Hi, in choosing the best structure to analyze, I’m choosing the cluster with the lowest z-score (most negative). However, the HADDOCK score is positive with a high restraint energy. I ran my complexes using the Easy and Prediction interface after retrieving active/passive residues from CPORT.
I read that to deduce the score, 10% of the restraint energy should be subtracted from it. Why is that so?
Is there a way I can improve the score?
Thank you.
The restraint energy is part of the score.
Substracting it is only if you want to get a score without it.
And if your restraint energy is very high, it means your restraints are not satisfied… Bioinformatics predictions are far from perfect.
Thank you for your reply! Is there a certain cutt-off point to labeling a restraint energy as being high?
Its tricky to establish a cutoff since these values are relative and not an absolute measure.
Try reviewing your restraints and looking for information in the literature. 
As already said, it is indeed tricky - you will have to analyse your models and see which data/restraints are satisfied and which not.
Giving a hard cutoff is not really doable as there might be many scenarios possible, e.g.
Those two example might lead to the same restraint energy, but would be very different in the way they satisfy (or not) the restraints.