Your HPS DDR3 controller generated with Quartus® II software version 13.0 or 13.0sp1 may experience a calibration failure and produce the following debug messages in the debug output text file:
test_load_patterns(0,ALL) => (85 == 255) => 0
Guaranteed read test failed
SEQ.C: Calibration Failed
SEQ.C: Error Stage : 1
SEQ.C: Error Substage: 1
SEQ.C: Error Group : 0
There is a known issue where the HPS Vref pins draw high current causing the Vref voltage to drop and DDR3 calibration to fail.