The direct refinement against NOESY intensities is more CPU intensive than distance-restrained refinement. Several means have been implemented to reduce the CPU time requirements.
The tolerance statement specifies the maximum distance that an NMR-active atom is allowed to move until the relaxation matrix pseudoenergy is recalculated. If the tolerance is larger than 0, the pseudoenergy is not calculated at every step. The optimal value of the tolerance depends on the energy parameters, weights on the relaxation matrix pseudoenergy, masses of the atoms, and annealing temperature. Too large a value for the tolerance (i.e., the relaxation matrix pseudoenergy is recalculated too rarely) heats the system and induces large temperature fluctuations, and the molecule may be trapped in the starting conformation. A value of 0.05 Å is a good starting point.
The largest reduction in computation time is achieved by the introduction of a distance cutoff for the relaxation matrix and gradient calculations. To a good approximation, the size of a 2D NOE cross peak between spins i and j is affected only by the relaxation pathways via spins close to i or j. Thus, individual distance cutoff spheres are used around i and j for the calculation of and the contribution to the gradient due to this cross peak. For every pair of spins, a relaxation matrix is generated and diagonalized separately.
The cutoff determines the number of cross relaxation pathways that are included in the calculation. Its optimal value depends on the longest mixing time and the rotational correlation time of the refined molecule. For 200 ms and 2.3 ns, a value of 4.5 Å is sufficient. The cutoff can also be specified relative to the actual distance between the protons i and j. In this case, the distance between the two protons is measured, and the cutoff is set to the distance times the specified factor.