Xtrige log file of P21


The full list of Patterson peaks is:

  x      y      z            height   p-value(height)
( 0.500, 0.500, 0.000 ) :   56.002   (2.915e-05)
( 0.483, 0.500, 0.034 ) :    6.152   (6.778e-01)


 If the observed pseudo translationals are crystallographic
 the following spacegroups and unit cells are possible:

 space group                operator         unit cell of reference setting 
 C 1 2 1 (a-1/4,b-1/4,c)       x+1/2, y+1/2, z  (186.38, 103.16, 295.88,  90.00, 98.79, 90.00)

Xtrige log file of P2

The full list of Patterson peaks is:
The Xtrige log is as follows,

  x      y      z            height   p-value(height)
( 0.500, 0.500, 0.000 ) :   56.000   (2.916e-05)
( 0.483, 0.500, 0.034 ) :    6.151   (6.781e-01)


 If the observed pseudo translationals are crystallographic
 the following spacegroups and unit cells are possible:

 space group                operator         unit cell of reference setting 
              C 1 2 1       x+1/2, y+1/2, z  (186.38, 103.16, 295.88,  90.00, 98.79, 90.00)


Results from rotation functions for P2 (Search two monomers in ASU)

******************************
*******************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION             2.2.4 ***
*************************************************************************************

---------------------
ANISOTROPY CORRECTION
---------------------

   No refinement of parameters

-------------------------------
DATA FOR FAST ROTATION FUNCTION
-------------------------------

   Outliers with a probability less than 1e-06 will be rejected
   There were 2 (0.0000%) reflections rejected

      H    K    L   reso            F     probability
      5    5   62   4.48       42.404       4.049e-07
     18    2  -26   8.12      112.092       7.520e-09

   Space-Group Name (Number):   P 1 2 1 (3)
   Resolution of All Data (Number):       3.82 49.18 (87989)
   Resolution of Selected Data (Number):  3.82 49.18 (87985)

--------------------------
ENSEMBLE FOR DECOMPOSITION
--------------------------

      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8
   Unit Cell:  394.48  295.80  293.03   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

-------------------
WILSON DISTRIBUTION
-------------------

   Parameters set for Wilson log-likelihood calculation
   E = 0 and variance 1 for each reflection
   Without correction for SigF to the variances,
      Wilson log(likelihood) = - number of acentrics (83981)
                               - half number of centrics (4004/2)
                             = -85983
   With correction for SigF,
      Wilson log(likelihood) = -89650.5


   Configuring ensembles
   ---------------------

      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8
   Unit Cell:  914.73  520.03  508.93   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

------------------------------
FAST ROTATION FUNCTION #1 OF 1
------------------------------

   Search Ensemble: 1
   Known MR solutions
   (empty solution set - no components)

   Fraction of asymmetric unit modelled: 1.0047
      of which the "moving" fraction is 1.0047

   Fraction of asymmetric unit modelled (after correction): 0.99
      of which the "moving" fraction is 0.99


   Spherical Harmonics
   -------------------
   Elmn for Data
   Elmn Calculation for Data
   0%                                                                        100%
   |=========================================================================| DONE

   Elmn for Search Ensemble
   Elmn Calculation for Search Ensemble
   0%                                                                          100%
   |===========================================================================| DONE


   Scanning the Range of Beta Angles
   ---------------------------------
   Performing a 1.3513 degree search.
   Clmn Calculation
   0%                                                                   100%
   |====================================================================| DONE

   Top 59 rotations before clustering will be rescored
   Calculating Likelihood for RF #1 of 1
   0%                                                           100%
   |============================================================| DONE

   Scoring 500 randomly sampled rotations
   Generating Statistics for RF #1 of 1
   0%                                                                       100%
   |========================================================================| DONE

   Mean Score (Sigma):       -7144.27   (152.138)
   Highest Score (Z-score):  -2269.9   (32.0392)


