What does final generated models with TM-score of DMPfold signify in "sequence.ema.txt" file?
This is described briefly in the paper. The four quantities are inputs to the estimator of model accuracy:


nres is the sequence length.
neff is an effective sequence count, or how deep the alignment was.
dpscore is how well the final model matches the initial distance prediction.
dpscorenorm is a normalised version of the above.


Don't worry too much about directly interpreting these. They are only given for completion. The important line is Estimated TM-score of ../final_1.pdb is 0.5, indicating that DMPfold just about thinks this is a decent model.

The "sequence.ema.txt" is more raw output giving the probability of the TM-score being in each bin. "rawdistpred.1" is the distance predictions from the first iteration. Always use "rawdistpred.1" as input to the TM-score predictor as this is how it was trained.