| 40 | + /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:FreeR_flag |
|
| 41 | +Miller array info: /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/1I2T_F.mtz:FreeR_flag |
|
| 42 | +Observation type: None |
|
| 43 | +Type of data: int, size=31567 |
|
| 44 | +Type of sigmas: None |
|
| 45 | +Number of Miller indices: 31567 |
|
| 46 | +Anomalous flag: False |
|
| 47 | +Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) |
|
| 48 | +Space group: P 21 21 21 (No. 19) |
|
| 49 | +Systematic absences: 0 |
|
| 50 | +Centric reflections: 3486 |
|
| 51 | +Resolution range: 30.5703 1.041 |
|
| 52 | +Completeness in resolution range: 1 |
|
| 53 | +Completeness with d_max=infinity: 1 |
|
| 54 | +Wavelength: 9.9990 |
|
| 55 | + |
|
| 56 | +Test (R-free flags) flag value: 0 |
|
| 57 | + |
|
| 58 | +Number of work/free reflections by resolution: |
|
| 59 | + work free %free |
|
| 60 | + bin 1: 19.0862 - 2.2418 [3340/3340] 3188 152 4.6% |
|
| 61 | + bin 2: 2.2418 - 1.7798 [3216/3217] 3050 166 5.2% |
|
| 62 | + bin 3: 1.7798 - 1.5549 [3147/3150] 2995 152 4.8% |
|
| 63 | + bin 4: 1.5549 - 1.4128 [3136/3137] 2983 153 4.9% |
|
| 64 | + bin 5: 1.4128 - 1.3116 [3144/3146] 2979 165 5.2% |
|
| 65 | + bin 6: 1.3116 - 1.2343 [3134/3134] 2981 153 4.9% |
|
| 66 | + bin 7: 1.2343 - 1.1725 [3107/3107] 2951 156 5.0% |
|
| 67 | + bin 8: 1.1725 - 1.1214 [3108/3114] 2950 158 5.1% |
|
| 68 | + bin 9: 1.1214 - 1.0783 [3103/3128] 2951 152 4.9% |
|
| 69 | + bin 10: 1.0783 - 1.0411 [3014/3083] 2860 154 5.1% |
|
| 70 | + overall 29888 1561 5.0% |
|
| 71 | + |
|
| 72 | + ----------Processing PDB file(s)---------- |
|
| 73 | + |
|
| 74 | + Monomer Library directory: |
|
| 75 | + "/programs/x86_64-linux/phenix/1.13-2998/phenix-1.13-2998/modules/chem_data/mon_lib" |
|
| 76 | + Total number of atoms: 602 |
|
| 77 | + Number of models: 1 |
|
| 78 | + Model: "" |
|
| 79 | + Number of chains: 2 |
|
| 80 | + Chain: "A" |
|
| 81 | + Number of atoms: 472 |
|
| 82 | + Number of conformers: 1 |
|
| 83 | + Conformer: "" |
|
| 84 | + Number of residues, atoms: 61, 472 |
|
| 85 | + Classifications: {'peptide': 61} |
|
| 86 | + Modifications used: {'COO': 1} |
|
| 87 | + Link IDs: {'PTRANS': 3, 'TRANS': 57} |
|
| 88 | + Chain: "A" |
|
| 89 | + Number of atoms: 130 |
|
| 90 | + Number of conformers: 1 |
|
| 91 | + Conformer: "" |
|
| 92 | + Number of residues, atoms: 130, 130 |
|
| 93 | + Classifications: {'water': 130} |
|
| 94 | + Link IDs: {None: 129} |
|
| 95 | + Time building chain proxies: 0.35, per 1000 atoms: 0.58 |
|
| 96 | + Number of scatterers: 602 |
|
| 97 | + At special positions: 0 |
|
| 98 | + Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) |
|
| 99 | + Space group: P 21 21 21 (No. 19) |
|
| 100 | + Number of sites at special positions: 0 |
|
| 101 | + Number of scattering types: 4 |
|
| 102 | + Type Number sf(0) |
|
| 103 | + S 3 16.00 |
|
| 104 | + O 216 8.00 |
|
| 105 | + N 85 7.00 |
|
| 106 | + C 298 6.00 |
|
| 107 | + sf(0) = scattering factor at diffraction angle 0. |
|
| 108 | + |
|
| 109 | + Number of disulfides: simple=0, symmetry=0 |
|
| 110 | + Custom bonds: |
|
| 111 | + Warning: Ignoring bond with distance_ideal = None: |
|
| 112 | + atom_selection_1 = None |
|
| 113 | + atom_selection_2 = None |
|
| 114 | + Total number of custom bonds: 0 |
|
| 115 | + Custom angles: |
|
| 116 | + Warning: Ignoring angle with angle_ideal = None: |
|
| 117 | + atom_selection_1 = None |
|
| 118 | + atom_selection_2 = None |
|
| 119 | + atom_selection_3 = None |
|
| 120 | + Total number of custom angles: 0 |
|
| 121 | + Custom dihedrals: |
|
| 122 | + Warning: Ignoring dihedral with angle_ideal = None: |
|
| 123 | + atom_selection_1 = None |
|
| 124 | + atom_selection_2 = None |
|
| 125 | + atom_selection_3 = None |
|
| 126 | + atom_selection_4 = None |
|
| 127 | + Total number of custom dihedrals: 0 |
|
| 128 | + Custom planarities: |
|
| 129 | + Warning: Ignoring planarity with with sigma <= 0: |
|
| 130 | + atom_selection = None |
|
| 131 | +None |
|
| 132 | + Total number of custom planarities: 0 |
|
| 133 | + Custom parallelities: |
|
| 134 | +Warning: Ignoring parallelity with empty atom selection. |
|
| 135 | + Total number of custom parallelities: 0 |
|
| 136 | + |
|
| 137 | + Automatic linking |
|
| 138 | + Parameters for automatic linking |
|
| 139 | + Linking & cutoffs |
|
| 140 | + Metal : False - 3.50 |
|
| 141 | + Amimo acid : False - 1.90 |
|
| 142 | + Carbohydrate : True - 1.99 |
|
| 143 | + Ligands : True - 1.99 |
|
| 144 | + Small molecules : False - 1.98 |
|
| 145 | + Amino acid - RNA/DNA : False |
|
| 146 | + |
|
| 147 | + Number of custom bonds: simple=0, symmetry=0 |
|
| 148 | + Time building additional restraints: 0.11 |
|
| 149 | + Conformation dependent library (CDL) restraints added in 24.1 milliseconds |
|
| 150 | + |
|
| 151 | + Adding C-beta torsion restraints... |
|
| 152 | + Number of C-beta restraints generated: 116 |
|
| 153 | + |
|
| 154 | + Time building geometry restraints manager: 0.14 seconds |
|
| 155 | + |
|
