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If there are multiple structures that have not converged, try increasing the maximum cycles and the refinements in the conf.yaml file, and running pipeline-refinement again. You can also open the .res files for the structures that did not refine to convergence and see if they are looking sensible or have solved/refined to nonsense. If that is the case, you will need to refine them finish off the refinement manually. But after you do this and have all your cifs ready, providing they stay in the same space group as the reference structure, you can move on to pipeline-cif
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