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. 2005 Aug 8;33(14):4496–4506. doi: 10.1093/nar/gki730

Figure 4.

Figure 4

Test protocol 2—L-BFGS minimization of non-bonded energy along 1–5 normal modes. Shaded bars indicate the initial cRMS values before refinement. This is substantially more efficient than unconstrained Cartesian minimization, but not entirely stable—structures sometimes end up in worse states when additional normal modes are used.