Re: [ccp4bb] Low resolution and high anisotropy

2022-10-27 Thread Clemens Vonrhein
Dear Lande,

On Wed, Oct 26, 2022 at 08:09:10AM +0100, Lande Fu wrote:
> I noticed STARANISO processd the data all the way down to 1.7A, with
> very poor stats on high resolution shell.

Were you looking at the second table in the original email? It is not
in a format I recognize as coming from STARANISO ... maybe this is
from the UCLA server or some manual procedure?

Cheers

Clemens



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Re: [ccp4bb] Low resolution and high anisotropy

2022-10-26 Thread Martin Malý

Dear Shenyuan Xu,

I dealt with a similar problem recently. In my particular case, a 
combination of the correction with STARANISO and a subsequent molecular 
replacement with the MoRDa pipeline helped me a lot. MoRDa was able to 
suggest how to place individual protein domains separately in the unit 
cell and which model templates to choose. Then I rebuilt carefully the 
main chain(s).


I have heard several times that BUSTER is very smart in the refinement 
of low-resolution structures. But I do not have personal experience.


By the way, regarding the reported completeness after the STARANISO 
correction, is it spherical or ellipsoidal?


Good luck!
Martin


On 24. 10. 22 3:43, Xu, Shenyuan wrote:

Dear CCP4 community,

I have encountered a dataset, which I thought should be easy to solve. 
The volume of the cell unit seems to be expanded after image 271, 
which I think is caused by radiation damage. After removing the last 
few images, the scaled statistics seem good with the resolution set at 
3:07 A:


d_max  d_min   #obs  #uniq   mult.  %comp             r_mrg   
r_meas    r_pim   r_anom   cc1/2 cc_ano
 91.54   8.33   3086   1197    2.58  98.44     345.2    51.3  0.101   
 0.133    0.086    0.145   0.973*  -0.148
  8.33   6.61   3005   1225    2.45  99.51     256.5    27.3  0.160   
 0.212    0.138    0.260   0.923*  -0.140
  6.61   5.78   2883   1190    2.42  98.43      92.9     9.4  0.278   
 0.368    0.237    0.461   0.541*  -0.165
  5.78   5.25   3195   1217    2.63  99.10      75.6     8.1  0.283   
 0.369    0.233    0.436   0.618*  -0.107
  5.25   4.87   3192   1206    2.65  99.42      92.5     8.3  0.281   
 0.367    0.232    0.427   0.856*  -0.187
  4.87   4.59   3230   1213    2.66  99.02     118.4    10.3  0.288   
 0.378    0.240    0.456   0.870*  -0.053
  4.59   4.36   2797   1156    2.42  92.93     137.0    12.2  0.309   
 0.410    0.266    0.496   0.843*  -0.239
  4.36   4.17   2694   1118    2.41  93.17     280.2    16.2  0.419   
 0.575    0.392    0.847   0.491*  -0.142
  4.17   4.01   3102   1188    2.61  95.50     133.6     9.9  0.392   
 0.516    0.330    0.622   0.663*  -0.268
  4.01   3.87   3224   1205    2.68  98.69     120.4     7.3  0.406   
 0.539    0.349    0.687   0.791*  -0.126
  3.87   3.75   2939   1181    2.49  98.91      90.7     6.8  0.491   
 0.652    0.425    0.810   0.691*  -0.042
  3.75   3.64   1981   1021    1.94  82.34      87.3     5.0  0.557   
 0.756    0.506    0.885   0.540*  -0.018
  3.64   3.54   2374   1082    2.19  89.13     194.6    11.2  0.502   
 0.675    0.447    0.973   0.625*  -0.237
  3.54   3.46   2622   1122    2.34  92.35     310.5    10.1  0.432   
 0.585    0.392    0.851   0.603*  -0.154
  3.46   3.38   1739    945    1.84  76.58      48.2     3.6  0.930   
 1.247    0.822    1.542   0.444*  -0.046
  3.38   3.31   2847   1240    2.30  98.57      85.4     4.2  0.691   
 0.930    0.616    1.242   0.523*  -0.060
  3.31   3.24   2838   1153    2.46  97.88      70.8     3.3  0.693   
 0.934    0.620    1.341   0.362*   0.006
  3.24   3.18   3097   1212    2.56  97.66      71.4     2.5  0.692   
 0.924    0.605    1.173   0.526*   0.044
  3.18   3.12   3204   1216    2.63  99.10      79.6     3.7  0.668   
 0.886    0.576    1.338   0.440*  -0.081
  3.12   3.07   3059   1172    2.61  98.16      73.5     2.4  0.714   
 0.945    0.612    1.633   0.362*  -0.177
 91.50   3.07  57108  23259    2.46  95.22     138.4    10.8  0.383   
 0.513    0.336    0.671   0.656*  -0.149


