Re: [ccp4bb] Antw: Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Of course - none of us has given the best advice of all! Try to find a better ordered crystal! Eleanor On 2 July 2017 at 19:59, Matthias Barone wrote: > Beside the good propositions of fixing the environment, flip the peptide, > or using PDB_REDO, I would suggest the

[ccp4bb] Antw: Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Beside the good propositions of fixing the environment, flip the peptide, or using PDB_REDO, I would suggest the following additional attempts: Try 1) setting the OCC of the sidechain (CG and further) below 0.3 or mutate directly to Ala. See which ones remain visible in a diff map and bring

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Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

I do agree with Eleanor. When I was solving structure at 2.16A resolution, outlier residues were having stearic clash or required side chain flipping. At 2.76A resolution, hydrogen bonds would be difficult to visulize. I found phenix.refine more user friendly. You may too find it useful. Vipul

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Dear Meytal, PHENIX-REFINE has an option for Ramachandran outlier refine. If you check this on, it will do the work. But after this refinement, you must check every residues to make sure residues are in the density. Thank you Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Dear Meytal, Perhaps the problem can be solved by increasing the restraint weight in Refmac, perhaps your model needs more substantial rebuilding. Look at hydrogen bonding, you may need to flip a few peptides. Also a wrongly fitted side-chain may distort the backbone enough to cause a

[ccp4bb] Ramachandran oultliers increase upon restrained refinement

Dear all, I am refining a 2.76A structure using refmac5. I keep fixing the Ramachandran outliers down to 18 (1.9%), however, upon restrained refinement, the outliers increase back to 35. Do you have any suggestions how can I fix my structure? Thanks, Meytal Galilee