Strange output for configuration number 7

[WildJimmy]

When using the initial positions provided by the professor for structure 7, I end up with a plot like this

Has anyone else had this issue? This is not the form of in the paper and it needs some additional tuning correct?

[s4il3sh]

Is not there some kind of line drawing features in 3d connecting those dots? It would be helpful to understand it easier.