reconfigure qFit segment

[stephaniewankowicz]

1) Remove collapse identical conformers: this leads to handing backbone atoms

2) Re-create refinement script to group occupancy of segment alt locs

In the output of qFit, we require all alt locs in the same segment to have the same occupancy but then allow each one to refine independently and we remove individual residues in the normalized occ script. This leads to unconnected backbone atoms.

An occupancy restraint file should be made as an output of qFit requiring all atoms in the same segment, with the same alt loc to be fed into refinement.

This occupancy restraint file will be used during the occupancy refine loop, updating if we remove the entire alt loc segment.

It will then be removed for the final refinement.

[stephaniewankowicz]

This issue has been closed with #298