Hi, I agree with Tom. Here is an example. A 3ifk structure deposited in PDB (resolution 2.03A) has the following statistics: - reported Rwork/Rfree = 0.237/0.293 - recomputed Rwork/Rfree (using phenix.model_vs_data) = 0.2306/0.2835 - Molprobity scores (computed using phenix.model_vs_data): Ramachandran plot, number of: outliers : 4 (2.35 %) allowed : 1 (0.59 %) favored : 165 (97.06 %) Rotamer outliers : 28 (18.67 %) Cbeta deviations >0.25A : 10 All-atom clashscore : 61.61 (steric overlaps >0.4A per 1000 atoms) After running this model through PHENIX AutoBuild and then refining it with phenix.refine using fix_rotamers option and H atoms added, I'm getting the following numbers: - Rwork/Rfree = 0.2097/0.2402 - Molprobity scores: Ramachandran plot, number of: outliers : 2 (1.18 %) allowed : 2 (1.18 %) favored : 166 (97.65 %) Rotamer outliers : 5 (3.57 %) Cbeta deviations >0.25A : 1 All-atom clashscore : 37.14 (steric overlaps >0.4A per 1000 atoms) As you can see, the change is pretty significant and no manual work at all to achieve it! Good luck! Pavel. P.S.: All files are here: http://cci.lbl.gov/~afonine/example_3ifk/ 3ifk.mtz - original data file pdb3ifk.ent - model from PDB pdb3ifk.mvd - result of "phenix.model_vs_data 3ifk.mtz pdb3ifk.ent > pdb3ifk.mvd " command autobuild.mvd - result of "phenix.model_vs_data autobuild.pdb 3ifk.mtz > autobuild.mvd " command autobuild.pdb - model after AutoBuild and phenix.refine On 8/31/10 7:08 PM, Thomas C. Terwilliger wrote:
Hi Fengyun,
That does look like a lot of outliers to me. You could try improving the model by "rebuilding in place" with autobuild with the keyword "rebuild_in_place=True" which will try to rebuild your model without changing the sequence alignment. This procedure takes a while and it is useful to use a multiprocessor machine with nproc=5.
You should also have a careful look at your model, as some manual rebuilding might improve it a lot.
All the best, Tom T
Hi everyone,
I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28. However, the geometry is not that good, the followings are the output from phenix.model_vs_data,
Stereochemistry statistics (mean, max, count): bonds : 0.0080 0.0547 3244 angles : 1.1669 12.1085 4374 dihedrals : 15.7241 85.6280 1202 chirality : 0.0706 0.2831 536 planarity : 0.0036 0.0246 573 non-bonded (min) : 2.1217 Ramachandran plot, number of: outliers : 17 (4.02 %) allowed : 37 (8.75 %) favored : 369 (87.23 %) Rotamer outliers : 30 (8.62 %) goal:< 1% Cbeta deviations>0.25A : 0 All-atom clashscore : 40.51 (steric overlaps>0.4A per 1000 atoms)
I tried to use fix_rotamer=True, but it doesn't help at all. As to the rotamer outliers, the value is far higher than the ideal one. Does that mean I need to manually adjust the model? Or will autobuild help improve the geometry?
Thanks! Fengyun
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