[phenixbb] Only one solution in AutoMR with very negative LLG

Daniel Mattle dmattle at mb.au.dk
Tue Mar 15 08:57:42 PDT 2011


Hey,

I played around with the RMSD value that helped at least for me. Try to make it higher.

Best,

Daniel

On 15.03.2011, at 16:45, Zhang yu wrote:

> 
> Hi, Pozharski
> 
> I attached part of log file.
> 
> 
> Fast Rotation Function Table: 1
>    -------------------------------
>    #SET        Top    (Z)      Second    (Z)       Third    (Z)
>    1      -1129.09  32.53         ---    ---         ---    ---
>    ---- ----------  -----  ----------  -----  ----------  -----
> 
> ---------------
> FINAL SELECTION
> ---------------
> 
>    Mean used for final selection = -5302.48
>    Cutoff used for final selection = -2172.44
>    Number of sets stored before final selection = 1
>    Number of solutions stored before final selection = 1
>    Number of sets stored (deleted) after final selection = 1 (0)
>    Number of solutions stored (deleted) after final selection = 1 (0)
> 
> 
>    Select by Percentage of Top value: 75
>    Top TF = -5085.32
>    Mean TF used for final selection = -7813.43
>    LLG Cutoff used for final selection = -5767.35
>    Number of solutions stored before final selection = 1
>    Number of solutions stored (deleted) after final selection = 1 (0)
>    Top TFZ = 21.3024
> 
> -----------------
> TABLES OF RESULTS
> -----------------
> 
> 
>    Fast Translation Function Table: Space Group P 1 2 1
>    ----------------------------------------------------
>    #SET #TRIAL      Top    (Z)    Second    (Z)     Third    (Z)    Ensemble
>       1      1 -5085.32 (21.30)        -      -         -      -    1
>    ---- ------ 
> 
> 
> 
> Solutions:
> =====================
> Solution #1:  Likelihood Gain -4625.06
> ENSE 1 - EULER  326.300,  61.849,  83.068 - FRAC    0.529,  -0.001,   0.102
> 
> 
> 
> Unit cell: (186.376, 103.164, 295.884, 90, 98.789, 90)
> Space group: P 1 2 1 (No. 3)
> 
> SPACE GROUP OF SOLUTION: 'P 1 2 1'
> 
> By the way, the Xtrige in Phenix tells that translational pseudo-symmetry is very likely present.  I also attached the log file.
> 
> Twinning and intensity statistics summary (acentric data):
> 
> Statistics independent of twin laws
>   <I^2>/<I>^2 : 2.148
>   <F>^2/<F^2> : 0.803
>   <|E^2-1|>   : 0.729
>   <|L|>, <L^2>: 0.391, 0.215
>   Multivariate Z score L-test: 9.366
> 
>  The multivariate Z score is a quality measure of the given
>  spread in intensities. Good to reasonable data are expected
>  to have a Z score lower than 3.5.
>  Large values can indicate twinning, but small values do not
>  necessarily exclude it.
> 
> 
> 
> No (pseudo)merohedral twin laws were found.
> 
> 
> Patterson analyses
>   - Largest peak height   : 56.002
>    (corresponding p value : 2.915e-05)
> 
> 
> The analyses of the Patterson function reveals a significant off-origin
> peak that is 56.00 % of the origin peak, indicating pseudo translational symmetry.
> The chance of finding a peak of this or larger height by random in a 
> structure without pseudo translational symmetry is equal to the 2.9153e-05.
> The detected tranlational NCS is most likely also responsible for the elevated intensity ratio.
> See the relevant section of the logfile for more details.
> The results of the L-test indicate that the intensity statistics
> are significantly different than is expected from good to reasonable,
> untwinned data.
> As there are no twin laws possible given the crystal symmetry, there could be
> a number of reasons for the departure of the intensity statistics from normality.
> Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems
>  as well as bad data quality might be possible reasons.
> It could be worthwhile considering reprocessing the data.
> 
> 
> Yu Zhang
> 
> 
> 2011/3/15 Ed Pozharski <epozh001 at umaryland.edu>
> On Mon, 2011-03-14 at 18:32 -0400, Zhang yu wrote:
> > I am working on a DNA-protein complex, the protein apo structure is
> > already known. Recently I got a dataset of the DNA-protein complex, I
> > tried to find a solution by autoMR in Phenix with the known protein
> > coordinate as template. I got only one solution with very negative LLG
> > (around -4000), and after rigid body refinement, the both Rwork and
> > Rfree is around 0.55.  Was there anyone in the same situation as me?
> > What does that mean if there is just one solution while with very high
> > negative LLG?
> 
> Could mean several things, but one thing is for sure - R~55% suggests
> that molecular replacement did not work.  One possibility is that your
> protein undergoes conformational change when it binds to DNA.  If it has
> distinct domains, you may be able to get a solution if running them as
> separate models.
> 
> Negative LLG could mean that you did not correctly guess the unit cell
> content.  Or maybe the space group is wrong.  You may want to post the
> phaser log-file, since it's not obvious to me what you mean by only one
> solution.  What were the Z-scores at rotation/translation steps?
> 
> --
> "I'd jump in myself, if I weren't so good at whistling."
>                               Julian, King of Lemurs
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110315/2da9f7ec/attachment-0003.htm>


More information about the phenixbb mailing list