I generated several loop conformations using the 'loop'
routine. The top file is similar to example 3 of the manual, with
the addition of gemetrical constraints on the end of loops.
I am refining 20 a.a. out of a 27-loop segment.
The refined loop conformations still have residues
located in unfavorable regions of the phi/psi plot, i.e. phi> 0 (non
Gly, or Asn). Typically, there are 1-4 residues in these regions.
Only 2% of my conformations have all residues with phi<0.
Are such occurrencies typical of the refinement procedure? If not,
how can I prevent this for happening?
Thanks
Germana
Germana Paterlini
Dept. of Medicinal Chemistry
Minneapolis, MN 55455