The System I/O Configuration register (CCFG_SYSIO) configures I/O lines in System I/O mode (such as JTAG, ERASE, USB, etc.) or as general purpose I/O lines. Enabling or disabling the corresponding I/O lines in peripheral mode or in PIO mode (PIO_PER or PIO_PDR registers) in the PIO controller as no effect. However, the direction (input or output), pull-up, pull-down and other mode control is still managed by the PIO controller.