It's I think termed a heuristic approach, it tries to find lowest energy docking. If it does not meet a minimum, the position is changed and the docking is tried again until it succeeds or gives up and moves on. The packages are build from a knowledge base where each ligand is typecast and estimated for a time to resolve. Some package quick and slow but always in a way that the end time is ending in a median of 3 hours. You could get to 50% in minutes and then the next 50% takes 3 hours. That causes the estimated and remaining runtime to recompute continuously.

If it's really a brand new system, then the times will fluctuate for a couple of days. It will start out with an estimate of how much time it will take based on the benchmarks that run when first booting BOINC on the system, but they're always a little off. It will get better with time as BOINC figures out how fast the system will actually run.

That said, don't expect too much of the estimates. There are multiple sizes of workunits, so if one is taking longer or shorter than estimate to complete, it doesn't indicate something is wrong. If it takes more than twice the length of an estimate, though, that's when I'd start checking to see if any progress is actually being made...

2 things to that

1) You might have to rerun the client benchmark, although 3 days plus start projection and getting 12 hours to finish is too big for that to be the explanation.
2) The runtime prediction can be improved by adding the "fraction done exact" line to the app_config.xml in the WCG project folder.

<app_config>
   <app>
      <name>arp1</name>
      <max_concurrent>1</max_concurrent>
      <fraction_done_exact/>
   </app>
 </app_config>

All it needs is to copy the code above into a flat text ASCII editor like notepad or nano and then save the file with the name app_config.xml into the worldcommunitygrig.org project data folder and read in the config with the Boinc Manager (BM). Certainly the rerun of the benchmark from the BM does not require programming skills what a 12 year old couldn't. OTOH, if you're fine, you're fine.

Crunch On.

Guys I am sorry, I don't understand programming, I guess I need a 12 year old, but I prefer mine to be scotch (and no, if you are from that country north of England, DO NOT send me your children)

Everything seems to work here, and if it ain't broke... don't go breaking it. I know some of you are VERY skilled in computer software. My expertise was 25 years as an Electrician, so how many 10 story buildings can some of you wire up from the ground? We all have our talents. Mine isn't programming computers sorry. I just want to be helpful, I am disabled now, so hopefully this still lets me help others. Sorry guys.