Table 1. Nodes per extension and average time per number of residues.
The default choices for the maximum number of point per extension, p max, for each loop length are shown in bold. Time is the average time per loop for about 100 loops in each case, including real-space refinement. The success rate is calculated as the percentage of times that Loopy actually returned a solution. R.m.s.d. Cα is the root-mean-square deviation from the final structure for all built loops after real-space refinement.
| pmax | ||||||
|---|---|---|---|---|---|---|
| Length | 2 | 3 | 4 | 5 | 6 | |
| 4 | Time (h:min:s) | 0:0:10 | 0:0:12 | 0:0:14 | 0:0:15 | 0:0:16 |
| Success (%) | 98.1 | 99.1 | 99.1 | 99.1 | 99.1 | |
| R.m.s.d. Cα (Å) | 0.08 | 0.06 | 0.06 | 0.05 | 0.06 | |
| 6 | Time (h:min:s) | 0:0:13 | 0:0:19 | 0:0:30 | 0:0:52 | 0:1:24 |
| Success (%) | 94.3 | 99.1 | 99.1 | 100.0 | 100.0 | |
| R.m.s.d. Cα (Å) | 0.12 | 0.09 | 0.08 | 0.08 | 0.07 | |
| 8 | Time (h:min:s) | 0:0:17 | 0:0:46 | 0:2:49 | ||
| Success (%) | 93.4 | 100.0 | 100.0 | |||
| R.m.s.d. Cα (Å) | 0.29 | 0.08 | 0.06 | |||
| 10 | Time (h:min:s) | 0:0:25 | 0:3:20 | |||
| Success (%) | 85.7 | 99.0 | ||||
| R.m.s.d. Cα (Å) | 0.25 | 0.08 | ||||
| 12 | Time(h:min:s) | 0:0:50 | 0:6:01 | |||
| Success(%) | 76.9 | 97.1 | ||||
| R.m.s.d. Cα (Å) | 0.37 | 0.09 | ||||
| 14 | Time (h:min:s) | 0:2:14 | 2–3 h | |||
| Success (%) | 76.7 | — | ||||
| R.m.s.d. Cα (Å) | 0.37 | — | ||||