Fri May  9 10:09:57 PDT 2008
T0395
Make started Fri May  9 10:10:43 PDT 2008
Running on cheep.cse.ucsc.edu

Fri May  9 10:27:40 PDT 2008 Kevin Karplus

This is reported to be a monomer that binds ATP and FMN.
Blast does not find a close hit.

Fri May  9 17:51:44 PDT 2008 Kevin Karplus

There are good templates for most of the length, but some floppy N and
C termini:

2oq2A, 2goyA, ... 
Phosphoadenylyl sulphate (PAPS) reductase-like family.

try1-opt3 looks pretty good, but needs some break reduction.

Wed May 14 19:17:36 PDT 2008 Kevin Karplus

try2-opt3 has somewhat better breaks, but not by much.

I'll start some meta-server predictions from the server models.
The consensus MQA like Zhang-Server and METATASSER models, while the
MQAU one likes the LEE-Server and SAM-T08-server.

 Thu May 15 09:38:25 PDT 2008 Kevin Karplus

MQAC1-opt3 scores best with the try2 costfcn, partly because it has
almost no breaks.  It seems to be built mainly from LEE-SERVER_TS3.
Mon May 19 22:35:54 PDT 2008   SAM-T08-MQAO hand QA T0395 Submitted
Mon May 19 22:35:54 PDT 2008   SAM-T08-MQAU hand QA T0395 Submitted
Mon May 19 22:35:54 PDT 2008   SAM-T08-MQAC hand QA T0395 Submitted

Sat May 24 21:08:35 PDT 2008 Kevin Karplus

I'd like to work on the undertaker-only models for a bit, before
tossing in the metaserver models.

For try3, I'll start from the gromacs-optimized models.

Sun May 25 09:13:08 PDT 2008 Kevin Karplus

try3-opt3 scores better than the models from the metaserver, but still
has worse clashes and breaks than I'd like to see.  Let's try
polishing a bit more, again from the gromacs-optimized models, but
with soft_clashes and breaks turned up.

Sun May 25 16:34:29 PDT 2008 Kevin Karplus

try4-opt3 has lower breaks and clashes, though MQAC1-opt3 has lower
breaks still.  I should probably try optimizing now including the
metaserver models, 

Mon May 26 04:44:28 PDT 2008 Kevin Karplus

try5 seems to be based mainly on try4, and scores better with
undertaker, though rosetta still likes try4-opt3.gromacs0.repack-nonPC
best, probably because the clashes are slightly less there, though
breaks are worse.

Looking at 5 of the models:
	try5-opt3
	MQAC1-opt3
	MQAU1-opt3
	try1-opt3
	alignment 1 (from T0395-2oq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m)

I see that try5-opt3 has not moved much from try1-opt3.  If I want to
sample different N and C termini, I'll have to start over from alignments.
The models all agree fairly well for I41-E227, though the loop
closures vary a little.  I like try5-opt3 around P52, with the double
H-bonds G55.N-S51.O and N54.N-S51.O, and I hope it is right.

I think I'll do another run from alignments for try6, but with
constraints for sheets and helices for the core region taken from
try5-opt3.

Mon May 26 08:29:10 PDT 2008 Kevin Karplus

try6 gets quite different N and C termini from the other models, but
its guts are not as nice as try5, so I'll make a chimera of try5 and
try6, then reoptimize that.  Try5-opt3 will be used for I41-E227,
try6-opt3 for the rest.

The chimera has some bad clashes, but that should be fixable.

Mon May 26 11:05:23 PDT 2008 Kevin Karplus

try7-opt3 looks like it has loosened up the N- and C-termini way too much.
I have no confidence in it.  I might have to try fixing the chimera
again with lower clash penalties.

Maybe I can add an extra sheet constraint:

SheetConstraint E134	D136	L290	W288	Hbond	D136

Mon May 26 16:09:14 PDT 2008 Kevin Karplus

The extra strand of the sheet did not form (it was unlikely anyway,
adding an antiparallel strand to a parallel sheet), but try8-opt3
scores ok now, though try8-opt3.gromacs0 scores a bit better with the
try5 costfcn.

Mon May 26 17:33:34 PDT 2008 Kevin Karplus

I'll polish up try8 as try9, and see if there is anything else I want
to do with this model.


Mon May 26 18:35:16 PDT 2008 Kevin Karplus

I think I like try9 better than try5.

Maybe I should do one polishing run from all the models.

Mon May 26 21:00:23 PDT 2008 Kevin Karplus

I think I'll submit

ReadConformPDB T0395.try10-opt3.pdb		best score from try5-try6 chimera
ReadConformPDB T0395.try5-opt3.pdb		
ReadConformPDB T0395.MQAC1-opt3.pdb		from LEE-SERVER_TS3
ReadConformPDB T0395.MQAU1-opt3.pdb		from SAM-T08-server_TS1
ReadConformPDB T0395.try7-opt3.gromacs0.repack-nonPC.pdb	best rosetta score


try10, try5, and try7 don't use metaserver results