Atoms not displayed after refinement

Hi. I am working on system which includes protein monomer, small molecule and 10 bp DNA. I want to refine my system, so I used HADDOCK 2.4 for this. But after the refinement, I saw that the C atom of the small molecule was not displayed. Related images are attached.
Before refinement:

After refinement:

First I kept the small molecule and protein in the same chain. When I got this result, I defined the small molecule and protein as separate molecules in different chains. However, the result has not changed.

I am also adding my input and output files. What can be the problem?

output.pdb (278.1 KB) input.pdb (431.4 KB)

Check the content of your PDB files. The atom is there, it is simply not displayed properly.

The input file has CONECT statements. If you remove those my guess is that you also won’t see the atom displayed properly