Table 2.
Refinement statistics of test protein structures with and without the hydrogen bond restraint
| Refinement without a hydrogen-bond restrainta | Refinement with optimized hydrogen bond restraintsb | |||||
| PDB code | Rfree (%) | R (%) | Rfree − R (%) | Rfree (%) | R (%) | Rfree − R (%) |
| 2CHR | 26.18 | 17.94 | 8.24 | 24.35 | 19.46 | 4.89 |
| 1A7B | 31.64 | 22.85 | 8.79 | 29.06 | 23.98 | 5.08 |
| 2BCT | 28.16 | 21.13 | 7.03 | 26.78 | 21.58 | 5.20 |
| 1A9B | 30.69 | 25.57 | 5.12 | 29.83 | 25.44 | 4.39 |
| 1A43 | 27.72 | 22.07 | 5.65 | 26.77 | 21.93 | 4.84 |
| 1AVC | 27.11 | 19.64 | 7.47 | 26.44 | 19.63 | 6.81 |
| 6PFK | 24.02 | 16.78 | 7.24 | 23.54 | 16.93 | 6.61 |
| 1AWU | 35.24 | 33.58 | 1.66 | 34.19 | 32.62 | 1.57 |
| 1AS3 | 27.18 | 21.86 | 5.32 | 26.67 | 21.76 | 4.91 |
| 1AB4 | 31.16 | 23.13 | 8.03 | 30.65 | 22.82 | 7.83 |
PDB, Protein Data Bank.
a R-factors are calculated in a consistent manner in this table and differ slightly from those of Table 1, which were calculated in the original structure determinations by the original authors using a variety of scaling procedures and refinement protocols.
b Hydrogen bond restraint parameters were optimized against each of these training proteins individually.