   Top Peaks With Clustering
   -------------------------
   #       Rank of the peak after rescoring search points
   (#)     Rank of the peak before rescoring search points
   LLG     Log-Likelihood Gain
   Z-Score Number of standard deviations of LLG above the mean
   FSS     Fast Search Score

   You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
   There was 1 site over 75% of top
   The sites over 75% are:
   #     (#)   Euler1 Euler2 Euler3   LLG   Z-score Split #Group   raw/top 
   1     1      326.1   62.4   83.0 -2269.90   32.04   0.0     23 100.0/100.0
                213.9  117.6  263.0




   Fast Rotation Function Table: 1
   -------------------------------
   #SET        Top    (Z)      Second    (Z)       Third    (Z)
   1      -2269.90  32.04         ---    ---         ---    ---
   ---- ----------  -----  ----------  -----  ----------  -----

---------------
FINAL SELECTION
---------------

   Mean used for final selection = -7144.27
   Cutoff used for final selection = -3488.49

   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)

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

Results from rotation functions for P2 (Search one monomer in ASU)

*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION             2.2.4 ***
*************************************************************************************

---------------------
ANISOTROPY CORRECTION
---------------------

   No refinement of parameters

-------------------------------
DATA FOR FAST ROTATION FUNCTION
-------------------------------

   Outliers with a probability less than 1e-06 will be rejected
   There were 2 (0.0000%) reflections rejected

      H    K    L   reso            F     probability
      5    5   62   4.48       42.404       4.049e-07
     18    2  -26   8.12      112.092       7.520e-09

   Space-Group Name (Number):   P 1 2 1 (3)
   Resolution of All Data (Number):       3.82 49.18 (87989)
   Resolution of Selected Data (Number):  3.82 49.18 (87985)

--------------------------
ENSEMBLE FOR DECOMPOSITION
--------------------------

      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8
   Unit Cell:  323.84  274.82  261.37   90.00   90.00   90.00


   Electron Density Calculation
   0%      100%
   |=======| DONE

-------------------
WILSON DISTRIBUTION
-------------------

   Parameters set for Wilson log-likelihood calculation
   E = 0 and variance 1 for each reflection
   Without correction for SigF to the variances,
      Wilson log(likelihood) = - number of acentrics (83981)
                               - half number of centrics (4004/2)
                             = -85983
   With correction for SigF,
      Wilson log(likelihood) = -89650.5


   Configuring ensembles
   ---------------------
- ÏÔʾÒýÓÃÎÄ×Ö -
      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8
   Unit Cell:  714.35  518.29  464.48   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

------------------------------
FAST ROTATION FUNCTION #1 OF 1
------------------------------

   Search Ensemble: 1
   Known MR solutions
   (empty solution set - no components)

   Fraction of asymmetric unit modelled: 0.831924
      of which the "moving" fraction is 0.831924


   Spherical Harmonics
   -------------------
   Elmn for Data
   Elmn Calculation for Data
   0%                                                                        100%
   |=========================================================================| DONE

   Elmn for Search Ensemble
   Elmn Calculation for Search Ensemble
   0%                                                                          100%
   |===========================================================================| DONE


   Scanning the Range of Beta Angles
   ---------------------------------
   Performing a 1.5476 degree search.
   Clmn Calculation
   0%                                                          100%
   |===========================================================| DONE

   Top 41 rotations before clustering will be rescored
   Calculating Likelihood for RF #1 of 1
   0%                                         100%
   |==========================================| DONE

   Scoring 500 randomly sampled rotations
   Generating Statistics for RF #1 of 1
   0%                                                                       100%
   |========================================================================| DONE

   Mean Score (Sigma):       -4412.88   (151.158)
   Highest Score (Z-score):  -893.783   (23.2809)


   Top Peaks With Clustering
   -------------------------
   #       Rank of the peak after rescoring search points
   (#)     Rank of the peak before rescoring search points
   LLG     Log-Likelihood Gain
   Z-Score Number of standard deviations of LLG above the mean
   FSS     Fast Search Score