| 156 | + NOTE: a complete listing of the restraints can be obtained by requesting |
|
| 157 | + output of .geo file. |
|
| 158 | + |
|
| 159 | + Histogram of bond lengths: |
|
| 160 | + 1.22 - 1.35: 161 |
|
| 161 | + 1.35 - 1.48: 94 |
|
| 162 | + 1.48 - 1.61: 217 |
|
| 163 | + 1.61 - 1.74: 0 |
|
| 164 | + 1.74 - 1.87: 6 |
|
| 165 | + Bond restraints: 478 |
|
| 166 | + Sorted by residual: |
|
| 167 | + bond pdb=" C GLY A1069 " |
|
| 168 | + pdb=" OXT GLY A1069 " |
|
| 169 | + ideal model delta sigma weight residual |
|
| 170 | + 1.231 1.363 -0.132 2.00e-02 2.50e+03 4.36e+01 |
|
| 171 | + bond pdb=" CG MET A1024 " |
|
| 172 | + pdb=" SD MET A1024 " |
|
| 173 | + ideal model delta sigma weight residual |
|
| 174 | + 1.803 1.874 -0.071 2.50e-02 1.60e+03 8.11e+00 |
|
| 175 | + bond pdb=" CG MET A1035 " |
|
| 176 | + pdb=" SD MET A1035 " |
|
| 177 | + ideal model delta sigma weight residual |
|
| 178 | + 1.803 1.873 -0.070 2.50e-02 1.60e+03 7.94e+00 |
|
| 179 | + bond pdb=" SD MET A1035 " |
|
| 180 | + pdb=" CE MET A1035 " |
|
| 181 | + ideal model delta sigma weight residual |
|
| 182 | + 1.791 1.849 -0.058 2.50e-02 1.60e+03 5.41e+00 |
|
| 183 | + bond pdb=" SD MET A1024 " |
|
| 184 | + pdb=" CE MET A1024 " |
|
| 185 | + ideal model delta sigma weight residual |
|
| 186 | + 1.791 1.842 -0.051 2.50e-02 1.60e+03 4.10e+00 |
|
| 187 | + ... (remaining 473 not shown) |
|
| 188 | + |
|
| 189 | + Histogram of bond angle deviations from ideal: |
|
| 190 | + 96.82 - 105.53: 15 |
|
| 191 | + 105.53 - 114.23: 281 |
|
| 192 | + 114.23 - 122.94: 314 |
|
| 193 | + 122.94 - 131.65: 32 |
|
| 194 | + 131.65 - 140.35: 3 |
|
| 195 | + Bond angle restraints: 645 |
|
| 196 | + Sorted by residual: |
|
| 197 | + angle pdb=" CA GLY A1069 " |
|
| 198 | + pdb=" C GLY A1069 " |
|
| 199 | + pdb=" OXT GLY A1069 " |
|
| 200 | + ideal model delta sigma weight residual |
|
| 201 | + 121.00 140.35 -19.35 3.00e+00 1.11e-01 4.16e+01 |
|
| 202 | + angle pdb=" O GLY A1069 " |
|
| 203 | + pdb=" C GLY A1069 " |
|
| 204 | + pdb=" OXT GLY A1069 " |
|
| 205 | + ideal model delta sigma weight residual |
|
| 206 | + 118.00 99.51 18.49 3.00e+00 1.11e-01 3.80e+01 |
|
| 207 | + angle pdb=" CA HIS A1068 " |
|
| 208 | + pdb=" CB HIS A1068 " |
|
| 209 | + pdb=" CG HIS A1068 " |
|
| 210 | + ideal model delta sigma weight residual |
|
| 211 | + 113.80 118.12 -4.32 1.00e+00 1.00e+00 1.86e+01 |
|
| 212 | + angle pdb=" CB GLN A1011 " |
|
| 213 | + pdb=" CG GLN A1011 " |
|
| 214 | + pdb=" CD GLN A1011 " |
|
| 215 | + ideal model delta sigma weight residual |
|
| 216 | + 112.60 119.69 -7.09 1.70e+00 3.46e-01 1.74e+01 |
|
| 217 | + angle pdb=" OE1 GLN A1011 " |
|
| 218 | + pdb=" CD GLN A1011 " |
|
| 219 | + pdb=" NE2 GLN A1011 " |
|
| 220 | + ideal model delta sigma weight residual |
|
| 221 | + 122.60 119.13 3.47 1.00e+00 1.00e+00 1.21e+01 |
|
| 222 | + ... (remaining 640 not shown) |
|
| 223 | + |
|
| 224 | + Histogram of dihedral angle deviations from ideal: |
|
| 225 | + 0.01 - 16.59: 280 |
|
| 226 | + 16.59 - 33.16: 16 |
|
| 227 | + 33.16 - 49.74: 3 |
|
| 228 | + 49.74 - 66.32: 1 |
|
| 229 | + 66.32 - 82.89: 1 |
|
| 230 | + Dihedral angle restraints: 301 |
|
| 231 | + sinusoidal: 124 |
|
| 232 | + harmonic: 177 |
|
| 233 | + Sorted by residual: |
|
| 234 | + dihedral pdb=" CB MET A1062 " |
|
| 235 | + pdb=" CG MET A1062 " |
|
| 236 | + pdb=" SD MET A1062 " |
|
| 237 | + pdb=" CE MET A1062 " |
|
| 238 | + ideal model delta sinusoidal sigma weight residual |
|
| 239 | + -60.00 -108.96 48.96 3 1.50e+01 4.44e-03 8.71e+00 |
|
| 240 | + dihedral pdb=" CA PHE A1028 " |
|
| 241 | + pdb=" C PHE A1028 " |
|
| 242 | + pdb=" N ALA A1029 " |
|
| 243 | + pdb=" CA ALA A1029 " |
|
| 244 | + ideal model delta harmonic sigma weight residual |
|
| 245 | + -180.00 -167.77 -12.23 0 5.00e+00 4.00e-02 5.98e+00 |
|
| 246 | + dihedral pdb=" CB GLN A1011 " |
|
| 247 | + pdb=" CG GLN A1011 " |
|
| 248 | + pdb=" CD GLN A1011 " |
|
| 249 | + pdb=" OE1 GLN A1011 " |
|
| 250 | + ideal model delta sinusoidal sigma weight residual |
|
| 251 | + 180.00 97.11 82.89 2 3.00e+01 1.11e-03 5.25e+00 |
|
| 252 | + ... (remaining 298 not shown) |
|
| 253 | + |
|
| 254 | + Histogram of chiral volume deviations from ideal: |
|
| 255 | + 0.000 - 0.031: 40 |
|
| 256 | + 0.031 - 0.062: 21 |
|
| 257 | + 0.062 - 0.094: 13 |
|
| 258 | + 0.094 - 0.125: 1 |
|
| 259 | + 0.125 - 0.156: 1 |
|
| 260 | + Chirality restraints: 76 |
|
| 261 | + Sorted by residual: |
|
| 262 | + chirality pdb=" CB ILE A1065 " |
|
| 263 | + pdb=" CA ILE A1065 " |
|
| 264 | + pdb=" CG1 ILE A1065 " |
|
| 265 | + pdb=" CG2 ILE A1065 " |
|
| 266 | + both_signs ideal model delta sigma weight residual |
|
| 267 | + False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.06e-01 |
|
| 268 | + chirality pdb=" CB ILE A1066 " |
|
| 269 | + pdb=" CA ILE A1066 " |
|
| 270 | + pdb=" CG1 ILE A1066 " |
|
| 271 | + pdb=" CG2 ILE A1066 " |
|
| 272 | + both_signs ideal model delta sigma weight residual |
|
| 273 | + False 2.64 2.53 0.11 2.00e-01 2.50e+01 3.06e-01 |
|
| 274 | + chirality pdb=" CA TYR A1018 " |
|
| 275 | + pdb=" N TYR A1018 " |
