Table 2.
Overview of refinement targets from all 40 targets. Group 1 (1–5), group 2 (6–21), group 3 (22–32), and group 4 (33–40). Improved cases with lower RMSD are highlighted in bold.
| No. | PDB | Residues | LBS RMSD (Å) | Protein RMSD (Å) | |||||
|---|---|---|---|---|---|---|---|---|---|
| LBS residues |
Initial | Refined | Control* | Initial | Refined | Control* | |||
| 1 | ItowA | 131 | 17 | 0.87 | 0.46 | 1.39 | 1.20 | 1.07 | 1.41 |
| 2 | 1lpzB | 234 | 21 | 0.73 | 0.35 | 1.25 | 1.69 | 1.64 | 1.72 |
| 3 | 1tz8A | 114 | 11 | 0.50 | 0.41 | 0.48 | 1.69 | 1.68 | 1.70 |
| 4 | 1g9vA | 141 | 21 | 1.38 | 0.50 | 1.55 | 1.72 | 1.35 | 1.78 |
| 5 | 1r55A | 203 | 15 | 0.88 | 0.57 | 1.12 | 1.90 | 1.87 | 1.90 |
| Group | 1 avg. | 0.87 | 0.46 | 1.16 | 1.64 | 1.52 | 1.70 | ||
| 6 | 1hq2A | 158 | 25 | 2.01 | 1.37 | 2.37 | 2.18 | 1.81 | 2.23 |
| 7 | 1oweA | 245 | 20 | 1.44 | 0.55 | 1.91 | 2.44 | 2.34 | 2.44 |
| 8 | 1q1gA | 243 | 13 | 1.16 | 1.29 | 1.47 | 2.51 | 2.49 | 2.48 |
| 9 | 1tt1A | 251 | 15 | 1.07 | 0.58 | 1.17 | 2.53 | 2.17 | 2.35 |
| 10 | 1ke5A | 298 | 15 | 1.15 | 0.85 | 0.82 | 2.54 | 2.43 | 2.40 |
| 11 | 1oytH | 257 | 18 | 3.04 | 0.40 | 3.35 | 2.60 | 2.24 | 2.62 |
| 12 | 1p62B | 241 | 30 | 1.70 | 1.59 | 1.58 | 2.64 | 2.60 | 2.55 |
| 13 | 1jjeA | 220 | 17 | 2.42 | 2.28 | 2.42 | 2.77 | 2.66 | 2.74 |
| 14 2bm2A | 242 | 15 | 3.02 | 1.31 | 3.22 | 3.16 | 2.97 | 3.13 | |
| 15 | lygcH | 254 | 21 | 2.80 | 0.55 | 3.07 | 3.18 | 2.98 | 3.20 |
| 16 | ls3vA | 186 | 17 | 1.70 | 0.64 | 1.39 | 3.22 | 3.19 | 3.20 |
| 17 | lk3uA | 268 | 21 | 5.80 | 0.59 | 5.92 | 3.34 | 1.94 | 3.36 |
| 18 | lulcA | 253 | 14 | 5.08 | 3.54 | 5.12 | 3.35 | 3.16 | 3.39 |
| 19 | 1unlA | 292 | 20 | 1.27 | 0.93 | 1.65 | 3.41 | 3.36 | 3.46 |
| 20 | lv0pA | 286 | 19 | 1.94 | 1.32 | 1.72 | 3.68 | 3.61 | 3.72 |
| 21 | lw2gA | 208 | 13 | 1.54 | 1.00 | 2.26 | 3.73 | 3.82 | 3.81 |
| Group 2 avg. | 2.32 | 1.17 | 2.47 | 2.96 | 2.74 | 2.94 | |||
| 22 | lsqnA | 251 | 20 | 0.95 | 0.43 | 1.00 | 4.02 | 4.01 | 4.01 |
| 23 | 2br1A | 271 | 16 | 1.11 | 0.71 | 1.30 | 4.10 | 4.09 | 4.10 |
| 24 | lm2zA | 255 | 22 | 1.42 | 0.86 | 1.28 | 4.12 | 4.06 | 4.15 |
| 25 | lsl9A | 253 | 24 | 1.96 | 0.80 | 2.14 | 4.14 | 4.01 | 4.26 |
| 26 | 1ia1A | 192 | 35 | 1.81 | 1.64 | 1.93 | 4.41 | 4.34 | 4.44 |
| 27 | lv48A | 283 | 18 | 3.52 | 1.15 | 3.26 | 4.51 | 4.38 | 4.55 |
| 28 | 1u4dA | 273 | 14 | 1.29 | 0.91 | 1.80 | 4.53 | 4.51 | 4.67 |
| 29 | ln46A | 251 | 25 | 1.62 | 1.26 | 1.49 | 4.60 | 4.56 | 4.61 |
| 30 | lgkcA | 163 | 15 | 2.51 | 1.25 | 3.56 | 4.63 | 4.43 | 4.66 |
| 31 | lz95A | 246 | 24 | 1.32 | 1.09 | 1.40 | 5.15 | 4.63 | 4.71 |
| 32 | lkzkA | 99 | 15 | 7.83 | 2.03 | 7.87 | 5.52 | 3.74 | 5.41 |
| Group 3 avg. | 2.30 | 1.10 | 2.46 | 4.52 | 4.25 | 4.51 | |||
| 33 | lsj0A | 245 | 21 | 3.13 | 2.59 | 3.14 | 6.21 | 6.09 | 6.32 |
| 34 | lig3A | 254 | 12 | 1.86 | 1.87 | 1.52 | 6.30 | 5.57 | 5.64 |
| 35 | lhnnA | 261 | 32 | 5.52 | 5.48 | 5.70 | 6.39 | 6.33 | 6.46 |
| 36 | lnavA | 263 | 23 | 1.92 | 1.50 | 1.78 | 6.45 | 6.03 | 6.09 |
| 37 | lhvyA | 288 | 24 | 8.07 | 7.89 | 8.39 | 7.24 | 7.25 | 7.35 |
| 38 | 2bsmA | 208 | 18 | 3.97 | 2.60 | 3.67 | 8.76 | 8.62 | 8.80 |
| 39 | lsg0A | 230 | 22 | 1.27 | 1.08 | 1.20 | 9.41 | 9.48 | 9.45 |
| 40 | llrhA | 160 | 15 | 7.58 | 7.97 | 7.94 | 10.96 | 11.04 | 11.12 |
| Group 4 avg. | 4.17 | 3.89 | 4.17 | 7.72 | 7.55 | 7.65 | |||
| Total avg. | 2.50 | 1.60 | 2.64 | 4.17 | 3.96 | 4.16 | |||
*
Control = simulations without distance restraints and with positional restraints.