Mon Jun  5 11:51:29 PDT 2006
T0317
Make started Mon Jun  5 11:52:11 PDT 2006
Running on cheep.cse.ucsc.edu

Mon Jun  5 12:50:59 PDT 2006 Kevin Karplus

Fairly strong blast hits almost full length
	1wrmA	33%id over 130 residues (E-value 4.3e-14)
	1yz4A	32%id over 128 residues (E-value 1.3e-13)
	1m3gA	33%id over 129 residues (E-value 1.6e-13)

Mon Jun  5 13:44:12 PDT 2006 Kevin Karplus
Top hits with HMMs are
	1wrmA
	1yz4A
	1vhrA
	1mkp
	
Mon Jun  5 20:50:10 PDT 2006 Kevin Karplus

The try1-opt2 model is very close to the 1wrmA alignment.

There may not be much to do with this one, though rosetta think that
some more work is needed before it can be repacked well.  Perhaps I'll
do another polishing run after seeing some of the server-based models.

Wed Jun 21 20:01:23 PDT 2006 Kevin Karplus

The try1-opt2 model agrees extremely well with the top server models
(ROBETTA and PROTINFO) so I'm doing a polishing run with breaks and
clashes turned up, and constraints, maybe_metal, and maybe_ssbond removed.
try2 running on cheep.

Wed Jun 21 20:59:24 PDT 2006 Kevin Karplus

try2-opt2 closes the gaps and reduces the clashes.
The worst remaining breaks are
	T0317.try2-opt2.pdb.gz breaks before (T0317)P48 with cost 0.839464
	T0317.try2-opt2.pdb.gz breaks before (T0317)G49 with cost 0.728284
	T0317.try2-opt2.pdb.gz breaks before (T0317)E133 with cost 0.647431

There are very few differences between try1-opt2 and try2-opt2, so I
think I might as well submit.

Wed Jun 21 21:14:16 PDT 2006 Kevin Karplus

submitted
	try2-opt2
	try1-opt2
	align 1 (1wrmA)
	align 2 (1yz4A)
	align 3 (1vhrA)