Hi Pavelphenix.reduce doesn't work well in my hands. I used "automatically add H's" in the phenix GUI instead. The other steps were exactly as you outlined (no water update). Thank you. Ezequiel PS: phenix.reduce reads my file, but it output a pdb file with the added H's with "0" in the second column (and "new" in the last column) El Martes, 15 de diciembre, 2015 20:35:32, Pavel Afonine escribió: Hi Ezequiel, version: dev-2247: Final: r_work = 0.1753 r_free = 0.2040 vs version: dev-2247: Final: r_work = 0.1663 r_free = 0.2017 look the same in a sense that if you 100 refinements each one starting with a slightly perturbed model you will get 100 slightly different refined models with both, Rwork and Rfree, varying withing about 1% at this resolution. Having said that I can postulate that r_work = 0.1753 is the same as r_work = 0.1663, and r_free = 0.2040 is the same as r_free = 0.2017. For some discussion see pages 75-77 here: http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf and "Improved target weight optimization in phenix.refine" here: http://phenix-online.org/newsletter/CCN_2011_07.pdf Now, before I proceed commenting, question: did you follow exactly the steps 1)-2)-3) that I outlined in my previous email? Otherwise it does not make much sense to compare results obtained using different refinement settings. Pavel On 12/15/15 12:00, Ezequiel Noguera wrote: Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between versions? version: dev-2247 Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321 Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593 version: 1.9-1692 Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

Hi Pavel,I made a mistake with the output from phenix.reduce, now it works well. In my first attempt, the output from phenix.reduce was a file whose only content was: "USER  MOD reduce.3.24.130724 H: found=0, std=0, add=0, rem=0, adj=0". It was solved when I renamed the input pdb. I took erroneously the first file as an input for phenix.refine and it produced an error (obviously). Now I repeated the refinement following exactly your instructions. I got the same results (as expected). version: dev-2247 Final: r_work = 0.1755 r_free = 0.2044 bonds = 0.030 angles = 0.598 version: 1.9-1692 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321 El Martes, 15 de diciembre, 2015 22:07:15, Pavel Afonine escribió: Hi Ezequiel phenix.reduce doesn't work well in my hands. I used "automatically add H's" in the phenix GUI instead. "automatically add H's" in the phenix GUI uses phenix.reduce to add H. The machinery that actually add H is exactly the same. PS: phenix.reduce reads my file, but it output a pdb file with the added H's with "0" in the second column (and "new" in the last column) Does this create any problem? Pavel