|
| 276 | + pdb=" C TYR A1018 " |
|
| 277 | + pdb=" CB TYR A1018 " |
|
| 278 | + both_signs ideal model delta sigma weight residual |
|
| 279 | + False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.07e-01 |
|
| 280 | + ... (remaining 73 not shown) |
|
| 281 | + |
|
| 282 | + Planarity restraints: 84 |
|
| 283 | + Sorted by residual: |
|
| 284 | + delta sigma weight rms_deltas residual |
|
| 285 | + plane pdb=" CA SER A1040 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 |
|
| 286 | + pdb=" C SER A1040 " -0.019 2.00e-02 2.50e+03 |
|
| 287 | + pdb=" O SER A1040 " 0.007 2.00e-02 2.50e+03 |
|
| 288 | + pdb=" N PRO A1041 " 0.006 2.00e-02 2.50e+03 |
|
| 289 | + delta sigma weight rms_deltas residual |
|
| 290 | + plane pdb=" CD ARG A1020 " -0.010 2.00e-02 2.50e+03 9.40e-03 1.10e+00 |
|
| 291 | + pdb=" NE ARG A1020 " 0.016 2.00e-02 2.50e+03 |
|
| 292 | + pdb=" CZ ARG A1020 " -0.004 2.00e-02 2.50e+03 |
|
| 293 | + pdb=" NH1 ARG A1020 " 0.005 2.00e-02 2.50e+03 |
|
| 294 | + pdb=" NH2 ARG A1020 " -0.006 2.00e-02 2.50e+03 |
|
| 295 | + delta sigma weight rms_deltas residual |
|
| 296 | + plane pdb=" CA GLN A1043 " 0.005 2.00e-02 2.50e+03 9.14e-03 8.35e-01 |
|
| 297 | + pdb=" C GLN A1043 " -0.016 2.00e-02 2.50e+03 |
|
| 298 | + pdb=" O GLN A1043 " 0.006 2.00e-02 2.50e+03 |
|
| 299 | + pdb=" N LEU A1044 " 0.005 2.00e-02 2.50e+03 |
|
| 300 | + ... (remaining 81 not shown) |
|
| 301 | + |
|
| 302 | + Histogram of nonbonded interaction distances: |
|
| 303 | + 2.29 - 2.81: 225 |
|
| 304 | + 2.81 - 3.33: 667 |
|
| 305 | + 3.33 - 3.86: 1265 |
|
| 306 | + 3.86 - 4.38: 1575 |
|
| 307 | + 4.38 - 4.90: 2246 |
|
| 308 | + Nonbonded interactions: 5978 |
|
| 309 | + Sorted by model distance: |
|
| 310 | + nonbonded pdb=" O HOH A1131 " |
|
| 311 | + pdb=" O HOH A1149 " |
|
| 312 | + model vdw |
|
| 313 | + 2.288 2.440 |
|
| 314 | + nonbonded pdb=" O HOH A1146 " |
|
| 315 | + pdb=" O HOH A1151 " |
|
| 316 | + model vdw |
|
| 317 | + 2.297 2.440 |
|
| 318 | + nonbonded pdb=" O HOH A1130 " |
|
| 319 | + pdb=" O HOH A1177 " |
|
| 320 | + model vdw |
|
| 321 | + 2.297 2.440 |
|
| 322 | + nonbonded pdb=" O HOH A1139 " |
|
| 323 | + pdb=" O HOH A1143 " |
|
| 324 | + model vdw |
|
| 325 | + 2.298 2.440 |
|
| 326 | + nonbonded pdb=" OD2 ASP A1059 " |
|
| 327 | + pdb=" O HOH A1173 " |
|
| 328 | + model vdw |
|
| 329 | + 2.299 2.440 |
|
| 330 | + ... (remaining 5973 not shown) |
|
| 331 | + |
|
| 332 | + NOTE: a complete listing of the restraints can be obtained by requesting |
|
| 333 | + output of .geo file. |
|
| 334 | + |
|
| 335 | +============================== Scattering factors ============================= |
|
| 336 | + |
|
| 337 | + |
|
| 338 | + ----------X-ray scattering dictionary---------- |
|
| 339 | + |
|
| 340 | +Number of scattering types: 4 |
|
| 341 | + Type Number sf(0) Gaussians |
|
| 342 | + S 3 15.96 2 |
|
| 343 | + O 216 7.97 2 |
|
| 344 | + N 85 6.97 2 |
|
| 345 | + C 298 5.97 2 |
|
| 346 | + sf(0) = scattering factor at diffraction angle 0. |
|
| 347 | + |
|
| 348 | +Number of scatterers: 602 |
|
| 349 | +At special positions: 0 |
|
| 350 | +Unit cell: (32.969, 38.166, 51.062, 90, 90, 90) |
|
| 351 | +Space group: P 21 21 21 (No. 19) |
|
| 352 | + |
|
| 353 | + ----------F(model) initialization---------- |
|
| 354 | + |
|
| 355 | + start: r(all,work,free)=0.2720 0.2733 0.2502 n_refl.: 31449 |
|
| 356 | + re-set all scales: r(all,work,free)=0.2720 0.2733 0.2502 n_refl.: 31449 |
|
| 357 | + remove outliers: r(all,work,free)=0.2722 0.2734 0.2502 n_refl.: 31445 |
|
| 358 | +bulk-solvent and scaling: r(all,work,free)=0.1978 0.1984 0.1864 n_refl.: 31445 |
|
| 359 | + remove outliers: r(all,work,free)=0.1977 0.1983 0.1864 n_refl.: 31444 |
|
| 360 | +|-Mask optimization: start----------------------------------------------------| |
|
| 361 | +| Solvent (probe) radius= 1.11 Shrink truncation radius= 0.90 | |
|
| 362 | +| all data: 500 lowest resolution reflections: | |
|
| 363 | +| r_work= 0.1983 r_free= 0.1864 r_work= 0.2432 | |
|
| 364 | +|-----------------------------------------------------------------------------| |
|
| 365 | + |
|
| 366 | +r_solv= 0.00 r_shrink= 0.00 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 367 | +r_solv= 0.10 r_shrink= 0.00 r_work=0.2008 r_free=0.1943 r_work_low=0.3020 |
|
| 368 | +r_solv= 0.20 r_shrink= 0.00 r_work=0.2000 r_free=0.1930 r_work_low=0.2725 |
|
| 369 | +r_solv= 0.30 r_shrink= 0.00 r_work=0.1992 r_free=0.1917 r_work_low=0.2512 |
|
| 370 | +r_solv= 0.40 r_shrink= 0.00 r_work=0.1985 r_free=0.1902 r_work_low=0.2362 |
|
| 371 | +r_solv= 0.50 r_shrink= 0.00 r_work=0.1982 r_free=0.1890 r_work_low=0.2416 |
|
| 372 | +r_solv= 0.60 r_shrink= 0.00 r_work=0.1983 r_free=0.1887 r_work_low=0.2547 |
|
| 373 | +r_solv= 0.70 r_shrink= 0.00 r_work=0.1987 r_free=0.1886 r_work_low=0.2696 |
|
| 374 | +r_solv= 0.80 r_shrink= 0.00 r_work=0.1992 r_free=0.1890 r_work_low=0.2839 |
|
| 375 | +r_solv= 0.90 r_shrink= 0.00 r_work=0.1998 r_free=0.1895 r_work_low=0.2974 |
|
| 376 | +r_solv= 1.00 r_shrink= 0.00 r_work=0.2004 r_free=0.1902 r_work_low=0.3092 |
