Duplicate conformations not collapsed in qfit_protein output-2NLV Tyr18, ChainA

[ss199514]

When qfit_protein is run on 2NLV, multiconformer_model2 has A-E conformations for Tyr18, Chain A. A and B conf are identical (RMSD-0) but not collapsed in the output. Replicate as below:

Pull from dev:

1. In the original 2nlv.pdb, remove alternate conformation B in residues 17,18 and 77 for both chains ​

2. Do 5 rounds of refinement in phenix using the model from step 1​

3. Create a composite omit map using 2nlv.mtz in phenix​

4. Run qfit_protein using the composite omit map and refined 2nlb model file like such:​

qfit_protein composite_omit_map.mtz -l 2FOFCWT,PH2FOFCWT 2nlv_refine_001_refine_003.pdb

Output file attached
multiconformer_model2.txt