I used Mrbump to do the MR, most sequence identities of the starting 
templates are more than 0.85, and some of them are structures 
predicted from alpha fold 2. But after refinement (including 
jelly-body, proSmart, TLC), the best R/Free R stuck at around 
0.42/0.45. Inspecting the electron density map shows that the model 
does not fit the electron density well. The space group is P1, Cell is 
58.49 63.97 91.60 91.71 91.86 99.47, should be 5 or 6 molecules in the 
asymmetric unit.


I checked the data quality, it said the data is highly anisotropy. Then
I searched the CCP4 forum and used theSTARANISO Server and UCLA 
server, but still cannot improve the refinement. The data 
statistics after drawing ellipsoidal resolution limits is good:


 
 resolution   observed     redundancy    completenes  rmerge         
i/sigma
            before/after  before/after   before/after  before/after   
before/after
    7.90     4957  1185     3.5  3.3    97.3%   92.6%    13.0%  12.7% 
   11.9   7.2
    5.58     8023  2397     3.0  3.6    98.6%   98.9%    30.3%  11.8% 
    5.5   7.5
    4.56    11176  2624     3.3  3.1    99.1%   97.5%    57.1%  18.2% 
    3.7   6.3
    3.95    11694  3213     2.9  3.1    94.0%   99.0%    53.1%  27.5% 
    4.2   4.3
    3.53    12065  3524     2.6  3.0    92.8%   99.0%    49.8%  45.9% 
    3.2   2.8
    3.22    12828  4098     2.5  3.2    93.8%   99.1%    69.3%  53.2% 
    2.1   2.7
    2.98    17566  4628     3.2  3.3    98.6%   99.1%    98.1%  60.0% 

Re: [ccp4bb] Low resolution and high anisotropy

2022-10-26 Thread Eleanor Dodson
How to deal with poor data is a challenge. Look at the images - see at what
resolution there is detectable diffraction.
Then run a self rotation function.Do you expect a trimer? dimer? etc and
does the self rotation give any clues?
Are your models dimers? trimers? etc.
Eleanor

On Wed, 26 Oct 2022 at 08:09, Lande Fu <
8bc2565720d4-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Shenyuan,
>
>
> I noticed STARANISO processd the data all the way down to 1.7A, with very
> poor stats on high resolution shell. I have two suggesstions:
> 1.You may want to reivse the raw images to check the anisotropy (that all
> spots are distributed in an flat ellipse).
> 2. If you can  scale&merge the data with Aimless suite in CCP4, check
> "Anisotropic deltaB" value below summary table.
>
>
> For MR, there is too much to tell and it's better to improve data
> processing first.
>
>
>
>
>
> regards,
> Lande
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] Low resolution and high anisotropy

2022-10-26 Thread Lande Fu
Hello Shenyuan,


I noticed STARANISO processd the data all the way down to 1.7A, with very poor 
stats on high resolution shell. I have two suggesstions: 
1.You may want to reivse the raw images to check the anisotropy (that all spots 
are distributed in an flat ellipse). 
2. If you can  scale&merge the data with Aimless suite in CCP4, check 
"Anisotropic deltaB" value below summary table.


