Hi Tong, I replied to your email yesterday. Did you get it? Just in case below is a verbatim copy of my yesterday's reply to you: **** Hi ??, hm, this shouldn't normally happen! Could you please send me relevant inputs so I can reproduce the problem and see what exactly is happening? Also explain how you run autobuild and then phenix.refine. Pavel On 7/20/12 5:43 AM, ?? wrote:

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong?

Pavel On 7/20/12 6:56 PM, herohonan wrote:

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong?

(After AutoBuild, I modified the structure and added the substrate moleculars into the structure by hand. I thought the increase of the R value was resulted from the inapposite position of the substrates. But the R value still increased when I ran the Phenix Refine just by inputting the output of the AutoBuild without any manual modification.)

-- Tong Huo Ph.D candidate College of Life Sciences Nankai University Tianjin, China

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