|
| 377 | +r_solv= 1.10 r_shrink= 0.00 r_work=0.2009 r_free=0.1908 r_work_low=0.3185 |
|
| 378 | +r_solv= 1.20 r_shrink= 0.00 r_work=0.2013 r_free=0.1915 r_work_low=0.3244 |
|
| 379 | +r_solv= 1.30 r_shrink= 0.00 r_work=0.2017 r_free=0.1919 r_work_low=0.3282 |
|
| 380 | +r_solv= 1.40 r_shrink= 0.00 r_work=0.2021 r_free=0.1921 r_work_low=0.3301 |
|
| 381 | +r_solv= 0.00 r_shrink= 0.10 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 382 | +r_solv= 0.10 r_shrink= 0.10 r_work=0.2008 r_free=0.1943 r_work_low=0.3020 |
|
| 383 | +r_solv= 0.20 r_shrink= 0.10 r_work=0.2000 r_free=0.1930 r_work_low=0.2725 |
|
| 384 | +r_solv= 0.30 r_shrink= 0.10 r_work=0.1992 r_free=0.1917 r_work_low=0.2512 |
|
| 385 | +r_solv= 0.40 r_shrink= 0.10 r_work=0.1985 r_free=0.1902 r_work_low=0.2362 |
|
| 386 | +r_solv= 0.50 r_shrink= 0.10 r_work=0.1982 r_free=0.1890 r_work_low=0.2416 |
|
| 387 | +r_solv= 0.60 r_shrink= 0.10 r_work=0.1983 r_free=0.1887 r_work_low=0.2547 |
|
| 388 | +r_solv= 0.70 r_shrink= 0.10 r_work=0.1987 r_free=0.1886 r_work_low=0.2696 |
|
| 389 | +r_solv= 0.80 r_shrink= 0.10 r_work=0.1992 r_free=0.1890 r_work_low=0.2839 |
|
| 390 | +r_solv= 0.90 r_shrink= 0.10 r_work=0.1998 r_free=0.1895 r_work_low=0.2974 |
|
| 391 | +r_solv= 1.00 r_shrink= 0.10 r_work=0.2004 r_free=0.1902 r_work_low=0.3092 |
|
| 392 | +r_solv= 1.10 r_shrink= 0.10 r_work=0.2009 r_free=0.1908 r_work_low=0.3185 |
|
| 393 | +r_solv= 1.20 r_shrink= 0.10 r_work=0.2013 r_free=0.1915 r_work_low=0.3244 |
|
| 394 | +r_solv= 1.30 r_shrink= 0.10 r_work=0.2017 r_free=0.1919 r_work_low=0.3282 |
|
| 395 | +r_solv= 1.40 r_shrink= 0.10 r_work=0.2021 r_free=0.1921 r_work_low=0.3301 |
|
| 396 | +r_solv= 0.00 r_shrink= 0.20 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 397 | +r_solv= 0.10 r_shrink= 0.20 r_work=0.2008 r_free=0.1943 r_work_low=0.3020 |
|
| 398 | +r_solv= 0.20 r_shrink= 0.20 r_work=0.2000 r_free=0.1930 r_work_low=0.2725 |
|
| 399 | +r_solv= 0.30 r_shrink= 0.20 r_work=0.1992 r_free=0.1917 r_work_low=0.2512 |
|
| 400 | +r_solv= 0.40 r_shrink= 0.20 r_work=0.1985 r_free=0.1902 r_work_low=0.2362 |
|
| 401 | +r_solv= 0.50 r_shrink= 0.20 r_work=0.1982 r_free=0.1890 r_work_low=0.2416 |
|
| 402 | +r_solv= 0.60 r_shrink= 0.20 r_work=0.1983 r_free=0.1887 r_work_low=0.2547 |
|
| 403 | +r_solv= 0.70 r_shrink= 0.20 r_work=0.1987 r_free=0.1886 r_work_low=0.2696 |
|
| 404 | +r_solv= 0.80 r_shrink= 0.20 r_work=0.1992 r_free=0.1890 r_work_low=0.2839 |
|
| 405 | +r_solv= 0.90 r_shrink= 0.20 r_work=0.1998 r_free=0.1895 r_work_low=0.2974 |
|
| 406 | +r_solv= 1.00 r_shrink= 0.20 r_work=0.2004 r_free=0.1902 r_work_low=0.3092 |
|
| 407 | +r_solv= 1.10 r_shrink= 0.20 r_work=0.2009 r_free=0.1908 r_work_low=0.3185 |
|
| 408 | +r_solv= 1.20 r_shrink= 0.20 r_work=0.2013 r_free=0.1915 r_work_low=0.3244 |
|
| 409 | +r_solv= 1.30 r_shrink= 0.20 r_work=0.2017 r_free=0.1919 r_work_low=0.3282 |
|
| 410 | +r_solv= 1.40 r_shrink= 0.20 r_work=0.2021 r_free=0.1921 r_work_low=0.3301 |
|
| 411 | +r_solv= 0.00 r_shrink= 0.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 412 | +r_solv= 0.10 r_shrink= 0.30 r_work=0.2016 r_free=0.1953 r_work_low=0.3304 |
|
| 413 | +r_solv= 0.20 r_shrink= 0.30 r_work=0.2016 r_free=0.1955 r_work_low=0.3276 |
|
| 414 | +r_solv= 0.30 r_shrink= 0.30 r_work=0.2010 r_free=0.1946 r_work_low=0.3013 |
|
| 415 | +r_solv= 0.40 r_shrink= 0.30 r_work=0.2000 r_free=0.1932 r_work_low=0.2660 |
|
| 416 | +r_solv= 0.50 r_shrink= 0.30 r_work=0.1990 r_free=0.1916 r_work_low=0.2412 |
|
| 417 | +r_solv= 0.60 r_shrink= 0.30 r_work=0.1982 r_free=0.1900 r_work_low=0.2313 |
|
| 418 | +r_solv= 0.70 r_shrink= 0.30 r_work=0.1981 r_free=0.1886 r_work_low=0.2402 |
|
| 419 | +r_solv= 0.80 r_shrink= 0.30 r_work=0.1983 r_free=0.1881 r_work_low=0.2578 |
|
| 420 | +r_solv= 0.90 r_shrink= 0.30 r_work=0.1988 r_free=0.1883 r_work_low=0.2731 |
|
| 421 | +r_solv= 1.00 r_shrink= 0.30 r_work=0.1994 r_free=0.1889 r_work_low=0.2870 |
|
| 422 | +r_solv= 1.10 r_shrink= 0.30 r_work=0.2000 r_free=0.1896 r_work_low=0.2997 |
|
| 423 | +r_solv= 1.20 r_shrink= 0.30 r_work=0.2006 r_free=0.1904 r_work_low=0.3110 |
|
| 424 | +r_solv= 1.30 r_shrink= 0.30 r_work=0.2010 r_free=0.1910 r_work_low=0.3207 |
|
| 425 | +r_solv= 1.40 r_shrink= 0.30 r_work=0.2014 r_free=0.1916 r_work_low=0.3262 |
|
| 426 | +r_solv= 0.00 r_shrink= 0.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 427 | +r_solv= 0.10 r_shrink= 0.40 r_work=0.2016 r_free=0.1952 r_work_low=0.3305 |
|
| 428 | +r_solv= 0.20 r_shrink= 0.40 r_work=0.2016 r_free=0.1953 r_work_low=0.3299 |
|
| 429 | +r_solv= 0.30 r_shrink= 0.40 r_work=0.2017 r_free=0.1956 r_work_low=0.3277 |
|
| 430 | +r_solv= 0.40 r_shrink= 0.40 r_work=0.2010 r_free=0.1948 r_work_low=0.2980 |
|
| 431 | +r_solv= 0.50 r_shrink= 0.40 r_work=0.1999 r_free=0.1930 r_work_low=0.2610 |
|
| 432 | +r_solv= 0.60 r_shrink= 0.40 r_work=0.1988 r_free=0.1914 r_work_low=0.2377 |
|
| 433 | +r_solv= 0.70 r_shrink= 0.40 r_work=0.1981 r_free=0.1896 r_work_low=0.2319 |
|
| 434 | +r_solv= 0.80 r_shrink= 0.40 r_work=0.1981 r_free=0.1880 r_work_low=0.2434 |
|
| 435 | +r_solv= 0.90 r_shrink= 0.40 r_work=0.1984 r_free=0.1879 r_work_low=0.2597 |
|
| 436 | +r_solv= 1.00 r_shrink= 0.40 r_work=0.1990 r_free=0.1882 r_work_low=0.2751 |
|
| 437 | +r_solv= 1.10 r_shrink= 0.40 r_work=0.1995 r_free=0.1889 r_work_low=0.2880 |
|
| 438 | +r_solv= 1.20 r_shrink= 0.40 r_work=0.2001 r_free=0.1897 r_work_low=0.3000 |
|
| 439 | +r_solv= 1.30 r_shrink= 0.40 r_work=0.2006 r_free=0.1904 r_work_low=0.3123 |
|
| 440 | +r_solv= 1.40 r_shrink= 0.40 r_work=0.2011 r_free=0.1911 r_work_low=0.3218 |
|
| 441 | +r_solv= 0.00 r_shrink= 0.50 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 442 | +r_solv= 0.10 r_shrink= 0.50 r_work=0.2016 r_free=0.1952 r_work_low=0.3305 |
|
| 443 | +r_solv= 0.20 r_shrink= 0.50 r_work=0.2016 r_free=0.1953 r_work_low=0.3301 |
|
| 444 | +r_solv= 0.30 r_shrink= 0.50 r_work=0.2017 r_free=0.1956 r_work_low=0.3301 |
|
| 445 | +r_solv= 0.40 r_shrink= 0.50 r_work=0.2014 r_free=0.1957 r_work_low=0.3131 |
|
| 446 | +r_solv= 0.50 r_shrink= 0.50 r_work=0.2004 r_free=0.1938 r_work_low=0.2737 |
|
| 447 | +r_solv= 0.60 r_shrink= 0.50 r_work=0.1992 r_free=0.1921 r_work_low=0.2436 |
|
| 448 | +r_solv= 0.70 r_shrink= 0.50 r_work=0.1983 r_free=0.1900 r_work_low=0.2321 |
|
| 449 | +r_solv= 0.80 r_shrink= 0.50 r_work=0.1981 r_free=0.1883 r_work_low=0.2383 |
|
| 450 | +r_solv= 0.90 r_shrink= 0.50 r_work=0.1983 r_free=0.1877 r_work_low=0.2530 |
|
| 451 | +r_solv= 1.00 r_shrink= 0.50 r_work=0.1988 r_free=0.1878 r_work_low=0.2690 |
|
| 452 | +r_solv= 1.10 r_shrink= 0.50 r_work=0.1993 r_free=0.1885 r_work_low=0.2827 |
|
| 453 | +r_solv= 1.20 r_shrink= 0.50 r_work=0.1999 r_free=0.1894 r_work_low=0.2945 |
|
| 454 | +r_solv= 1.30 r_shrink= 0.50 r_work=0.2004 r_free=0.1901 r_work_low=0.3078 |
|
| 455 | +r_solv= 1.40 r_shrink= 0.50 r_work=0.2009 r_free=0.1909 r_work_low=0.3188 |
|
| 456 | +r_solv= 0.00 r_shrink= 0.60 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 457 | +r_solv= 0.10 r_shrink= 0.60 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 458 | +r_solv= 0.20 r_shrink= 0.60 r_work=0.2016 r_free=0.1952 r_work_low=0.3304 |
|
| 459 | +r_solv= 0.30 r_shrink= 0.60 r_work=0.2017 r_free=0.1955 r_work_low=0.3325 |
|
| 460 | +r_solv= 0.40 r_shrink= 0.60 r_work=0.2018 r_free=0.1962 r_work_low=0.3309 |
|
| 461 | +r_solv= 0.50 r_shrink= 0.60 r_work=0.2014 r_free=0.1959 r_work_low=0.3076 |
|
| 462 | +r_solv= 0.60 r_shrink= 0.60 r_work=0.2005 r_free=0.1946 r_work_low=0.2727 |
|
| 463 | +r_solv= 0.70 r_shrink= 0.60 r_work=0.1993 r_free=0.1918 r_work_low=0.2444 |
|
| 464 | +r_solv= 0.80 r_shrink= 0.60 r_work=0.1984 r_free=0.1898 r_work_low=0.2395 |
|
| 465 | +r_solv= 0.90 r_shrink= 0.60 r_work=0.1981 r_free=0.1881 r_work_low=0.2414 |
|
| 466 | +r_solv= 1.00 r_shrink= 0.60 r_work=0.1984 r_free=0.1870 r_work_low=0.2535 |
|
| 467 | +r_solv= 1.10 r_shrink= 0.60 r_work=0.1988 r_free=0.1876 r_work_low=0.2667 |
|
| 468 | +r_solv= 1.20 r_shrink= 0.60 r_work=0.1994 r_free=0.1885 r_work_low=0.2799 |
|
| 469 | +r_solv= 1.30 r_shrink= 0.60 r_work=0.1999 r_free=0.1892 r_work_low=0.2932 |
|
| 470 | +r_solv= 1.40 r_shrink= 0.60 r_work=0.2004 r_free=0.1902 r_work_low=0.3069 |
|
| 471 | +r_solv= 0.00 r_shrink= 0.70 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 472 | +r_solv= 0.10 r_shrink= 0.70 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 473 | +r_solv= 0.20 r_shrink= 0.70 r_work=0.2016 r_free=0.1952 r_work_low=0.3305 |
|
| 474 | +r_solv= 0.30 r_shrink= 0.70 r_work=0.2017 r_free=0.1954 r_work_low=0.3325 |
|
| 475 | +r_solv= 0.40 r_shrink= 0.70 r_work=0.2018 r_free=0.1962 r_work_low=0.3342 |
|
| 476 | +r_solv= 0.50 r_shrink= 0.70 r_work=0.2016 r_free=0.1961 r_work_low=0.3168 |
|
| 477 | +r_solv= 0.60 r_shrink= 0.70 r_work=0.2009 r_free=0.1956 r_work_low=0.2864 |
|
| 478 | +r_solv= 0.70 r_shrink= 0.70 r_work=0.1997 r_free=0.1925 r_work_low=0.2547 |
|
| 479 | +r_solv= 0.80 r_shrink= 0.70 r_work=0.1987 r_free=0.1904 r_work_low=0.2429 |
|
| 480 | +r_solv= 0.90 r_shrink= 0.70 r_work=0.1982 r_free=0.1885 r_work_low=0.2420 |
|
| 481 | +r_solv= 1.00 r_shrink= 0.70 r_work=0.1983 r_free=0.1868 r_work_low=0.2488 |
|
| 482 | +r_solv= 1.10 r_shrink= 0.70 r_work=0.1987 r_free=0.1873 r_work_low=0.2599 |
|
| 483 | +r_solv= 1.20 r_shrink= 0.70 r_work=0.1992 r_free=0.1882 r_work_low=0.2745 |
|
| 484 | +r_solv= 1.30 r_shrink= 0.70 r_work=0.1997 r_free=0.1889 r_work_low=0.2882 |
|
| 485 | +r_solv= 1.40 r_shrink= 0.70 r_work=0.2002 r_free=0.1898 r_work_low=0.3019 |
|
| 486 | +r_solv= 0.00 r_shrink= 0.80 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 487 | +r_solv= 0.10 r_shrink= 0.80 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 488 | +r_solv= 0.20 r_shrink= 0.80 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 489 | +r_solv= 0.30 r_shrink= 0.80 r_work=0.2017 r_free=0.1953 r_work_low=0.3325 |
|
| 490 | +r_solv= 0.40 r_shrink= 0.80 r_work=0.2019 r_free=0.1961 r_work_low=0.3376 |
|
| 491 | +r_solv= 0.50 r_shrink= 0.80 r_work=0.2018 r_free=0.1962 r_work_low=0.3280 |
|
