It looks like the problem is caused by the 875 bytes consumed by your array of logic_structs . The chip only has 1k of ram and some of that is used by the arduino start up code.
Your struct consists of 5 bytes (Boolean is a byte), you could increase your array size by using 15 bits for cycle and 1 bit for the logic level. This would increase the max array size to around from 175 to around 440. But it would reduce the maximum value of cycles to 32k If this is an approach that you want to take and your not already familiar with bitfields, have a look at using that to manage the data in your structure.