DEFS sd [0.03] sf [0.2] su [0.01] ss [0.05] maxsof DEFS may be used to change the default effective standard deviations for the following DFIX, SAME, SADI, CHIV, FLAT, DELU and SIMU restraints, and is useful when these are to be varied systematically to establish the optimum values for a large structure (e.g. using R(free)). sd is the default for s in the SADI and DFIX instructions (excluding DFIX instructions with negative d, for which the default s remains at 0.1), and also for s1 and s2 in the SAME instruction. sf is the default effective standard deviation for CHIV and FLAT, su is the default for both s1 and s2 in DELU, fand ss is the default s or SIMU. The default st for SIMU is set to twice the default s.
maxsof is the maximum allowed value that an occupation factor can refine to; occupation factors that are fixed or tied to free variables are not restricted. It is possible to change this parameter (to say 1.1 to allow for hydrogen atoms) when refining both occupation factors and U's for solvent water in proteins (a popular but not uncontroversial way of improving the R factor).
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