You have to look at total enterprise value. That is common market cap plus debt. WNR is already at around $2 billion. That is alot for 2 refineries totaling about 170kBPD and a rusting yorktown that is shut down. WNR is currently valued at over $1000 per BPD capacity. Notice that some recent refinery transactions took place at around $200-$400. So no, i think you are wrong that WNR is still less than its peers. VLO is certainly much cheaper.
The downgrade that tanked the stock during options expiration is an example of how the pros short a stock, drive its price down, and come back in long on the turnaround. Ain't America grand? No offense to the true Americans who fight and die most every day so these Wal St. pukes can get rich. But alas, I stray from your question. WNR needs to put its financial house in order before we see a 20.00 stock. The heavy debt load has only been manageable because borrowing costs have been so low. Over the next few qtrs., interest rates will begin to rise and WNR will have a tougher time paying off debt w/ ballooning interest. The recent restructuring of their loan for the Yorktown facility only dealt with the removal of restrictive maintenance requirements- it did not help w/ loan duration or interest rates. The Yorktown facility is older and has had a history of breakdowns and minor fires. As a resident of SE VA, I can follow the local news pertaining to Yorktown fairly easily. In order to bring the facility back online, it would take a significant influx of money, which WNR does not have. I believe the company's recent explanation of narrow crack spreads on the east coast simply a smokescreen. The good news for owning the facility is that there will probably never be another east coast refinery built. If they can partner w/someone that has deeper pockets, keeping the facility may make sense. The co. seems to want to streamline and rid itself of financial burdens. This combo of widening spreads and good potential of lowered debt can jump the eps significantly. The longer term question is how the country plans to grow itself.