Table 2.
Initial values of GDT-HA, RMSD, MolProbity and SphereGrinder and change after refinement from sampling in the presence of DPPC lipid bilayers.
| 1j4n | 1py6 | 1qj8 | 3odu | 3vg9 | 4hyj | 4kr8 | 4n6h | Average | |
|---|---|---|---|---|---|---|---|---|---|
| GDT-HA | |||||||||
| Initial | 63.55 | 59.58 | 51.69 | 43.13 | 43.43 | 47.14 | 66.25 | 62.38 | 54.64±3.33 |
| Refined (Δ) RWplus | 1.61 | 3.86 | 11.65 | 1.32 | −2.18 | 1.59 | −1.25 | 3.63 | 2.53±1.50 |
| Refined (Δ) DFIRE | 1.31 | 3.97 | 10.98 | 1.08 | −2.35 | 1.69 | −1.18 | 3.71 | 2.40±1.44 |
| Refined (Δ) HDGBv3 | 1.21 | 3.42 | 10.98 | 1.82 | −2.44 | 1.91 | −1.18 | 3.21 | 2.37±1.42 |
| Refined (Δ) HDGBvdW | 1.31 | 3.53 | 10.81 | 1.74 | −2.10 | 1.59 | −1.99 | 3.63 | 2.32±1.43 |
| RMSD [Å] | |||||||||
| Initial | 3.52 | 1.87 | 3.53 | 4.97 | 4.69 | 4.13 | 2.07 | 2.08 | 3.36±0.43 |
| Refined (Δ) RWplus | −0.14 | −0.08 | −0.47 | −0.12 | −0.02 | −0.06 | −0.06 | −0.24 | −0.15±0.05 |
| Refined (Δ) DFIRE | −0.11 | −0.08 | −0.47 | −0.11 | −0.02 | −0.06 | −0.05 | −0.24 | −0.14±0.05 |
| Refined (Δ) HDGBv3 | −0.13 | −0.07 | −0.46 | −0.13 | −0.02 | −0.06 | −0.04 | −0.24 | −0.14±0.05 |
| Refined (Δ) HDGBvdW | −0.14 | −0.08 | −0.45 | −0.13 | −0.01 | −0.05 | −0.03 | −0.23 | −0.14±0.05 |
| MolProbity | |||||||||
| Refined RWplus | 0.97 | 0.64 | 0.65 | 1.60 | 1.01 | 0.69 | 0.86 | 0.50 | 0.87±0.12 |
| Refined DFIRE | 0.93 | 0.58 | 0.65 | 1.61 | 0.95 | 0.74 | 0.82 | 0.50 | 0.85±0.12 |
| Refined HDGBv3 | 0.93 | 0.64 | 0.65 | 0.84 | 0.96 | 0.81 | 0.84 | 0.50 | 0.77±0.06 |
| Refined HDGBvdW | 0.91 | 0.64 | 0.65 | 0.71 | 0.93 | 0.74 | 0.84 | 0.53 | 0.74±0.05 |
| SphereGrinder | |||||||||
| Initial | 83.62 | 89.29 | 71.53 | 72.64 | 69.50 | 75.68 | 82.38 | 89.96 | 79.33±2.85 |
| Refined (Δ) RWplus | 0.0 | 0.95 | 12.15 | −1.63 | −0.17 | 1.57 | 3.92 | 2.47 | 2.41±1.52 |
| Refined (Δ) DFIRE | −0.43 | 0.95 | 12.5 | −1.08 | 0.0 | −1.13 | 1.05 | 0.89 | 1.59±1.59 |
| Refined (Δ) HDGBv3 | −0.43 | 0.47 | 11.11 | −0.72 | 0.89 | −0.68 | 1.66 | 1.06 | 1.67±1.38 |
| Refined (Δ) HDGBvdW | 0.0 | 0.47 | 12.15 | −0.9 | −0.17 | −0.91 | 1.81 | 0.71 | 1.65±1.53 |
Values for GDT-HA, RMSD, and SphereGrinder are for models with respect to the native structure. For refined models using different scoring functions for structure selection (RWplus, DFIRE, HDGBv3, HDGBvdW) the changes ΔGDT-HA, ΔRMSD and ΔSphereGrinder relative to the initial values are given. MolProbity scores are only given for the refined models. In addition to individual values, the averages over all eight proteins (1j4n, 1py6, 1qj8, 3odu, 3vg9, 4hyj, 4kr8 and 4n6h) for each row are given in the last column.