For MR, there is too much to tell and it's better to improve data processing 
first.





regards,
Lande



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Re: [ccp4bb] Low resolution and high anisotropy

2022-10-24 Thread Mark J. van Raaij
The improvement in statistics by STARANISO is really spectacular, but I do 
wonder how much is caused by the directionally variable resolution limits and 
how much by the removal of solvent rings? The original data set statistics have 
big dips in CC1/2 at 6, 4.3 and 3.7 Å.
Also in the final statistics table, the completeness is really high, but I 
guess reflections from the "bad" direction(s) are not taken into account? It 
would be good to also know the spherical completeness and the CC1/2 values 
before going too far ahead with these data. Or perhaps better phrased: I'd 
simultaneously try to get a dataset from a better flash-cooled crystal while 
trying to get the most out of this dataset.

Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 24 Oct 2022, at 03:43, Xu, Shenyuan  wrote:
> 
> Dear CCP4 community,
> 
> I have encountered a dataset, which I thought should be easy to solve. The 
> volume of the cell unit seems to be expanded after image 271, which I think 
> is caused by radiation damage. After removing the last few images, the scaled 
> statistics seem good with the resolution set at 3:07 A:
> 
> d_max  d_min   #obs  #uniq   mult.  %comp r_mrg   r_meas 
>r_pim   r_anom   cc1/2   cc_ano
>  91.54   8.33   3086   11972.58  98.44 345.251.30.101
> 0.1330.0860.145   0.973*  -0.148
>   8.33   6.61   3005   12252.45  99.51 256.527.30.160
> 0.2120.1380.260   0.923*  -0.140
>   6.61   5.78   2883   11902.42  98.43  92.9 9.40.278
> 0.3680.2370.461   0.541*  -0.165
>   5.78   5.25   3195   12172.63  99.10  75.6 8.10.283
> 0.3690.2330.436   0.618*  -0.107
>   5.25   4.87   3192   12062.65  99.42  92.5 8.30.281
> 0.3670.2320.427   0.856*  -0.187
>   4.87   4.59   3230   12132.66  99.02 118.410.30.288
> 0.3780.2400.456   0.870*  -0.053
>   4.59   4.36   2797   11562.42  92.93 137.012.20.309
> 0.4100.2660.496   0.843*  -0.239
>   4.36   4.17   2694   11182.41  93.17 280.216.20.419
> 0.5750.3920.847   0.491*  -0.142
>   4.17   4.01   3102   11882.61  95.50 133.6 9.90.392
> 0.5160.3300.622   0.663*  -0.268
>   4.01   3.87   3224   12052.68  98.69 120.4 7.30.406
> 0.5390.3490.687   0.791*  -0.126
>   3.87   3.75   2939   11812.49  98.91  90.7 6.80.491
> 0.6520.4250.810   0.691*  -0.042
>   3.75   3.64   1981   10211.94  82.34  87.3 5.00.557
> 0.7560.5060.885   0.540*  -0.018
>   3.64   3.54   2374   10822.19  89.13 194.611.20.502
> 0.6750.4470.973   0.625*  -0.237
>   3.54   3.46   2622   11222.34  92.35 310.510.10.432
> 0.5850.3920.851   0.603*  -0.154
>   3.46   3.38   17399451.84  76.58  48.2 3.60.930
> 1.2470.8221.542   0.444*  -0.046
>   3.38   3.31   2847   12402.30  98.57  85.4 4.20.691
> 0.9300.6161.242   0.523*  -0.060
>   3.31   3.24   2838   11532.46  97.88  70.8 3.30.693
> 0.9340.6201.341   0.362*   0.006
>   3.24   3.18   3097   12122.56  97.66  71.4 2.50.692
> 0.9240.6051.173   0.526*   0.044
>   3.18   3.12   3204   12162.63  99.10  79.6 3.70.668
> 0.8860.5761.338   0.440*  -0.081
>   3.12   3.07   3059   11722.61  98.16  73.5 2.40.714
> 0.9450.6121.633   0.362*  -0.177
>  91.50   3.07  57108  232592.46  95.22 138.410.80.383
> 0.5130.3360.671   0.656*  -0.149
> 
> I used Mrbump to do the MR, most sequence identities of the starting 
> templates are more than 0.85, and some of them are structures predicted from 
> alpha fold 2. But after refinement (including jelly-body, proSmart, TLC), the 
> best R/Free R stuck at around 0.42/0.45. Inspecting the electron density map 
> shows that the model does not fit the electron density well. The space group 
> is P1, Cell is 58.49 63.97 91.60 91.71 91.86 99.47, should be 5 or 6 
> molecules in the asymmetric unit.
> 
> I checked the data quality, it said the data is highly anisotropy. Then
> I searched the CCP4 forum and used the STARANISO Server and UCLA server, but 
> still cannot improve the refinement. The data statistics after drawing 
> ellipsoidal resolution limits is good:
> 
>  
>  resolution   observed redundancycompletenesrmerge 
> i/sigma 
> before/after  before/after   before/afterbefore/after   
> before/after
> 7.90 4957  1185 3.5  3.397.3%   92.6%13.0%  12.7%11.9 
>   7.2
> 5.5