   You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
   There was 1 site over 75% of top
   The sites over 75% are:
   #     (#)   Euler1 Euler2 Euler3   LLG   Z-score Split #Group   raw/top 
   1     1       70.6   39.1   10.6 -893.78   23.28   0.0     13 100.0/100.0
                109.4  140.9  190.6




   Fast Rotation Function Table: 1
   -------------------------------
   #SET        Top    (Z)      Second    (Z)       Third    (Z)
   1       -893.78  23.28         ---    ---         ---    ---
   ---- ----------  -----  ----------  -----  ----------  -----

---------------
FINAL SELECTION
---------------

   Mean used for final selection = -4412.88
   Cutoff used for final selection = -1773.56

   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)

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

Results from rotation functions for P21 (Search two monomers in ASU)

*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION             2.2.4 ***
*************************************************************************************

---------------------
ANISOTROPY CORRECTION
---------------------

   No refinement of parameters

-------------------------------
DATA FOR FAST ROTATION FUNCTION
-------------------------------

   Outliers with a probability less than 1e-06 will be rejected
   There were 2 (0.0000%) reflections rejected

      H    K    L   reso            F     probability
      5    5   62   4.48       42.404       4.046e-07
     18    2  -26   8.12      112.092       7.516e-09

   Space-Group Name (Number):   P 1 21 1 (4)
   Resolution of All Data (Number):       3.82 49.18 (87983)
   Resolution of Selected Data (Number):  3.82 49.18 (87981)

--------------------------
ENSEMBLE FOR DECOMPOSITION
--------------------------

      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8
   Unit Cell:  323.83  274.82  261.37   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

-------------------
WILSON DISTRIBUTION
-------------------

   Parameters set for Wilson log-likelihood calculation
   E = 0 and variance 1 for each reflection
   Without correction for SigF to the variances,
      Wilson log(likelihood) = - number of acentrics (83976)
                               - half number of centrics (4005/2)
                             = -85978
   With correction for SigF,
      Wilson log(likelihood) = -89646.3


   Configuring ensembles
   ---------------------
     This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8

   Unit Cell:  714.35  518.29  464.48   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

------------------------------
FAST ROTATION FUNCTION #1 OF 1
------------------------------

   Search Ensemble: 1
   Known MR solutions
   (empty solution set - no components)

   Fraction of asymmetric unit modelled: 0.737308
      of which the "moving" fraction is 0.737308


   Spherical Harmonics
   -------------------
   Elmn for Data
   Elmn Calculation for Data
   0%                                                                        100%
   |=========================================================================| DONE

   Elmn for Search Ensemble
   Elmn Calculation for Search Ensemble
   0%                                                                          100%
   |===========================================================================| DONE


   Scanning the Range of Beta Angles
   ---------------------------------
   Performing a 1.54708 degree search.
   Clmn Calculation
   0%                                                          100%
   |===========================================================| DONE

   Top 47 rotations before clustering will be rescored
   Calculating Likelihood for RF #1 of 1
   0%                                               100%
   |================================================| DONE

   Scoring 500 randomly sampled rotations
   Generating Statistics for RF #1 of 1
   0%                                                                       100%
   |========================================================================| DONE

   Mean Score (Sigma):       -3258.27   (128.907)
   Highest Score (Z-score):  -242.259   (23.3968)


   Top Peaks With Clustering
   -------------------------
   #       Rank of the peak after rescoring search points
   (#)     Rank of the peak before rescoring search points
   LLG     Log-Likelihood Gain
   Z-Score Number of standard deviations of LLG above the mean
   FSS     Fast Search Score

   You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
   There was 1 site over 75% of top
   The sites over 75% are:
   #     (#)   Euler1 Euler2 Euler3   LLG   Z-score Split #Group   raw/top 
   1     1       70.7   39.1   10.6 -242.26   23.40   0.0     18 100.0/100.0
                109.3  140.9  190.6




