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

Zhang yu phenixzyfish at gmail.com
Tue Mar 15 08:45:30 PDT 2011

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         ---    ---         ---    ---
   ---- ----------  -----  ----------  -----  ----------  -----


   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


   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
   ---- ------

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)


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
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
a number of reasons for the departure of the intensity statistics from
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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