Wed Jul 9 09:55:28 PDT 2008 T0492 Make started Wed Jul 9 09:56:41 PDT 2008 Running on lopez.cse.ucsc.edu Wed Jul 9 10:01:01 PDT 2008 Kevin Karplus This looks like at least 2/3 a homology model to 2gcxA and 2h3jA. Wed Jul 9 13:23:17 PDT 2008 Kevin Karplus T0492 has 2gcxA and 2h3jA as strong hits (3e-10) and 1fx7A, 1qw1A, 2dtrA, and 2qq9A as weaker hits. try1-opt3 looks like a fairly decent model, except for the bad break before T12. It looks like there should be a constraint SheetConstraint C9 K14 K43 E38 Hbond I41 to help close the gap. Wed Jul 9 15:08:02 PDT 2008 Kevin Karplus try2 didn't seem to be enough, so for try3 I'll up the breaks weight and add some more constraints: Constraint A7.CB V13.CG1 3.1 3.13 4 Constraint A7.CB V72.CG2 3.2 3.22 4 Wed Jul 9 17:30:13 PDT 2008 Kevin Karplus try3 mostly closes the gaps, but gromacs does not like some of the other damage done. I should turn up clashes and breaks a bit more and reoptimize. Wed Jul 9 19:37:10 PDT 2008 Kevin Karplus I think I've reached the point of diminishing returns here. I may be able to do better with a slightly different loop for L47-P50, as there are two small gaps left there. I'll wait for the meta-server results, see if they change anything, then submit. Sun Jul 13 08:03:16 PDT 2008 Kevin Karplus The MQAC quality assessment likes pro-sp3-TASSER_TS3, Zhang-Server_TS2, ... The MQAU quality assessment likes SAM-T08-server_TS1, pro-sp3-TASSER_TS4, ... I started MQAU1, MQAC1, MQAU4, and MQAC4 metaserver runs. Sun Jul 13 10:16:25 PDT 2008 Kevin Karplus costfcn top models try4 MQAU4-opt3 try4-opt3 MQAC4-opt3 try3-opt3 MQAC1-opt3.gromacs0 MQAU1-opt3.gromacs0 try3 MQAU4-opt3 try4-opt3 try3-opt3 MQAC4-opt3 MQAC1-opt3.gromacs0 MQAU1-opt3.gromacs0 try2 MQAU4-opt3 try4-opt3 MQAC4-opt3 try3-opt3 MQAC1-opt3.gromacs0 MQAU1-opt3.gromacs0 try1 MQAU4-opt3 MQAU1-opt3 MQAC4-opt3 MQAC1-opt3 try4-opt3 try3-opt3 MQAC1 comes from MULTICOM-RANK_TS3, but the others (MQAU1, MQAC4, MQAU4) all come from SAM-T08-server_TS1. Maybe I should do MQAX1 and MQAX4 runs that exclude the SAM servers, to get a little more variety. Sun Jul 13 10:32:08 PDT 2008 Kevin Karplus MQAX1 and MQAX4 started. The current models are all very similar. When the MQAX models are done, I'll do one polishing run from all the gromacs models and then submit. Sun Jul 13 13:28:53 PDT 2008 Kevin Karplus Oops, I had a typo in the target, so the MQAX runs never started. I've started them now. Sun Jul 13 14:19:25 PDT 2008 Kevin Karplus MQAX4 is based on LOOPP_Server_TS1 MQAX1 is based on mariner1_TS3 Sun Jul 13 15:38:36 PDT 2008 Kevin Karplus Neither scores particularly well with the current cost functions. I've started a try5 to optimize from the gromacs0 and gromacs0.repack-nonPC models. I suspect that MQAU4-opt3.gromacs0 will be the model that gets polished. Sun Jul 13 16:14:37 PDT 2008 Kevin Karplus Indeed, that was the case: try5-opt3 polished MQAU4-op3.groamcs0, but rosetta still prefers MQAX4-opt3.gromacs0.repack-nonPC Sun Jul 13 16:23:46 PDT 2008 Kevin Karplus Submitted with comment: All the SAM+undertaker and the metaserver models were very similar. It isn't clear that any of the cost functions are precise enough to distinguish among them. The first model is a metaserver model, but from our own server (SAM-T08-server), optimized with undertaker, then gromacs, then undertaker again. The second model was generated entierly with SAM and undertaker. The last three models are all metaserver models, optimized with undertaker then gromacs (and for model 3, with sidechains repacked by rosetta). model 1 T0492.try5-opt3.pdb # < MQAU4-opt3.gromacs0 < SAM-T08-server_TS1 2 T0492.try4-opt3.pdb # < try3-opt3 < try2-opt3 < try1-opt3 < align(1fx7A) 3 T0492.MQAX4-opt3.gromacs0.repack-nonPC.pdb # < LOOPP_Server_TS1 # best Rosetta energy 4 T0492.MQAC1-opt3.gromacs0.pdb # < MULTICOM-RANK_TS3 5 T0492.MQAX1-opt3.gromacs0.pdb # < mariner1_TS3 Thu Jul 17 16:51:33 PDT 2008 SAM-T08-MQAO hand QA T0492 Submitted Thu Jul 17 16:51:34 PDT 2008 SAM-T08-MQAU hand QA T0492 Submitted Thu Jul 17 16:51:34 PDT 2008 SAM-T08-MQAC hand QA T0492 Submitted