Fig. 4

The differences in the essential dynamics of TEM-1 is visualized using a no outlier correction, b outlier removal, and c outlier selection. Outlier processing was done using a z-score cutoff of 1.96. Projections are colored by time series, with red being the beginning of the trajectory and blue being the end. Figure d shows the RMSIP between the essential subspaces of the outlier removal and selection modes with the no correction modes. We see that the essential subspace is very similar (\(> 0.9\) identity) for no correction and outlier removal indicating that the outlier do not appreciably impact the essential dynamics of the protein. The RMSIP between the no-correction and outlier selection space is much lower and in the projections we see that the first PC mode is dominated by a relaxation motion of the molecule at the beginning of the simulation