| 492 | +r_solv= 0.60 r_shrink= 0.80 r_work=0.2013 r_free=0.1965 r_work_low=0.3023 |
|
| 493 | +r_solv= 0.70 r_shrink= 0.80 r_work=0.2006 r_free=0.1946 r_work_low=0.2769 |
|
| 494 | +r_solv= 0.80 r_shrink= 0.80 r_work=0.1996 r_free=0.1917 r_work_low=0.2647 |
|
| 495 | +r_solv= 0.90 r_shrink= 0.80 r_work=0.1986 r_free=0.1894 r_work_low=0.2530 |
|
| 496 | +r_solv= 1.00 r_shrink= 0.80 r_work=0.1983 r_free=0.1870 r_work_low=0.2479 |
|
| 497 | +r_solv= 1.10 r_shrink= 0.80 r_work=0.1984 r_free=0.1866 r_work_low=0.2483 |
|
| 498 | +r_solv= 1.20 r_shrink= 0.80 r_work=0.1988 r_free=0.1873 r_work_low=0.2619 |
|
| 499 | +r_solv= 1.30 r_shrink= 0.80 r_work=0.1994 r_free=0.1881 r_work_low=0.2782 |
|
| 500 | +r_solv= 1.40 r_shrink= 0.80 r_work=0.1999 r_free=0.1891 r_work_low=0.2922 |
|
| 501 | +r_solv= 0.00 r_shrink= 0.90 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 502 | +r_solv= 0.10 r_shrink= 0.90 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 503 | +r_solv= 0.20 r_shrink= 0.90 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 504 | +r_solv= 0.30 r_shrink= 0.90 r_work=0.2016 r_free=0.1953 r_work_low=0.3318 |
|
| 505 | +r_solv= 0.40 r_shrink= 0.90 r_work=0.2019 r_free=0.1960 r_work_low=0.3386 |
|
| 506 | +r_solv= 0.50 r_shrink= 0.90 r_work=0.2019 r_free=0.1963 r_work_low=0.3345 |
|
| 507 | +r_solv= 0.60 r_shrink= 0.90 r_work=0.2016 r_free=0.1968 r_work_low=0.3126 |
|
| 508 | +r_solv= 0.70 r_shrink= 0.90 r_work=0.2011 r_free=0.1955 r_work_low=0.2890 |
|
| 509 | +r_solv= 0.80 r_shrink= 0.90 r_work=0.2002 r_free=0.1933 r_work_low=0.2820 |
|
| 510 | +r_solv= 0.90 r_shrink= 0.90 r_work=0.1991 r_free=0.1904 r_work_low=0.2658 |
|
| 511 | +r_solv= 1.00 r_shrink= 0.90 r_work=0.1984 r_free=0.1873 r_work_low=0.2538 |
|
| 512 | +r_solv= 1.10 r_shrink= 0.90 r_work=0.1983 r_free=0.1866 r_work_low=0.2429 |
|
| 513 | +r_solv= 1.20 r_shrink= 0.90 r_work=0.1986 r_free=0.1869 r_work_low=0.2538 |
|
| 514 | +r_solv= 1.30 r_shrink= 0.90 r_work=0.1991 r_free=0.1875 r_work_low=0.2702 |
|
| 515 | +r_solv= 1.40 r_shrink= 0.90 r_work=0.1996 r_free=0.1886 r_work_low=0.2851 |
|
| 516 | +r_solv= 0.00 r_shrink= 1.00 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 517 | +r_solv= 0.10 r_shrink= 1.00 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 518 | +r_solv= 0.20 r_shrink= 1.00 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 519 | +r_solv= 0.30 r_shrink= 1.00 r_work=0.2016 r_free=0.1953 r_work_low=0.3312 |
|
| 520 | +r_solv= 0.40 r_shrink= 1.00 r_work=0.2019 r_free=0.1960 r_work_low=0.3388 |
|
| 521 | +r_solv= 0.50 r_shrink= 1.00 r_work=0.2019 r_free=0.1962 r_work_low=0.3390 |
|
| 522 | +r_solv= 0.60 r_shrink= 1.00 r_work=0.2017 r_free=0.1970 r_work_low=0.3216 |
|
| 523 | +r_solv= 0.70 r_shrink= 1.00 r_work=0.2014 r_free=0.1961 r_work_low=0.3012 |
|
| 524 | +r_solv= 0.80 r_shrink= 1.00 r_work=0.2007 r_free=0.1945 r_work_low=0.2936 |
|
| 525 | +r_solv= 0.90 r_shrink= 1.00 r_work=0.1997 r_free=0.1917 r_work_low=0.2852 |
|
| 526 | +r_solv= 1.00 r_shrink= 1.00 r_work=0.1988 r_free=0.1878 r_work_low=0.2655 |
|
| 527 | +r_solv= 1.10 r_shrink= 1.00 r_work=0.1984 r_free=0.1868 r_work_low=0.2433 |
|
| 528 | +r_solv= 1.20 r_shrink= 1.00 r_work=0.1985 r_free=0.1865 r_work_low=0.2470 |
|
| 529 | +r_solv= 1.30 r_shrink= 1.00 r_work=0.1989 r_free=0.1869 r_work_low=0.2628 |
|
| 530 | +r_solv= 1.40 r_shrink= 1.00 r_work=0.1994 r_free=0.1881 r_work_low=0.2771 |
|
| 531 | +r_solv= 0.00 r_shrink= 1.10 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 532 | +r_solv= 0.10 r_shrink= 1.10 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 533 | +r_solv= 0.20 r_shrink= 1.10 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 534 | +r_solv= 0.30 r_shrink= 1.10 r_work=0.2016 r_free=0.1952 r_work_low=0.3308 |
|
| 535 | +r_solv= 0.40 r_shrink= 1.10 r_work=0.2018 r_free=0.1959 r_work_low=0.3383 |
|
| 536 | +r_solv= 0.50 r_shrink= 1.10 r_work=0.2020 r_free=0.1962 r_work_low=0.3411 |
|
| 537 | +r_solv= 0.60 r_shrink= 1.10 r_work=0.2018 r_free=0.1971 r_work_low=0.3285 |
|
| 538 | +r_solv= 0.70 r_shrink= 1.10 r_work=0.2017 r_free=0.1966 r_work_low=0.3122 |
|
| 539 | +r_solv= 0.80 r_shrink= 1.10 r_work=0.2011 r_free=0.1954 r_work_low=0.3052 |
|
| 540 | +r_solv= 0.90 r_shrink= 1.10 r_work=0.2002 r_free=0.1932 r_work_low=0.3026 |
|
| 541 | +r_solv= 1.00 r_shrink= 1.10 r_work=0.1994 r_free=0.1883 r_work_low=0.2830 |
|
| 542 | +r_solv= 1.10 r_shrink= 1.10 r_work=0.1986 r_free=0.1868 r_work_low=0.2513 |
|
| 543 | +r_solv= 1.20 r_shrink= 1.10 r_work=0.1984 r_free=0.1868 r_work_low=0.2434 |
|
| 544 | +r_solv= 1.30 r_shrink= 1.10 r_work=0.1987 r_free=0.1866 r_work_low=0.2542 |
|
| 545 | +r_solv= 1.40 r_shrink= 1.10 r_work=0.1992 r_free=0.1873 r_work_low=0.2684 |
|
| 546 | +r_solv= 0.00 r_shrink= 1.20 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 547 | +r_solv= 0.10 r_shrink= 1.20 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 548 | +r_solv= 0.20 r_shrink= 1.20 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 549 | +r_solv= 0.30 r_shrink= 1.20 r_work=0.2016 r_free=0.1952 r_work_low=0.3307 |
|
