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Check of Data and Initial
Structure and Determination of Weights

This procedure checks the initial value and determines the ideal
weight (and if a phase restraint is used)
between and . The procedure
should be carried out before running
any refinement on the system. The weight is determined by running a
brief molecular dynamics calculation without
and then comparing the norm of the gradient of
and the norm of the gradient of .
The program will display the weight. A similar procedure should be
applied when using targets other than the crystallographic
residual (Eq. 13.1).

If the minimizer exits with “line search abandoned" and very large van der Waals energies (in the thousands of kcal mole ), the structure probably has bad contacts. The output of X-PLOR provides a list of bad contacts . One should check the molecule and symmetry-related molecules on the graphics and fix the problem. If this is inconvenient, try the following procedure: use the “repel" nonbonded energy function (see Section 4.1) for the first several steps of minimization. One should replace the minimization statement in the example above with the following statements:

parameter nbonds repel=0.89 rcon=4. end end {*This turns on the repulsive *} {*function. *} minimize powell nstep=40 drop=40.0 end {* This switches back to the Lennard-Jones function.*} parameter nbonds repel=0.0 end end minimize powell nstep=40 drop=40.0 end

*Xplor-NIH 2024-09-13*