[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