I used SWISS-MODEL to create protein models for a bacterial transporter protein , that i want to use for further docking and MD simulation studies. The created model is failing the structure validation test i.e. Verify3D and ERRAT. I tried energy minimization using UCSF Chimera but no significant improvement. The template on which this model is made itself is failing the structure validation tests and is a low confidence model. Any suggestions what should be the next step?

I thought of using Modeler to create new models but their is no similar template in PDB. So what should be done?