| 550 | +r_solv= 0.40 r_shrink= 1.20 r_work=0.2018 r_free=0.1957 r_work_low=0.3374 |
|
| 551 | +r_solv= 0.50 r_shrink= 1.20 r_work=0.2020 r_free=0.1961 r_work_low=0.3417 |
|
| 552 | +r_solv= 0.60 r_shrink= 1.20 r_work=0.2019 r_free=0.1970 r_work_low=0.3333 |
|
| 553 | +r_solv= 0.70 r_shrink= 1.20 r_work=0.2019 r_free=0.1968 r_work_low=0.3196 |
|
| 554 | +r_solv= 0.80 r_shrink= 1.20 r_work=0.2013 r_free=0.1960 r_work_low=0.3114 |
|
| 555 | +r_solv= 0.90 r_shrink= 1.20 r_work=0.2005 r_free=0.1942 r_work_low=0.3138 |
|
| 556 | +r_solv= 1.00 r_shrink= 1.20 r_work=0.1997 r_free=0.1889 r_work_low=0.2941 |
|
| 557 | +r_solv= 1.10 r_shrink= 1.20 r_work=0.1989 r_free=0.1870 r_work_low=0.2617 |
|
| 558 | +r_solv= 1.20 r_shrink= 1.20 r_work=0.1985 r_free=0.1871 r_work_low=0.2457 |
|
| 559 | +r_solv= 1.30 r_shrink= 1.20 r_work=0.1985 r_free=0.1864 r_work_low=0.2471 |
|
| 560 | +r_solv= 1.40 r_shrink= 1.20 r_work=0.1991 r_free=0.1870 r_work_low=0.2634 |
|
| 561 | +r_solv= 0.00 r_shrink= 1.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 562 | +r_solv= 0.10 r_shrink= 1.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 563 | +r_solv= 0.20 r_shrink= 1.30 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 564 | +r_solv= 0.30 r_shrink= 1.30 r_work=0.2016 r_free=0.1952 r_work_low=0.3307 |
|
| 565 | +r_solv= 0.40 r_shrink= 1.30 r_work=0.2018 r_free=0.1957 r_work_low=0.3370 |
|
| 566 | +r_solv= 0.50 r_shrink= 1.30 r_work=0.2020 r_free=0.1960 r_work_low=0.3418 |
|
| 567 | +r_solv= 0.60 r_shrink= 1.30 r_work=0.2019 r_free=0.1970 r_work_low=0.3358 |
|
| 568 | +r_solv= 0.70 r_shrink= 1.30 r_work=0.2019 r_free=0.1970 r_work_low=0.3237 |
|
| 569 | +r_solv= 0.80 r_shrink= 1.30 r_work=0.2015 r_free=0.1965 r_work_low=0.3155 |
|
| 570 | +r_solv= 0.90 r_shrink= 1.30 r_work=0.2007 r_free=0.1950 r_work_low=0.3221 |
|
| 571 | +r_solv= 1.00 r_shrink= 1.30 r_work=0.1999 r_free=0.1895 r_work_low=0.3035 |
|
| 572 | +r_solv= 1.10 r_shrink= 1.30 r_work=0.1991 r_free=0.1872 r_work_low=0.2676 |
|
| 573 | +r_solv= 1.20 r_shrink= 1.30 r_work=0.1986 r_free=0.1874 r_work_low=0.2504 |
|
| 574 | +r_solv= 1.30 r_shrink= 1.30 r_work=0.1984 r_free=0.1864 r_work_low=0.2449 |
|
| 575 | +r_solv= 1.40 r_shrink= 1.30 r_work=0.1990 r_free=0.1868 r_work_low=0.2594 |
|
| 576 | +r_solv= 0.00 r_shrink= 1.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 577 | +r_solv= 0.10 r_shrink= 1.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 578 | +r_solv= 0.20 r_shrink= 1.40 r_work=0.2015 r_free=0.1952 r_work_low=0.3306 |
|
| 579 | +r_solv= 0.30 r_shrink= 1.40 r_work=0.2016 r_free=0.1952 r_work_low=0.3306 |
|
| 580 | +r_solv= 0.40 r_shrink= 1.40 r_work=0.2017 r_free=0.1955 r_work_low=0.3357 |
|
| 581 | +r_solv= 0.50 r_shrink= 1.40 r_work=0.2019 r_free=0.1959 r_work_low=0.3411 |
|
| 582 | +r_solv= 0.60 r_shrink= 1.40 r_work=0.2019 r_free=0.1968 r_work_low=0.3389 |
|
| 583 | +r_solv= 0.70 r_shrink= 1.40 r_work=0.2020 r_free=0.1972 r_work_low=0.3300 |
|
| 584 | +r_solv= 0.80 r_shrink= 1.40 r_work=0.2017 r_free=0.1971 r_work_low=0.3218 |
|
| 585 | +r_solv= 0.90 r_shrink= 1.40 r_work=0.2011 r_free=0.1960 r_work_low=0.3323 |
|
| 586 | +r_solv= 1.00 r_shrink= 1.40 r_work=0.2003 r_free=0.1905 r_work_low=0.3169 |
|
| 587 | +r_solv= 1.10 r_shrink= 1.40 r_work=0.1995 r_free=0.1881 r_work_low=0.2785 |
|
| 588 | +r_solv= 1.20 r_shrink= 1.40 r_work=0.1989 r_free=0.1874 r_work_low=0.2593 |
|
| 589 | +r_solv= 1.30 r_shrink= 1.40 r_work=0.1984 r_free=0.1866 r_work_low=0.2447 |
|
| 590 | +r_solv= 1.40 r_shrink= 1.40 r_work=0.1989 r_free=0.1866 r_work_low=0.2549 |
|
| 591 | + |
|
| 592 | +|-Mask optimization: final----------------------------------------------------| |
|
| 593 | +| Solvent (probe) radius= 0.70 Shrink truncation radius= 0.30 | |
|
| 594 | +| all data: 500 lowest resolution reflections: | |
|
| 595 | +| r_work= 0.1981 r_free= 0.1886 r_work= 0.2402 | |
|
| 596 | +|-----------------------------------------------------------------------------| |
|
| 597 | + |
|
| 598 | +|--(resolution: 1.04 - 19.08 A, n_refl.=31444 (all), 4.96 % free)------------| |
|
| 599 | +| | |
|
| 600 | +| r_work= 0.1981 r_free= 0.1886 coordinate error (max.-lik. estimate): 0.09 A | |
|
| 601 | +| | |
|
| 602 | +| normalized target function (ml) (work): 4.640880 | |
|
| 603 | +| target function (ml) not normalized (work): 138683.431375 | |
|
| 604 | +| target function (ml) not normalized (free): 7189.821067 | |
|
| 605 | +|-----------------------------------------------------------------------------| |
|
| 606 | + |
|
| 607 | +End of input processing |
|
| 608 | + |
|
| 609 | +======================= ROSETTA/PHENIX X-ray refinement ======================= |
|
| 610 | + |
|
| 611 | +Output directory: |
|
| 612 | + /nfs/staff/key/software_tests/PHENIX.ROSETTA.REFINE_linux/rosetta_refine_4 |
|
| 613 | + |
|
| 614 | + ----------Setting up input files for Rosetta---------- |
|
| 615 | + |
|
| 616 | +|-starting model--------------------------------------------------------------| |
|
| 617 | +| target_work(ml) = 4.64088 r_work = 0.1981 r_free = 0.1886 | |
