Ports are not coming up.

If port speed is not configured, all ports of the SRX5K-IOC4-MRATE operate as four 10-Gigabit Ethernet interfaces by default as below,

xe-5/0/0:0              up    down
xe-5/0/0:1              up    down
xe-5/0/0:2              up    down
xe-5/0/0:3              up    down
xe-5/0/1:0              up    down
xe-5/0/1:1              up    down
xe-5/0/1:2              up    down
xe-5/0/1:3              up    down

Configure the ports as below and restart the FPC.

[edit chassis fpc 5 pic 0]
root@b01-17# show

[edit chassis fpc 5 pic 0]
root@b01-17# set port 0 speed 40g

[edit chassis fpc 5 pic 0]
root@b01-17# set port 1 speed 40g

root@b01-17> request chassis fpc slot 5 restart
Restart initiated, use "show chassis fpc" to verify

If valid port speeds are configured, the MPC PICs operate at the configured speed as below

et-5/0/0                up    down
et-5/0/1                up    down
xe-5/1/0:0              up    down
xe-5/1/0:1              up    down

root@b01-17> show interfaces et-5/0/0
Physical interface: et-5/0/0, Enabled, Physical link is Down
  Interface index: 238, SNMP ifIndex: 618
  Link-level type: Ethernet, MTU: 1514, Speed: 40Gbps, BPDU Error: None,