[phenixbb] ramachandran_restraints

Pavel Afonine pafonine at lbl.gov
Tue Dec 28 10:29:57 PST 2010

  Hi Jose,

what happens if after a round of refinement with Ramachandran restraints 
you do another round of refinement without Ramachandran restraints?


On 12/28/10 4:56 AM, José Trincão wrote:
> Dear all,
> I am refining a structure to 2.9 A, with pretty bad experimental data (P1, ~5400 residues in the A.U. (4 mol), anisotropic, fairly incomplete...). I have been running phenix.refine with NCS, 1 ADP per residue, lower target weights, TLS. My R/Rfree are stuck at about 2.4/3.05. I was getting around 2% ramachandran outliers at every cycle so I have been giving the nightly builds a shot. Now I get 0.2% outliers without changing any parameters for the ramachandra_restraints but it is forcing some of the peptide bonds out of the density. What can I tweak to improve the refinement?
> Thanks all in advance!
> Jose
> José Trincão, PhD	CQFB at FCT-UNL
> 2829-516 Caparica, Portugal

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