[phenixbb] merohedral twinned refinement
Peter Zwart
phzwart at gmail.com
Mon Jan 18 08:16:34 PST 2010
>
> 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the
> molecules will crash.Besides,the overall FOM ( lower than 0.4) and the
> R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg.
try P31 or otherwise P1. You should get a solution in those groups.
It could of course mean that there are OD type issues, but I would not
jump there yet.
Can you send the intensity statistics from xtriage?
P
>
> 4. TLS refinement also did not imrove the results.
>
> 5. There are totally 88 aa in my protein, I could build 86 aa clearly.
>
> The intensity ststistics is attached in the message.
>
> J.X. QI
>
> ************************************************************************
>
> Shell I/Sigma in resolution shells:
> Lower Upper % of of reflections with I / Sigma less than
> limit limit 0 1 2 3 5 10 20 >20 total
> 50.00 4.95 0.9 1.5 1.9 2.4 2.8 4.0 9.5 90.5 100.0
> 4.95 3.93 0.0 0.2 0.3 0.5 0.8 2.0 6.6 93.4 100.0
> 3.93 3.44 0.2 0.3 0.6 1.0 2.5 5.4 15.4 84.6 100.0
> 3.44 3.12 0.0 0.2 0.5 0.7 2.5 7.6 22.7 77.3 100.0
> 3.12 2.90 0.3 1.0 2.1 3.2 7.2 17.6 41.4 58.6 100.0
> 2.90 2.73 0.0 0.7 2.0 3.2 9.9 20.8 52.9 47.1 100.0
> 2.73 2.59 0.0 1.4 2.9 5.7 12.4 30.0 60.8 39.2 100.0
> 2.59 2.48 0.7 1.6 4.7 7.7 16.3 36.0 71.5 28.5 100.0
> 2.48 2.38 0.6 2.1 5.0 10.2 21.9 42.0 76.2 23.8 100.0
> 2.38 2.30 0.8 2.3 7.4 12.7 25.3 49.4 83.4 16.6 100.0
> All hkl 0.4 1.1 2.7 4.7 10.0 21.1 43.4 56.6 100.0
>
>
>
>
> Summary of reflections intensities and R-factors by shells
> R linear = SUM ( ABS(I - <I>)) / SUM (I)
> R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2)
> Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) )
> In all sums single measurements are excluded
>
> Shell Lower Upper Average Average Norm. Linear Square
> limit Angstrom I error stat. Chi**2 R-fac R-fac
> 50.00 4.95 619.8 13.8 3.5 1.039 0.046 0.050
> 4.95 3.93 834.6 17.5 5.0 1.156 0.048 0.052
> 3.93 3.44 521.9 14.6 4.5 1.026 0.059 0.062
> 3.44 3.12 333.7 11.1 4.1 1.073 0.071 0.068
> 3.12 2.90 172.5 7.1 3.6 1.153 0.098 0.096
> 2.90 2.73 131.4 6.0 3.4 1.256 0.116 0.108
> 2.73 2.59 102.8 5.2 3.4 1.306 0.140 0.130
> 2.59 2.48 77.7 4.6 3.4 1.381 0.173 0.158
> 2.48 2.38 64.1 4.3 3.3 1.355 0.195 0.177
> 2.38 2.30 54.7 4.1 3.3 1.345 0.221 0.197
> All reflections 297.8 8.9 3.7 1.209 0.071 0.059
>
> Intensities of systematic absences
> h k l Intensity Sigma I/Sigma
>
> 0 0 2 -0.2 0.4 -0.5
> 0 0 4 0.1 1.0 0.1
> 0 0 5 0.4 1.4 0.3
> 0 0 7 1.1 2.5 0.4
> 0 0 8 0.4 2.1 0.2
> 0 0 10 7.3 3.4 2.2
> 0 0 11 6.0 3.5 1.7
> 0 0 13 -2.3 4.9 -0.5
> 0 0 14 6.1 4.3 1.4
> 0 0 16 8.1 5.1 1.6
> 0 0 17 3.9 4.9 0.8
> 0 0 19 0.8 4.5 0.2
> 0 0 20 4.0 4.6 0.9
> *********************************************************************
>
>
>
>
>
> 1. How do the intensity statistic look like?
> 2. How did you choose P3121?
> 3. Did you try solving and refining in P3?
> 4. TLS?
> 5. How complete is your model
>
>
>
>
>
> 2010/1/17 JXQI <jxqi at mail.im.ac.cn>:
>> Dear all,
>>
>> I have a 2.3A data set processed with HKL2000. The space group is P3121
>> with
>> 63% of solvent content and 1 molecule in the ASU. I used a 40% homology
>> model to do molecular replacement. Both the Phaser and Molrep gave similar
>> solution with good packing. After further refinement with phenix, the
>> built
>> model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to
>> 0.34/0.38.
>>
>> I rechedked the data set with xtriage and found the data set is merohedral
>> twinned (with twin law"-h,-k,l", the estimated twin fraction is about
>> 0.05).
>> When I used the twin law in further refinement, the R/Rfree were only
>> decreased to 0.32/0.36. Any suggestions are appreciated, thanks!
>>
>>
>> J.X. QI
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
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--
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
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