The refinement package has been used extensively to study a number of complexes of inhibitors with the thermostable endopeptidase thermolysin (e.g. Holmes, Tronrud & Matthews, 1983; Tronrud, Monzingo & Matthews, 1986). In different instances the resolution ranges from 2.3 to 1.6Å.
Because of the hexagonal space group and the size of the problem (Table 2), calculations of structure factors and crystallographic derivatives by conventional methods is time consuming. [Refinement of the native structure at 1.6Å resolution by the method of Hendrickson & Konnert (1980) required 21 c.p.u. hours per cycle (Holmes & Matthews, 1982). The present program package requires 0.7 to 1.5h per cycle, depending on the resolution. The ability of the present program package to specify the geometry of chemically unusual inhibitors is an advantage. In addition, it is also possible to define appropriate stereochemistry for inhibitors that are covalently bonded to the enzyme (e.g. Holmes, Tronrud & Matthews, 1983).
The refinement of an inhibitor complex normally requires 10 - 30 cycles of refinement. Little manual intervention is required because thermolysin normally does not change its conformation very much when inhibitors are bound. It is, of course, always necessary to monitor the configuration of the inhibitor during refinement and to check for changes in solvent structure concomitant with inhibitor binding.