## 3 Results and Discussion
### All-Atom Model
This massive deviation causes the necessity to apply the high rigidity value cited in Table 1 to match the average value of the experimental B-factors. Therefore, the application of such a small cutoff value is clearly not adequate for the proposed technique and the investigated protein, thus demanding larger spheres of influence. The 6 A and 8 A cases are capable of providing more information about global and localized flexibility. Most of the peaks in the computed profile of numerical B-factors exhibit some similarity with the experimental ones. The remaining cutoff values, i.e., 10, 12, 15, 20, 25, and 30 A, present very similar profiles, matching pretty well with the experimental B-factors. However, the amplitude of flexibility in some regions changes to some extent depending on the specific case, i.e., the specific cutoff value. As can be appreciated by comparing Figure 2a-c, the augment of the sphere of influence adds more details to the B-factors curves. Some of these increments are subtle, but they can contribute to the changes in the shape of the profile. These modifications can also highlight minor peaks not captured with other selected cutoffs. Three sections are also amplified in the lower panel of Figure 2 for better visualization: atoms 50-250, 350-600, and 750-1000. Overall, it can be noted that the trends provided by the numerical solutions meet fairly accurately with the experimental one. Some specific observations are cited:  
* in the region 50-250, the major experimental peaks agree with the numerical ones from the model with a cutoff value of 10 A onwards. For small fluctuations, it is hard to confirm a good representative relationship between the solutions;
* in the region 350-600, node 379 shows a high experimental B-factor, but none of the numerical solutions provides such increased flexibility. The models are not able to  
Figure 2: The numerical and experimental B-factor for all cases under analysis. The vertical lines indicate the C\({}^{\alpha}\) nodes. The experimental B-factors are shown with dotted-black lines. Three plots are displayed to avoid overlapping and facilitate visualization: (**a**) 4, 6, 8; (**b**) 10, 12, 15; (**c**) 20, 25, and 30 Å. Additionally, three sections are amplified for a better view of specific regions of the protein. capture this particular behavior. This can either be due to deficiencies in the simplified truss models or measurement errors in the experimental B-factors. Some other smaller peaks have similar patterns. At node 478, the effect that arises from increasing the cutoff value is clearly seen; \(\odot\) in the region 750-1000, nodes 991 and 992 present a substantial peak in all cases that go beyond the top of the chart. In that region, a dent extends outside the globular body region, making it similar to a cantilever beam attached to the main structure. This is commonly associated with the first natural mode of numerical solutions and it has high participation in many modes. At first sight, this solution does not present a real behavior according to the experimental B-factors. It is possible that damping related to the surrounding environment may play a role, leading to this discrepancy. The Pearson correlation coefficient is also applied to measure the correlation between the profile of experimental and numerical B-factors. Figure 3 displays the coefficients among all the numerical B-factors as well as against the experimental profile. The agreement between models with near-size cutoff values is confirmed, while larger differences in the selected cutoff make the numerical B-factors less correlated with each other. This observation is remarkably straightforward when comparing the models with extreme cutoff values, i.e., 4 and 30 A. Comparing the experimental value from the 10 A case onwards demonstrates a correlation coefficient higher than 0.56. The correlation coefficients of larger cutoff values are similar to those obtained with the coarse-grained model based on the C\({}^{\alpha}\) location [15].