   Fast Rotation Function Table: 1
   -------------------------------
   #SET        Top    (Z)      Second    (Z)       Third    (Z)
   1       -242.26  23.40         ---    ---         ---    ---
   ---- ----------  -----  ----------  -----  ----------  -----

---------------
FINAL SELECTION
---------------

   Mean used for final selection = -3258.27
   Cutoff used for final selection = -996.261

   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)

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

Results from rotation functions for P21 (Search One monomers in ASU)

*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION             2.2.4 ***
*************************************************************************************

---------------------
ANISOTROPY CORRECTION
---------------------

   No refinement of parameters

-------------------------------
DATA FOR FAST ROTATION FUNCTION
-------------------------------

   Outliers with a probability less than 1e-06 will be rejected
   There were 2 (0.0000%) reflections rejected

      H    K    L   reso            F     probability
      5    5   62   4.48       42.404       4.046e-07
     18    2  -26   8.12      112.092       7.516e-09

   Space-Group Name (Number):   P 1 21 1 (4)
   Resolution of All Data (Number):       3.82 49.18 (87983)
   Resolution of Selected Data (Number):  3.82 49.18 (87981)

--------------------------
ENSEMBLE FOR DECOMPOSITION
--------------------------

      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8
   Unit Cell:  323.83  274.82  261.37   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

-------------------
WILSON DISTRIBUTION
-------------------

   Parameters set for Wilson log-likelihood calculation
   E = 0 and variance 1 for each reflection
   Without correction for SigF to the variances,
      Wilson log(likelihood) = - number of acentrics (83976)
                               - half number of centrics (4005/2)
                             = -85978
   With correction for SigF,
      Wilson log(likelihood) = -89646.3


   Configuring ensembles
   ---------------------
      This pdb file contains 1 models
      The (input) RmsD of this model with respect to the real structure is 0.8

   Unit Cell:  714.35  518.29  464.48   90.00   90.00   90.00

   Electron Density Calculation
   0%      100%
   |=======| DONE

------------------------------
FAST ROTATION FUNCTION #1 OF 1
------------------------------

   Search Ensemble: 1
   Known MR solutions
   (empty solution set - no components)

   Fraction of asymmetric unit modelled: 0.737308
      of which the "moving" fraction is 0.737308


   Spherical Harmonics
   -------------------
   Elmn for Data
   Elmn Calculation for Data
   0%                                                                        100%
   |=========================================================================| DONE

   Elmn for Search Ensemble
   Elmn Calculation for Search Ensemble
   0%                                                                          100%
   |===========================================================================| DONE


   Scanning the Range of Beta Angles
   ---------------------------------
   Performing a 1.54708 degree search.
   Clmn Calculation
   0%                                                          100%
   |===========================================================| DONE

   Top 47 rotations before clustering will be rescored
   Calculating Likelihood for RF #1 of 1
   0%                                               100%
   |================================================| DONE

   Scoring 500 randomly sampled rotations
   Generating Statistics for RF #1 of 1
   0%                                                                       100%
   |========================================================================| DONE

   Mean Score (Sigma):       -3258.27   (128.907)
   Highest Score (Z-score):  -242.259   (23.3968)


   Top Peaks With Clustering
   -------------------------
   #       Rank of the peak after rescoring search points
   (#)     Rank of the peak before rescoring search points
   LLG     Log-Likelihood Gain
   Z-Score Number of standard deviations of LLG above the mean
   FSS     Fast Search Score

   You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
   There was 1 site over 75% of top
   The sites over 75% are:
   #     (#)   Euler1 Euler2 Euler3   LLG   Z-score Split #Group   raw/top 
   1     1       70.7   39.1   10.6 -242.26   23.40   0.0     18 100.0/100.0
                109.3  140.9  190.6




   Fast Rotation Function Table: 1
   -------------------------------
   #SET        Top    (Z)      Second    (Z)       Third    (Z)
   1       -242.26  23.40         ---    ---         ---    ---
   ---- ----------  -----  ----------  -----  ----------  -----

---------------
FINAL SELECTION
---------------

   Mean used for final selection = -3258.27
   Cutoff used for final selection = -996.261

   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)

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



Thanks a lot.

