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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb