We strongly advise you to use the default pre-processing options (in bold in the relevant section). Do you want to submit anyway?
If you use local distance difference test (lDDT), please cite the following reference:
Mariani, V., Biasini, M., Barbato, A., Schwede, T. lDDT: a
local superposition-free score for comparing protein
structures and models using distance difference tests.
Bioinformatics 29, 2722-2728 (2013).