Yu


2011/3/15 Francis E Reyes <Francis.Reyes@colorado.edu>
Go back to your xtriage log file... Post the section that looks similar to the one below...

The full list of Patterson peaks is:

 x      y      z            height   p-value(height)
( 0.500, 0.000, 0.233 ) :   26.198   (2.753e-03)
( 0.000, 0.338, 0.000 ) :    5.699   (7.800e-01)

 If the observed pseudo translationals are crystallographic
 the following spacegroups and unit cells are possible:

 space group                operator         unit cell of reference setting
 C 2 2 21 (-a,c,2*b)       x+1/2, y, z+1/4  (55.47, 73.64, 81.46,  90.00, 90.00, 90.00)



Systematic absences


Also, post the results of the rotation function.. What is the RFZ score and how did it compare to any other rotation solutions.


F




On Mar 15, 2011, at 1:13 PM, Zhang yu wrote:


It indicates that pseudo translational symmetry is present in the dataset. I didn't do anything when I first try MR. Is that possible I merged two lattice together during data process, or should I reprocess the data to P1?

I attached the scale log file,

 Shell Lower Upper Average      Average     Norm. Linear Square
 limit    Angstrom       I   error   stat. Chi**2  R-fac  R-fac
     50.00  10.29  1030.9    76.3    20.0  1.095  0.105  0.118
     10.29   8.18   791.3    52.2    18.1  1.108  0.093  0.101
      8.18   7.15   350.8    23.5    11.3  1.160  0.108  0.106
      7.15   6.49   195.8    17.1    11.4  1.090  0.138  0.131
      6.49   6.03   143.7    15.7    12.1  1.029  0.167  0.154
      6.03   5.67   130.8    15.6    13.2  1.101  0.187  0.173
      5.67   5.39   129.9    16.8    14.6  1.074  0.198  0.184
      5.39   5.16   136.0    17.9    15.6  1.078  0.202  0.186
      5.16   4.96   138.3    19.2    16.8  1.044  0.207  0.192
      4.96   4.79   150.9    20.7    18.0  1.082  0.209  0.191
      4.79   4.64   151.3    21.1    18.8  1.140  0.225  0.210
      4.64   4.50   143.1    22.4    20.3  1.070  0.236  0.226
      4.50   4.39   127.5    22.5    21.1  1.027  0.262  0.251
      4.39   4.28   117.7    22.8    22.3  1.051  0.291  0.279
      4.28   4.18   105.8    24.2    23.7  0.988  0.322  0.317
      4.18   4.09    93.0    25.0    24.9  0.947  0.365  0.371
      4.09   4.01    84.9    25.3    25.2  0.884  0.409  0.403
      4.01   3.94    76.6    27.4    27.3  0.843  0.457  0.490
      3.94   3.87    66.5    27.5    27.5  0.778  0.505  0.559
      3.87   3.80    59.3    28.9    28.8  0.766  0.575  0.696
 All reflections    222.9    26.7    19.5  1.037  0.165  0.128




2011/3/15 Francis E Reyes <Francis.Reyes@colorado.edu>
This is probably the most revealing to me.. What did you do about this when you did the MR?


On Mar 15, 2011, at 9:45 AM, Zhang yu wrote:

The analyses of the Patterson function reveals a significant off-origin
peak that is 56.00 % of the origin peak, indicating pseudo translational symmetry.

---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D





_______________________________________________
phenixbb mailing list
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_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb

---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D




_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb