Table 2.
Simulated annealing minimization of protein crystals using different force fields and a protocol described previously2, the average results for an independent validation set of another 25 proteins are shown. RMSD is the heavy-atom RMSD from the X-ray structure after the minimization converged, Quality Z-Score is the average of the three most sensitive WHAT IF checks28: Ramachandran plot (RAMCHK), backbone conformation (BBCCHK) and 3D packing quality (QUACHK).
| Force field | RMSD | Quality Z-Score |
|---|---|---|
| None | 0.000 | 0.348 |
| AMBER99 (23) | 0.440 | −0.581 |
| AMBER03 (27) | 0.437 | −0.364 |
| YAMBER2 (2) | 0.410 | −0.353 |
| YASARA | 0.379 | 0.616 |
A Z-score is simply the number of standard deviations away from the average, a negative value is assigned to models that are worse than the average high resolution X-ray structure (e.g. have more Ramachandran plot outliers).