Fine-tuning parameters allow some control of the inner-workings of the program. Used judiciously they may be used to bring the best matches to the top of the list.
The match precision is used in the voting stage. It specifies how close the coordinates and the base triplet distances need be in order to add a vote to a model in the hash table. Using high precision will cause the number of votes to drop but will produce only highly accurate matches. Using low precision matches will result in relaxed matches and higher scores.
Min. votes to qualify determines the number of votes a model has to get in order to be considered as a match after the voting stage is over. Raising this parameter too high may result in loss of matches. Lowering it may cause longer running times. Note that this parameter is directly tied in to the value chosen for the Match precision