In generations using 3D-SB parameters, molecules are iteratively optimized based on 2 rewards: the Docking Score and the Contact Score.
If generations with 3D-SB rewards yield disappointing results, a set-up issue that lead to unsatisfying reward optimization might be the cause!
The first thing to do is to check that your file preparation is correct (PDB, SDF, and water molecules in the PDB). Here is a description of the file preparation to follow: https://makyasupport.zendesk.com/hc/en-us/articles/18736724202524-Before-Makya-Preparation-of-the-Input-Files
(Don't hesitate to contact your Application Scientist if your file seems to have issues!)
Once the files are ready, below are some tips to find better results: