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Given that only a single NOE assignment is active at any point in time during pass 3, the question arises as to how to best treat the target distance in eq 3 in cases where a single NOE cross-peak arises from genuine overlap of two or more NOE interactions. Our choice is to leave the target distance unaltered, because, in most cases, cross-peaks do arise from only a single NOE interaction. If a cross-peak genuinely arises from say two NOE interactions of approximately equal intensity, this will be directly reflected in the final likelihoods computed by the PASD algorithm (see section on Final Assignment and Restraints Likelihoods). The distance correction to the upper distance bound for two equally probable assignments would be 12% at most (corresponding to a reduction by a factor of 2 in NOE intensity). However, because the NOE intensities are converted into loose distance ranges, such a correction, in the context of the PASD calculations, is unnecessary. If, on the other hand, the contribution of one of the two NOE interactions constitutes only a very small proportion of the NOE cross-peak intensity, and the NOE restraint associated with that cross-peak is classified as strong, then the weaker interaction would be excluded by the probabilistic inactivation mechanism employed by the PASD algorithm, with no untoward effect.
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A "good" TALOS prediction is defined as follows: either all 10 best database matches for that residue fall in a consistent region of the Ramachandran map, or 9 out of the 10 best database matches fall in a consistent region with φ < 0, and the one outlier also lies in the φ < 0 half of the Ramachandran map (cf. ref 25).
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A missing resonance assignment can have two possible consequences with regard to the generation of NOE assignments. If a particular NOE cross-peak cannot be assigned to any pairwise interaction due to a missing resonance assignment, the effect is entirely neutral because no incorrect information is incorporated into the NOE restraints list. If, on the other hand, a given NOE cross-peak has multiple possible assignments, because of chemical shift degeneracy, and the resonance assignment for one of the partners for the correct NOE assignment is absent, the resulting NOE restraint (which may comprise multiple possible NOE assignments) will be incorrect.
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