GTPase RsgA-30S ribosomal subunit-GMPPNP complex
In this example, which is also used within the scope of the PowerFit web server tutorial, the putative ribosome biogenesis GTPase RsgA (chain W of PDB entry 2ykr) was fitted into the cryo-EM density map of the full RsgA-30S ribosomal subunit-GMPPNP complex (EMDB entry 1884 - 9.8 Å resolution) with the default server parameters. The best 3 Fits all occupy the expected part of the density map with powerfit clearly favoring one particular orientation based on cross correlation score and sigma difference.

Run 2ykr_W - EMD-1884 (Example1)
Status: FINISHED
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Archive of the complete run: Example1.tgz
Archive of all autogenerated images: Example1_images.tgz
Please cite the following papers in your work:
G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin.
The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. J. Mol. Biol., Advanced Online Publication (2016).

G.C.P. van Zundert and A.M.J.J. Bonvin (2015)
Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit.
AIMS Biophysics 2, 73-87.
and add the following acknowledgment:
The H2020 e-Infrastructure projects West-Life (grant no. 675858), EGI-Engage-MobrainCC (grant no. 654142) and INDICO-DataCloud (grant no. 653549) are acknowledged for the use of their web portals, which make use of the EGI infrastructure.
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Solutions
The table below lists the 15 best non-redundant solutions found by correlation score. The first column shows the rank, column 2 the correlation score, column 3 the Fisher z-score column 4 the zscore as factor of standard deviations (z/σ), and column 5 the sigma difference to the best fit. (see N. Volkmann 2009, and Van Zundert and Bonvin 2016).
Rank (N) Cross Correlation Score Fisher z-score z-score/σ Sigma difference
(z1-zN)/σ
1 0.560 0.633 31.0 0.00
2 0.517 0.573 28.0 2.98
3 0.432 0.463 22.7 8.35
4 0.301 0.311 15.2 15.79
5 0.298 0.307 15.1 15.97
6 0.298 0.307 15.0 15.99
7 0.293 0.302 14.8 16.24
8 0.290 0.298 14.6 16.42
9 0.288 0.297 14.5 16.49
10 0.288 0.296 14.5 16.53
11 0.287 0.295 14.4 16.58
12 0.285 0.293 14.3 16.69
13 0.284 0.292 14.3 16.71
14 0.284 0.292 14.3 16.73
15 0.282 0.290 14.2 16.82
Images were generated with UCSF Chimera.
Fit 1
Rank 1
Cross Correlation Score 0.560
Fisher z-score 0.633
z-score/σ 31.0
Sigma difference (zN-zN+1)/σ 0.00
PDB Download
Fit 2
Rank 2
Cross Correlation Score 0.517
Fisher z-score 0.573
z-score/σ 28.0
Sigma difference (zN-zN+1)/σ 2.98
PDB Download
Fit 3
Rank 3
Cross Correlation Score 0.432
Fisher z-score 0.463
z-score/σ 22.7
Sigma difference (zN-zN+1)/σ 8.35
PDB Download
Fit 4
Rank 4
Cross Correlation Score 0.301
Fisher z-score 0.311
z-score/σ 15.2
Sigma difference (zN-zN+1)/σ 15.79
PDB Download
Fit 5
Rank 5
Cross Correlation Score 0.298
Fisher z-score 0.307
z-score/σ 15.1
Sigma difference (zN-zN+1)/σ 15.97
PDB Download
Fit 6
Rank 6
Cross Correlation Score 0.298
Fisher z-score 0.307
z-score/σ 15.0
Sigma difference (zN-zN+1)/σ 15.99
PDB Download
Fit 7
Rank 7
Cross Correlation Score 0.293
Fisher z-score 0.302
z-score/σ 14.8
Sigma difference (zN-zN+1)/σ 16.24
PDB Download
Fit 8
Rank 8
Cross Correlation Score 0.290
Fisher z-score 0.298
z-score/σ 14.6
Sigma difference (zN-zN+1)/σ 16.42
PDB Download
Fit 9
Rank 9
Cross Correlation Score 0.288
Fisher z-score 0.297
z-score/σ 14.5
Sigma difference (zN-zN+1)/σ 16.49
PDB Download
Fit 10
Rank 10
Cross Correlation Score 0.288
Fisher z-score 0.296
z-score/σ 14.5
Sigma difference (zN-zN+1)/σ 16.53
PDB Download