Once the NOESY spectrum and its gradient are calculated, the
relaxation energy
can be expressed as a function of the difference between
(functions of) observed and calculated intensities, and
analytic derivatives with respect to atomic coordinates can be
readily obtained by using the chain rule
where 
is the energy constant for the relaxation term,
and 
are respectively the calculated and observed intensities,
is an error estimate for 
,
is a weight factor, 
is the calibration factor
for each spectrum, and 
is the number of cross peaks in each spectrum.
The function 
is defined as the absolute value of the
difference between the nth powers of a and b, where b has an error
estimate 
:
The individual error estimates 
reflect the errors in
the peak volumes, usually subjective estimates, especially due
to noise and spectral overlap.
At present, the error estimates are also used to ascertain if a
measured intensity is to be used in the determination of the
overall calibration factor.
Values for the exponents of 
and m=2 (Eqs. 21.9
and 21.10) correspond to the refinement of the residual in X-ray
crystallography. These values tend to put a high weight on the
large intensities, resulting in a bad fit of intensities for which
the calculated value is too small. Following a suggestion
by James et al. (1991), use m=2 and
. A value of m=1 results in the refinement of the
R value directly, instead of the residual. The discontinuity of the
gradient may lead to instabilities during the refinement.
In addition to the overall weight 
, individual weights 
can be applied to each term in the sum in Eqs. 21.9
and 21.12, e.g.,
in order to increase the relative weight of the small intensities.
(It should be noted that this is achieved already by setting 
in Eq. 21.9.)
The scheme
corresponds to a
common weighting scheme
used in crystallography if experimental 
values are unreliable
or unavailable.
In the NMR case, however, there is no theoretical justification
for this weighting scheme. (In crystallography, the statistical error
of an intensity measurement 
is 
.)
The weights are scaled such that 
.
The calibration factor between observed and back-calculated intensities is determined simply as the ratio of the sums of all calculated and observed intensities:
This ratio can be determined separately for each spectrum, or overall for all data points. Volumes that are not very reliable (i.e., they have a large error estimate) can be excluded from the ratio. The calibration factor can be updated automatically at every step. For technical reasons, this does not allow the calculation of the exact derivatives at present, so the calibration should not be updated automatically at every step during conjugate gradient minimization. During annealing, the effects due to the error in the gradient are negligible.
