Table 1.

Troubleshooting table

Step	Problem	Possible reason	Solution
5	No structure of the individual protein is predicted by the I-TASSER protein structure prediction	No homologues templates are available	Provide restraint information immediately at first prediction step. Try to repeat the first prediction step with I-TASSER using all cross-linking restraints of the corresponding intraprotein cross-links
	The number of predicted models is < 5	The identified templates are very similar	Choose the model with the highest C-score
8, 25	Distance calculations can fail under certain conditions. In such a case, negative distance values will be reported	-1:The distance between the atoms exceeds the maximum distance defined in the command line with the parameter (-max) -2:The first atom is not solvent accessible -3:The second atom is not solvent accessible -4:Both atoms are not solvent accessible -5:The first atom is in a cavity which prohibits proper shortest path calculations	The values -2, -3, -4 and -5 should be replaced with the Euclidian distance between the two atoms. The value -1 should be replaced with a value higher than the maximum cutoff (e.g., 100) for future categorization (Step 10 and Step 26)
10 and 27	Most or all of the cross-links are incompatible with the preliminary model	Such a case is likely to be the result of a markedly different protein conformation in solution compared with the preliminary model. Alternatively, it could also indicate an unsuccessful cross-linking experiment	It is not recommended to continue with the protocol
24	Docking results at HADDOCK server have disappeared	Results are deleted at HADDOCK server after 1 week	Save all results immediately after getting the notification from the server about the completed job. Save the parameter file for each HADDOCK submission. It is possible to use the ‘File Upload’ interface for repeating the docking analysis at a later time point