I have submitted a 190 amino acid protein sequences with three domains. There is a loop region between the second and third domain that binds a zinc atom by liganding with two cysteine pairs in the linker region. I have added a restraint file in various forms (see file attachments), but the restraints in the linker region are not carried out in the models generated. The restraints should bring the two pairs of cysteines in the linker region close to one another by creating a large loop. If I just submit the sequence of the linker region, the program does apply the proper constraints. Why aren't these constraints applied in the whole protein? What am I doing incorrectly?