Output

ARP/wARP outputs several useful quantities. These are: the number of atoms merged, the number of atoms removed, the sphericity functions indicating whether atoms are well shaped - a value of about 0.05 to 0.10 (the lower the better) is reasonable, the result of improvement of the sphericity function if sphere-based real space refinement is used, the statistically significant threshold in difference density (if FIND cutsigma auto is provided) for addition of new atoms, the number of atoms added.

The auto option provides an attempt to be objective in adding atoms. The actual number of atoms to remove depends both on REMOVE cutsigma value and atoms number). If the user during reshuffling the structure asked for not enough removal, the result would be that not enough new atoms are found. If the requested number for removal is too high (but assumed to satisfy the formula given above) - more new atoms will be found. A situation where each cycle ARP/wARP removes less than about 2-3 atoms (for typical structure of 1,000 to 3,000 atoms) and finds the same number of new ones and the R factor does not change indicates that convergence has been achieved. There is no reason to run millions of cycles. Usually refinement essentially converges after 10 to 20 cycles. However if the density is still getting better the number of cycles can be increased to 50 or even 100.

A new feature in the automated scripts, is that at the end they also calculate and write to the files/ directory $\sigma_A$ weighted Fourier maps, extended to either the asymmetric unit or covering the protein model, if available. Also, the scripts output a one-line summary of the latest part of relevant logfiles, which allows the user to follow the convergence of the refinement.