Atoms SELECTED in KEY "active" are MINIMIZED against background of "passive" KEY atoms with the ENERGY terms turned ON. 'active' atoms are allowed to move and 'passive' atoms are there only to interact with 'active' atoms. The key 'passive' should include all 'active' atoms, otherwise 'active' atoms will not be treated properly.
When applying PAIR constraints take care that anchor do not become a part of the 'active' key. Anchors do not need to be included to the 'passive' key.
MINI_ANH minimizes anchors in an electron density map gradients. I recommand you to use this option a lot.
See for example the >utils/def_top_par_19.com file, which is the default macro invoked through the "DEFINE" item. You can redirect these calls by redifining the variable DEF_ALL. Try
> show vari DEF_ALL
to check the variable status.
> defin clas charge by topo > defin bond angle by auto > defin dihe improper by topo
DENSITY energy term is a negative correlation of a "real" atom with the density of the chosen map. For comfort model building see also the below session "Use of anchors" and the session "Load_xray_maps" in the part "Dialog mode accessories".
> ener density map 1 density scale 30.