L.S. nls  nrf  nextra  maxvec nls cycles of full-matrix least-squares refinement are performed, followed by a structure factor calculation. When L.S. (or CGLS) is combined with BLOC, each cycle involves refinement of a block of parameters which may be set up differently in different cycles. If no L.S. or CGLS instruction is given, 'L.S. 0' is assumed.
If nrf is positive it is the number of these cycles which should be performed before applying ANIS. This two-stage refinement is particularly suitable for the early stages of least-squares refinement; experience indicates that it is not advisable to let everything go at once!
Negative nrf indicates which reflections should be ignored during the refinement but used instead for the calculation of independent R-factors in the final structure factor summation; for example L.S. 4 -10 would ignore every 10th reflection for refinement purposes. The selection is based on the (merged) reflection list before applying OMIT and SHEL, and so should be independent of the operation of these two instructions (however only data which have not been suppressed by OMIT or SHEL contribute to the independent R-factors). This strategy should also make the selection of reflections to ignore independent of the computer. It is desirable to use the same negative value of nrf throughout, so that the values of 'R1(free)' and 'wR2(free)' are not biased by the 'memory' of the contribution of these reflections to earlier refinements. These independent R-factors may be used to calibrate the sigmas for the various classes of restraint, and provide a check as to whether the data are being 'over-refined' (primarily a problem for macromolecules with a poor data to parameter ratio). For further details see A.T. Brunger, Nature 355 (1992) 472-475. In SHELXL-93, these ignored reflections are treated in the same way as reflections suppressed with OMIT except for the calculation of R1(free) and wR2(free), i.e they are used in the calculation of R-indices based on all reflections, but not used for Fourier calculations.
nextra is the number of additional parameters which were derived from the data when performing empirical absorption corrections etc. It should be set to 8 (LAMI), 12 (HOPE) or 18 (EMPI) if SHELXA was used for this purpose, and to 44 for DIFABS (or 34 without the theta correction; N. Walker and D. Stuart, Acta Cryst., A39 (1983) 158-166). It ensures that the standard deviations and GooF are estimated correctly; they would be underestimated if the number of extra parameters is not specified. nextra is zero (and so can be omitted) if extra information in the form of indexed crystal faces or psi-scan data was used to apply an absorption correction.
maxvec refers to the maximum number of reflections processed simultaneously in the rate-determining calculations. Usually the program utilizes all available memory to process as many reflections as possible simultaneously, subject to a maximum of maxvec, which may not be larger than 511. For complicated reasons involving the handling of suppressed and 'R(free)' reflections and input/output buffering, some blocks may be smaller than the maximum, especially if the facilities for refinement against twinned or powder data are being used. It may be desirable to set maxvec to a smaller number than 511 to prevent unnecessary disk transfers when large structures are refined on virtual memory systems with limited physical memory.
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