arp_warp
ARP/wARP is a software project for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC. (Summary from the program web page.)
The official web page: http://www.embl-hamburg.de/ARP/.