|
| 618 | +|-----------------------------------------------------------------------------| |
|
| 619 | + |
|
| 620 | + Validation statistics (starting model): |
|
| 621 | + Ramachandran outliers = 0.00 % |
|
| 622 | + favored = 100.00 % |
|
| 623 | + Rotamer outliers = 2.04 % |
|
| 624 | + C-beta deviations = 0 |
|
| 625 | + Clashscore = 4.15 |
|
| 626 | + RMS(bonds) = 0.0000 |
|
| 627 | + RMS(angles) = 0.00 |
|
| 628 | + MolProbity score = 1.43 |
|
| 629 | + |
|
| 630 | + |
|
| 631 | +Rosetta command-line arguments: |
|
| 632 | + -parser:protocol /programs/x86_64-linux/rosetta/3.8/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml |
|
| 633 | + -s 1I2T_modified_rosetta_in.pdb |
|
| 634 | + -mtzfile 1I2T_modified_rosetta_data.mtz |
|
| 635 | + -run:preserve_header |
|
| 636 | + -crystal_refine |
|
| 637 | + -parser:script_vars symmdef=1I2T_modified_rosetta.symm |
|
| 638 | + -parser:script_vars bfactstrat=individual |
|
| 639 | + -parser:script_vars map_type=Auto |
|
| 640 | + -score:weights talaris2013_cart |
|
| 641 | + -nstruct 1 |
|
| 642 | + -database /programs/x86_64-linux/rosetta/3.8/main/database |
|
| 643 | + |
|
| 644 | +Generating 5 models on 1 processors... |
|
| 645 | + |
|
| 646 | + 1: r_work = 0.2200 r_free = 0.2181 energy = -694.96 rmsd = 0.946 *** |
|
| 647 | + 2: r_work = 0.2207 r_free = 0.2171 energy = -698.52 rmsd = 1.065 *** |
|
| 648 | + 3: r_work = 0.2206 r_free = 0.2139 energy = -704.21 rmsd = 0.970 *** |
|
| 649 | + 4: r_work = 0.2199 r_free = 0.2152 energy = -711.36 rmsd = 1.001 |
|
| 650 | + 5: r_work = 0.2231 r_free = 0.2205 energy = -703.18 rmsd = 1.156 |
|
| 651 | + |
|
| 652 | +|-after ROSETTA---------------------------------------------------------------| |
|
| 653 | +| target_work(ml) = 4.64366 r_work = 0.2206 r_free = 0.2139 | |
|
| 654 | +|-----------------------------------------------------------------------------| |
|
| 655 | + |
|
| 656 | + Validation statistics after ROSETTA: |
|
| 657 | + Ramachandran outliers = 0.00 % |
|
| 658 | + favored = 100.00 % |
|
| 659 | + Rotamer outliers = 0.00 % |
|
| 660 | + C-beta deviations = 0 |
|
| 661 | + Clashscore = 0.00 |
|
| 662 | + RMS(bonds) = 0.0000 |
|
| 663 | + RMS(angles) = 0.00 |
|
| 664 | + MolProbity score = 0.50 |
|
| 665 | + |
|
| 666 | + |
|
| 667 | + ----------Running phenix.refine (with null strategy)---------- |
|
| 668 | + |
|
| 669 | +start r_work=0.2898 r_free=0.2737 |
|
| 670 | +1_bss r_work=0.2120 r_free=0.2065 |
|
| 671 | +end r_work=0.2120 r_free=0.2065 |
|
| 672 | + Ramachandran outliers = 0.00 % |
|
| 673 | + favored = 100.00 % |
|
| 674 | + Rotamer outliers = 0.00 % |
|
| 675 | + C-beta deviations = 0 |
|
| 676 | + Clashscore = 9.34 |
|
| 677 | + RMS(bonds) = 0.1003 |
|
| 678 | + RMS(angles) = 1.77 |
|
| 679 | + MolProbity score = 1.49 |
|
| 680 | + Resolution = 1.04 |
|
| 681 | + R-work = 0.2120 |
|
| 682 | + R-free = 0.2065 |
|
| 683 | + |
|
| 684 | + ----------Final results---------- |
|
| 685 | + |
|
| 686 | + |
|
| 687 | +Refined model: 1I2T_modified_rosetta_phenix_001.pdb |
|
| 688 | +Final maps: 1I2T_modified_rosetta_phenix_001.mtz |
|
| 689 | + |
|
| 690 | +Elapsed time: 9291.2s |
|
| 691 | + |
|
| 692 | +Citation: |
|
| 693 | + |
|
| 694 | +DiMaio F., Echols N., Headd J.J., Terwilliger T.C., Adams P.D., and Baker D. |
|
| 695 | +(2013). Improved low-resolution crystallographic refinement with Phenix and |
|
| 696 | +Rosetta. Nat Methods 10, 1102-4. |
|
| 697 | + |
examples/phenix.rosetta_refine.md
| ... | ... | @@ -1 +1,31 @@ |
| 1 | -##coming soon |
|
| 1 | +## Running PHENIX with Rosetta |
|
| 2 | + |
|
| 3 | +Running PHENIX with Rosetta requires compatible versions of PHENIX and Rosetta to be installed and enabled in the shell environment. In the SBGrid environment, the default versions of Rosetta and PHENIX are compatible and tested. Other versions may also work together (nightly builds), but we don't typically test all possible combinations. |
|
| 4 | + |
|
| 5 | +### PHENIX regression test |
|
| 6 | + |
|
| 7 | +A quick check of PHENIX Rosetta integration can be made with the phenix_regression.test_rosetta_refine command. |
|
| 8 | + |
|
| 9 | + phenix_regression.test_rosetta_refine |
|
| 10 | + |
|
| 11 | +A successful test will output this : |
|
| 12 | + |
|
| 13 | +``` |
|
| 14 | +$ phenix_regression.test_rosetta_refine |
|
| 15 | +/programs/x86_64-linux/rosetta/3.8/main/source |
|
| 16 | +OK |
|
| 17 | +``` |
|
| 18 | + |
|
| 19 | +### phenix.rosetta_refine |
|
| 20 | + |
|
| 21 | +phenix.rosetta_refine can be run from the GUI or from the command line. |
|
| 22 | + |
|
| 23 | +We test rosetta with a small 61 aminoacid protein (1I2T, Poly-A binding protein, PABP). |
|
| 24 | +Our test dataset is available here : [1I2T.tar.bz2](1I2T.tar.bz2) |
|
| 25 | + |
|
| 26 | +This command should run to completion : |
|
| 27 | + |
|
| 28 | + phenix.rosetta_refine 1I2T.pdb 1I2T_F.mtz protocol=hires nproc=8 |
|
| 29 | + |
|
| 30 | +Here is the expected log output. |
|
| 31 | +[phenix.rosetta_refine.log](phenix.rosetta_refine.log) |