Re: [ccp4bb] Low resolution and high anisotropy

2022-10-24 Thread Tim Gruene
Dear Shenyuan Xu,

it is a good sign that the model and density to not match - at 3.07A,
one often only has model bias with a poor MR solution. You don't want
to start with refinement, better to start with model building: make the
model fit the density better, before you run refinement, and check
again for R/Rfree.

Best regards,
Tim


On Mon, 24 Oct 2022 09:43:19 +0800
"Xu, Shenyuan"  wrote:

> Inspecting the electron
> density map shows that the model does not fit the electron density
> well.


-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] AW: [ccp4bb] Low resolution and high anisotropy

2022-10-24 Thread Schreuder, Herman /DE
Dear Shenyuan,

I have two suggestions:

  1.  Is your protein a single or a multi-domain protein? If it is a 
multi-domain protein, you should search with the individual domains.
  2.  Given the low resolution, high anisotropy and expected large number of 
molecules in the asymmetric unit, you may have an exceptionally high solvent 
content, maybe >75%. Is the electron density of all molecules bad, or have a 
few molecules better electron density? If a few molecules have reasonable 
density, I would keep those and delete the molecules with bad density. 
Alternatively, I would start a MR search for only 3 or 4 molecules.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Xu, Shenyuan
Gesendet: Montag, 24. Oktober 2022 03:43
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Low resolution and high anisotropy

Dear CCP4 community,

I have encountered a dataset, which I thought should be easy to solve. The 
volume of the cell unit seems to be expanded after image 271, which I think is 
caused by radiation damage. After removing the last few images, the scaled 
statistics seem good with the resolution set at 3:07 A:

d_max  d_min   #obs  #uniq   mult.  %comp r_mrg   r_meas   
 r_pim   r_anom   cc1/2   cc_ano
 91.54   8.33   3086   11972.58  98.44 345.251.30.1010.133  
  0.0860.145   0.973*  -0.148
  8.33   6.61   3005   12252.45  99.51 256.527.30.1600.212  
  0.1380.260   0.923*  -0.140
  6.61   5.78   2883   11902.42  98.43  92.9 9.40.2780.368  
  0.2370.461   0.541*  -0.165
  5.78   5.25   3195   12172.63  99.10  75.6 8.10.2830.369  
  0.2330.436   0.618*  -0.107
  5.25   4.87   3192   12062.65  99.42  92.5 8.30.2810.367  
  0.2320.427   0.856*  -0.187
  4.87   4.59   3230   12132.66  99.02 118.410.30.2880.378  
  0.2400.456   0.870*  -0.053
  4.59   4.36   2797   11562.42  92.93 137.012.20.3090.410  
  0.2660.496   0.843*  -0.239
  4.36   4.17   2694   11182.41  93.17 280.216.20.4190.575  
  0.3920.847   0.491*  -0.142
  4.17   4.01   3102   11882.61  95.50 133.6 9.90.3920.516  
  0.3300.622   0.663*  -0.268
  4.01   3.87   3224   12052.68  98.69 120.4 7.30.4060.539  
  0.3490.687   0.791*  -0.126
  3.87   3.75   2939   11812.49  98.91  90.7 6.80.4910.652  
  0.4250.810   0.691*  -0.042
  3.75   3.64   1981   10211.94  82.34  87.3 5.00.5570.756  
  0.5060.885   0.540*  -0.018
  3.64   3.54   2374   10822.19  89.13 194.611.20.5020.675  
  0.4470.973   0.625*  -0.237
  3.54   3.46   2622   11222.34  92.35 310.510.10.4320.585  
  0.3920.851   0.603*  -0.154
  3.46   3.38   17399451.84  76.58  48.2 3.60.9301.247  
  0.8221.542   0.444*  -0.046
  3.38   3.31   2847   12402.30  98.57  85.4 4.20.6910.930  
  0.6161.242   0.523*  -0.060
  3.31   3.24   2838   11532.46  97.88  70.8 3.30.6930.934  
  0.6201.341   0.362*   0.006
  3.24   3.18   3097   12122.56  97.66  71.4 2.50.6920.924  
  0.6051.173   0.526*   0.044
  3.18   3.12   3204   12162.63  99.10  79.6 3.70.6680.886  
  0.5761.338   0.440*  -0.081
  3.12   3.07   3059   11722.61  98.16  73.5 2.40.7140.945  
  0.6121.633   0.362*  -0.177
 91.50   3.07  57108  232592.46  95.22 138.410.80.3830.513  
  0.3360.671   0.656*  -0.149

I used Mrbump to do the MR, most sequence identities of the starting templates 
are more than 0.85, and some of them are structures predicted from alpha fold 
2. But after refinement (including jelly-body, proSmart, TLC), the best R/Free 
R stuck at around 0.42/0.45. Inspecting the electron density map shows that the 
model does not fit the electron density well. The space group is P1, Cell is 
58.49 63.97 91.60 91.71 91.86 99.47, should be 5 or 6 molecules in the 
asymmetric unit.

I checked the data quality, it said the data is highly anisotropy. Then
I searched the CCP4 forum and used the STARANISO Server and UCLA server, but 
still cannot improve the refinement. The data statistics after drawing 
ellipsoidal resolution limits is good:

 
 resolution   observed redundancycompletenesrmerge 
i/sigma
before/after  before/after   before/afterbefore/after   
before/after
7.90 4957  1185 3.5  3.397.3%   92.6%13.0%  12.7%11.9   
7.2
5.58 8023  2397 3.0  3.698.6%   98.9%30.3%  11.8% 5.5   
7.5
4.5611176  2624 3.3  3.199.1%   97.5%57.1%  18.2% 3.7   
6.3
3.9511694  3213 2.9  3.194.0%   99.0%53.1%  27.5% 4.2   
4.3
3.5312065  3524 2.6  3.092.8%   99.0%49.8%  45.9% 3.2   

[ccp4bb] Low resolution and high anisotropy

2022-10-23 Thread Xu, Shenyuan
Dear CCP4 community,

I have encountered a dataset, which I thought should be easy to solve. The
volume of the cell unit seems to be expanded after image 271, which I think
is caused by radiation damage. After removing the last few images, the
scaled statistics seem good with the resolution set at 3:07 A:

