[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
>
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