HADDOCK server status for docking run PRE5-PUP2-MS-crosslinks

Status: FINISHED

Your HADDOCK run has successfully completed. The complete run can be downloaded as a gzipped tar file here. The file containing your docking parameters is here.

Please cite the following paper in your work:
G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and (2016). "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes."
J. Mol. Biol., 428, 720-725 (2015).

Questions / feedback ? ask.bioexcel.eu

Summary

HADDOCK clustered 189 structures in 8 cluster(s), which represents 94.5 % of the water-refined models HADDOCK generated. Note that currently the maximum number of models considered for clustering is 200.

The statistics of the top 10 clusters are shown below. The top cluster is the most reliable according to HADDOCK. Its Z-score indicates how many standard deviations from the average this cluster is located in terms of score (the more negative the better).

A graphical representation of the results is also provided at the bottom of the page.

Cluster 1

Cluster 8

Cluster 3

Cluster 2

Cluster 5

Cluster 4

Cluster 7

Cluster 6

Results analysis: The results and graphics presented below are based on water-refined models generated by HADDOCK. The clusters (indicated in color in the graphs) are calculated based on the interface-ligand RMSDs calculated by HADDOCK, with the interface defined automatically based on all observed contacts. The various structural analysis (FCC, i-RMSD and l-RMSD) are made with respect to the best HADDOCK model (the one with the lowest HADDOCK score).
Supplementary information:: i-RMSD -> interface-RMSD calculated on the backbone (CA,C,N,O,P) atoms of all residues involved in intermolecular contact using a 10Å cutoff
l-RMSD -> ligand-RMSD calculated on the backbone atoms (CA,C,N,O,P) of all (N>1) molecules after fitting on the backbone atoms of the first (N=1) molecule
FCC -> Fraction of common contacts. The intermolecular contacts are defined based on the best HADDOCK model using a 5Å cutoff (see Rodrigues et al, Proteins 2012)
a.u. -> Arbitrary Units
The cluster averages and standard deviations are indicated by colored dots with associated error bars. The average values are calculated on the best 4 structures of each clusters (based on the HADDOCK score).

Note that HADDOCK results are deleted after one week.

HADDOCK score	-124.7 +/- 3.5
Cluster size	110
RMSD from the overall lowest-energy structure	0.9 +/- 0.1
Van der Waals energy	-62.6 +/- 3.8
Electrostatic energy	-258.1 +/- 26.8
Desolvation energy	-10.4 +/- 2.7
Restraints violation energy	0.0 +/- 0.00
Buried Surface Area	2213.6 +/- 73.2
Z-Score	-1.7

Nr 1 best structure	Download structure
Nr 2 best structure	Download structure
Nr 3 best structure	Download structure
Nr 4 best structure	Download structure

HADDOCK score	-117.0 +/- 15.2
Cluster size	4
RMSD from the overall lowest-energy structure	0.8 +/- 0.5
Van der Waals energy	-59.1 +/- 13.2
Electrostatic energy	-251.7 +/- 49.7
Desolvation energy	-7.5 +/- 7.2
Restraints violation energy	0.0 +/- 0.00
Buried Surface Area	2174.0 +/- 319.0
Z-Score	-1.4

Nr 1 best structure	Download structure
Nr 2 best structure	Download structure
Nr 3 best structure	Download structure
Nr 4 best structure	Download structure

HADDOCK score	-89.6 +/- 2.4
Cluster size	16
RMSD from the overall lowest-energy structure	1.2 +/- 0.1
Van der Waals energy	-43.6 +/- 2.3
Electrostatic energy	-169.3 +/- 7.5
Desolvation energy	-12.1 +/- 5.2
Restraints violation energy	0.0 +/- 0.04
Buried Surface Area	1660.9 +/- 47.6
Z-Score	-0.3

HADDOCK score	-83.3 +/- 5.5
Cluster size	35
RMSD from the overall lowest-energy structure	1.4 +/- 0.4
Van der Waals energy	-39.4 +/- 3.3
Electrostatic energy	-138.7 +/- 36.0
Desolvation energy	-16.2 +/- 12.6
Restraints violation energy	0.1 +/- 0.08
Buried Surface Area	1483.1 +/- 153.4
Z-Score	-0.1

HADDOCK score	-70.4 +/- 5.3
Cluster size	6
RMSD from the overall lowest-energy structure	1.5 +/- 0.1
Van der Waals energy	-44.3 +/- 7.6
Electrostatic energy	-102.9 +/- 23.4
Desolvation energy	-5.5 +/- 6.6
Restraints violation energy	0.0 +/- 0.01
Buried Surface Area	1575.8 +/- 130.1
Z-Score	0.4

HADDOCK score	-65.1 +/- 7.0
Cluster size	10
RMSD from the overall lowest-energy structure	1.6 +/- 0.1
Van der Waals energy	-34.7 +/- 5.7
Electrostatic energy	-136.6 +/- 47.8
Desolvation energy	-3.1 +/- 7.7
Restraints violation energy	0.5 +/- 0.39
Buried Surface Area	1330.9 +/- 88.7
Z-Score	0.6

HADDOCK score	-53.4 +/- 5.7
Cluster size	4
RMSD from the overall lowest-energy structure	1.9 +/- 0.3
Van der Waals energy	-23.2 +/- 3.5
Electrostatic energy	-158.3 +/- 29.3
Desolvation energy	1.4 +/- 4.8
Restraints violation energy	0.2 +/- 0.12
Buried Surface Area	1323.3 +/- 152.0
Z-Score	1.1

HADDOCK score	-50.7 +/- 12.7
Cluster size	4
RMSD from the overall lowest-energy structure	1.8 +/- 0.1
Van der Waals energy	-25.6 +/- 3.9
Electrostatic energy	-123.5 +/- 56.6
Desolvation energy	-0.5 +/- 7.2
Restraints violation energy	0.4 +/- 0.34
Buried Surface Area	1163.3 +/- 132.0
Z-Score	1.2