d_max  d_min   #obs  #uniq   mult.  %comp r_mrg
r_measr_pim   r_anom   cc1/2   cc_ano
 91.54   8.33   3086   11972.58  98.44 345.251.30.101
 0.1330.0860.145   0.973*  -0.148
  8.33   6.61   3005   12252.45  99.51 256.527.30.160
 0.2120.1380.260   0.923*  -0.140
  6.61   5.78   2883   11902.42  98.43  92.9 9.40.278
 0.3680.2370.461   0.541*  -0.165
  5.78   5.25   3195   12172.63  99.10  75.6 8.10.283
 0.3690.2330.436   0.618*  -0.107
  5.25   4.87   3192   12062.65  99.42  92.5 8.30.281
 0.3670.2320.427   0.856*  -0.187
  4.87   4.59   3230   12132.66  99.02 118.410.30.288
 0.3780.2400.456   0.870*  -0.053
  4.59   4.36   2797   11562.42  92.93 137.012.20.309
 0.4100.2660.496   0.843*  -0.239
  4.36   4.17   2694   11182.41  93.17 280.216.20.419
 0.5750.3920.847   0.491*  -0.142
  4.17   4.01   3102   11882.61  95.50 133.6 9.90.392
 0.5160.3300.622   0.663*  -0.268
  4.01   3.87   3224   12052.68  98.69 120.4 7.30.406
 0.5390.3490.687   0.791*  -0.126
  3.87   3.75   2939   11812.49  98.91  90.7 6.80.491
 0.6520.4250.810   0.691*  -0.042
  3.75   3.64   1981   10211.94  82.34  87.3 5.00.557
 0.7560.5060.885   0.540*  -0.018
  3.64   3.54   2374   10822.19  89.13 194.611.20.502
 0.6750.4470.973   0.625*  -0.237
  3.54   3.46   2622   11222.34  92.35 310.510.10.432
 0.5850.3920.851   0.603*  -0.154
  3.46   3.38   17399451.84  76.58  48.2 3.60.930
 1.2470.8221.542   0.444*  -0.046
  3.38   3.31   2847   12402.30  98.57  85.4 4.20.691
 0.9300.6161.242   0.523*  -0.060
  3.31   3.24   2838   11532.46  97.88  70.8 3.30.693
 0.9340.6201.341   0.362*   0.006
  3.24   3.18   3097   12122.56  97.66  71.4 2.50.692
 0.9240.6051.173   0.526*   0.044
  3.18   3.12   3204   12162.63  99.10  79.6 3.70.668
 0.8860.5761.338   0.440*  -0.081
  3.12   3.07   3059   11722.61  98.16  73.5 2.40.714
 0.9450.6121.633   0.362*  -0.177
 91.50   3.07  57108  232592.46  95.22 138.410.80.383
 0.5130.3360.671   0.656*  -0.149

I used Mrbump to do the MR, most sequence identities of the starting
templates are more than 0.85, and some of them are structures predicted
from alpha fold 2. But after refinement (including jelly-body, proSmart,
TLC), the best R/Free R stuck at around 0.42/0.45. Inspecting the electron
density map shows that the model does not fit the electron density well.
The space group is P1, Cell is 58.49 63.97 91.60 91.71 91.86 99.47, should
be 5 or 6 molecules in the asymmetric unit.

I checked the data quality, it said the data is highly anisotropy. Then
I searched the CCP4 forum and used the STARANISO Server and UCLA server,
but still cannot improve the refinement. The data statistics after drawing
ellipsoidal resolution limits is good:

 
 resolution   observed redundancycompletenesrmerge
i/sigma
before/after  before/after   before/afterbefore/after
before/after
7.90 4957  1185 3.5  3.397.3%   92.6%13.0%  12.7%
 11.9   7.2
5.58 8023  2397 3.0  3.698.6%   98.9%30.3%  11.8%
5.5   7.5
4.5611176  2624 3.3  3.199.1%   97.5%57.1%  18.2%
3.7   6.3
3.9511694  3213 2.9  3.194.0%   99.0%53.1%  27.5%
4.2   4.3
3.5312065  3524 2.6  3.092.8%   99.0%49.8%  45.9%
3.2   2.8
3.2212828  4098 2.5  3.293.8%   99.1%69.3%  53.2%
2.1   2.7
2.9817566  4628 3.2  3.398.6%   99.1%98.1%  60.0%
1.6   2.7
2.7919405  4631 3.3  3.198.1%   96.8%   203.0%  70.3%
0.8   2.7
2.6320871  4001 3.3  2.598.1%   90.1%   760.1%  41.2%
0.3   3.4
2.5020352  5406 3.0  3.297.8%   97.3%   -99.9%  66.0%
0.0   2.6
2.3817281  5689 2.5  3.293.8%   98.2%   -99.9%  81.4%
0.0   1.8
2.2813198  3874 1.8  2.168.6%   88.0%   546.3% 193.2%
0.1   0.6
2.1910429  4961 1.4  2.652.5%   92.7%   -99.9%  31.0%
0.0   4.8
2.11 7776  4275 1.0  2.141.2%   90.1%   -99.9% 266.0%
0.0   0.6
2.04 5561  6084 0.7  2.930.9%   97.6%   531.4% 109.2%
0.1   1.1
1.97 3818  6700 0.4  3.123.4%   97.4%   -99.9%  85.8%
0.0   1.6
1.91 2269  5906 0.3  2.717.0%   83.9