[phenixbb] question on bad geometry

[Thomas C. Terwilliger]

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
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>