[phenixbb] bad geometry problem

[Qian Sarah]

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Hi Pavel Thank you so much! The information is VERY detailed and I learnt a
lot!
Thanks to phenixbb!




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> 2012/6/21 Pavel Afonine <pafonine at lbl.gov>
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>> Hi Sarah,
>>
>> thanks for sending me the data. I spent 15 minutes trying a few things
>> and here is the statistics I get:
>>
>> r_work = 0.2454 r_free = 0.2700
>> MOLPROBITY STATISTICS.
>>  ALL-ATOM CLASHSCORE : 13.60
>>  RAMACHANDRAN PLOT:
>>   OUTLIERS : 0.89  %
>>   ALLOWED  : 5.33  %
>>   FAVORED  : 93.78 %
>>  ROTAMER OUTLIERS : 8.64 %
>>  CBETA DEVIATIONS : 0
>>
>> which isn't that bad compared to the starting point:
>>
>> r_work = 0.2469 r_free = 0.2613
>> MOLPROBITY STATISTICS.
>>  ALL-ATOM CLASHSCORE : 48.87
>>  RAMACHANDRAN PLOT:
>>   OUTLIERS : 2.49  %
>>   ALLOWED  : 5.33  %
>>   FAVORED  : 92.18 %
>>  ROTAMER OUTLIERS : 29.47 %
>>  CBETA DEVIATIONS : 10
>>
>> Here is what I did (it's just one of possible ways of doing this; other
>> scenarios may works as good as this one or better!):
>>
>> - add H atoms:
>>
>> phenix.reduce model.pdb > model_H.pdb
>>
>> - then run a quick geometry regularization:
>>
>> phenix.pdbtools model_H.pdb --geom
>>
>> - then strip off H:
>>
>> phenix.reduce -trim model_H_regularized.pdb > start.pdb
>>
>> - then run refinement using NCS and Ramachandran plot restraints:
>>
>> phenix.refine start.pdb def_data.mtz main.ncs=true --overwrite
>> output.prefix=def2 main.number_of_mac=5 ramachandran_restraints=true
>> rama_potential=emsley strategy=individual_sites+**individual_adp
>>
>> - then take outcome of previous refinement and run the same refinement
>> plus weights optimization:
>>
>> phenix.refine def2_001.pdb def_data.mtz main.ncs=true --overwrite
>> output.prefix=def3 main.number_of_mac=5 ramachandran_restraints=true
>> rama_potential=emsley strategy=individual_sites+**individual_adp
>> optimize_xyz=true nproc=6
>>
>> Also, looking at the original maps I see a lot of places where simple
>> fixing in Coot is just obvious, for both - rotamers and Ramachandran
>> outliers. So you should do it first of all.
>>
>> Also, use Ramachandran restraints ONLY to preserve good starting model
>> and NOT to fix problems.
>>
>> All in all, geometry problems you were concerned about are all easily
>> fixable. One of the reason why these problems arise is that the map is
>> really looking like 3A resolution map, may be even worse; plus there are
>> places in the model that you need to fix manually (refinement would not be
>> able to fix them).
>>
>> I will send you the files off-list.
>>
>>
>> Pavel
>>
>> On 6/19/12 1:17 AM, Qian Sarah wrote:
>>
>>> Hi, this may not be a new problem, but I tried every stretagy that I
>>> know from bb, but the geometry is still very bad. So I wish I can get some
>>> help from here.
>>> Crystal information:
>>>  SAD data. Resolution 3.0.  There is no anisotropy in the data.
>>>  R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz file
>>> generated after the first refinement.)
>>>   RMS(bonds):0.02
>>>   RMS(angles): 1.453
>>>   Ramachandran outliers: 3.0%
>>>   Ramachandran favored: 91.2%
>>>   Rotamer outliers: 18.7% !!
>>>   Clashscore: 31.84
>>>   overall score: 3.47
>>>   I tried different strategies, like autobuild and then refine; set
>>> wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain
>>> romaters"etc, however the paramters are still very bad, especially the
>>> rotamer outliers. Then I rebuild them manually in coot,after refinement the
>>> parameters are even worse.
>>> p.s. phenix version: phenix-1.7.3-dev-1046.
>>> Thank you very much!
>>> best,
>>> Sarah
>>>
>>
>>
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