Hi Yarrow,
I was given these statistics in the pdb header:
Rwork Rfree Bonds Angles start .1588 .1838 .007 1.235 end .1454 .1780 .016 1.601
(1.37 A resolution) Looks ok. Did you update solvent using "ordered_solvent=true"? Did you remember to add have H atoms to your structure? Thanks Pavel,
No, I did not have these turned on. It appears that "ordered_solvent=true" is essentially a water checker in later stages of refinement (correct me if I am wrong). I will try turning this on.
refinement means changing your structure, and changing the structure means some map improvement. Since solvent is added using the maps (mFo-DFc and 2mFo-DFc) it is a good idea to re-check it (solvent) once the maps are updated. The result of such re-check may be some more good water added, or removing some wrong waters originally added to noise density peaks.
What are the advantages of adding H atoms if you are not going to refine them? (Bear with me--this is my first structure).
See pages from 27 here: http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf Let me know if it is still not entirely clear why you would need to use H-atoms in refinement. After updating water and adding H atoms the R-factors may drop by 1-3%.
1. I would like to find the optimized weighting factors in the log file but cannot. Instead I find the following (pasted below). I'm wondering why you are trying to find them? It is such a technical thing that changes from macro-cycle to macro-cycle... I was attempting to use the best weighting factors in subsequent rounds of refinement so that I did not have to optimize each time (because it takes a long time to run). Is this a good strategy?
I see. Although you can do it, it is good to keep in mind that these values can change between refinement runs. You can get this value for coordinate refinement and unfortunately this values is not printed out for ADP refinement (because of a formatting bug that I keep forgetting to fix). Good luck! Pavel.