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![[Figure 8]](qj5008fig8mag.jpg)
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Figure 8
Effect of top-out (equation 10) ![[link]](../../../../../../logos/arrows/d_arr.gif) or adaptive (equation 14) torsion restraints on the refinement of PDB entry 3fyj using an optimized PDB entry 3fhr as a reference for a grid search of angle range (30, 60, 90, 120, 150 or 180°), alpha (0, 0.1, 0.2, 0.3, 0.4 or 0.5) and spring constant (0, 50, 100, 150, 200, 250 or 300 kJ mol−1). All models were settled in ISOLDE for 50 000 time steps with gradual temperature reduction and then refined in Phenix as described in the main text. (a) Overview of the search space. Displayed surfaces are contours minimizing Rfree (green), MolProbity score (transparent orange), large backbone deviations from the exemplar (purple wireframe) and large side-chain deviations from the exemplar (blue). The approximate optimum balancing these parameters is illustrated as a red sphere. (b, c, d) Results for angle range 30° (black), 60° (orange) or 90° (green) with the spring constant fixed at 250 kJ mol−1. (b) Refined Rfree (solid lines) and Rwork (dashed lines). (c) MolProbity score (exemplar model = 1.29). (d) Number of remaining large side-chain (solid lines) or backbone (dashed lines) deviations from the exemplar model. Error bars are ±1 standard deviation. The shaded grey box indicates the approximate optimum region. |
![[Figure 8]](qj5008fig8.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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