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

Zhang yu phenixzyfish at gmail.com
Tue Mar 15 16:49:11 PDT 2011


*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
   ---------------------
- 显示引用文字 -
      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 at 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 at 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
>> 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
>>
>
> ---------------------------------------------
> 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 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/20110315/4fbed20d/attachment-0003.htm>


More information about the phenixbb mailing list