Dear Smith,
Given that your runs differ in presence of Individual B-factors, Occupanies, Optimize X-ray/sterochemistry weight in the first run, in the corresponding .eff file you should contain something like
strategy = *individual_sites *individual_sites_real_space rigid_body \
*individual_adp group_adp tls *occupancies group_anomalous
when in the second .eff file it should look like
strategy = *individual_sites *individual_sites_real_space rigid_body \
individual_adp group_adp tls occupancies group_anomalous
Pay attention to the stars.
Optimize X-ray flag should result in
optimize_xyz_weight = True
instead of
optimize_xyz_weight = False
Diff tools suggested by Tim should be useful to locate these small changes.
Best regards,
Oleg.