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If you are not sure about the I/O Banks Voltage supplies then there are some options to try.

NOTE: Missing VCCIO Voltage will not cause AXI GPIO to freeze, no matter if it is connected to MicroBlaze or Zynq Processing Block.

DONE LED

If there is on board LED directly connected to FPGA "DONE" output, then it is also possible to control it as long as it is possible to configure the FPGA (or PL portion of Zynq). For Zynq the PS subsystem is not needed if configuration is done via JTAG.

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