NMR Restraints Grid |
Result table
image | mrblock_id | pdb_id | cing | stage | position | type | subtype |
12463 | 1szy | cing | 1-original | 20 | protocol | structure calculation |
Distances: A-form NOEs for stem: cp ../stem/noes.inp noes.stem.inp Hand-edited noes.stem.inp to change segid b resid 1-7 to segid b resid 15-21, then removed segids Real NOES for loop: I'm artificially constraining the stem to A-form and there are no exchangeable NOEs in the loop (or between stem and loop) so I need concern myself only with nonexchangeable NOEs involving at least one loop proton. egrep 'resid ([8-9]|1[0-4])' ~/nmr/italy2-30c.int/noes.d2o.inp > noes.loop.inp.old cp noes.loop.inp.old noes.loop.inp Hand-edited Dihedrals: Hand-created dihedrals.d2x using values from - inspection of 31P-1H COSY (alpha-zeta) - inspection of aromatic-sugar region of NOESY (chi) - ~/nmr/italy2-30c.j/j2nu.out (nu0-nu4); left intermediate Js unconstrained and constrained U12 (75% C2'-endo) to C2'-endo - used A-form angles for G1 and C21, since I'm using A-form NOEs there dihedrals2xplor dihedrals.d2x > dihedrals.inp Template: Ran run.make-template. Moved make-template.??.out, template.??.pdb and make-template.summary to template/. Examined templates; template/template.07.pdb has the lowest energy (out of a not very large range) Linked template/template.07.pdb to template.pdb. Miscellaneous: Increased dgsa.inp's weighting of cdih term by 4x relative to the manual. Doing so eliminated almost all dihedral angle violations (although violations were usually only 5 degrees or so anyway) and did not increase (in fact may have reduced) NOE violations. Ran series of calculations varying times and timesteps in template.inp and dgsa.inp; see ../italy2.results/{template,dgsa}. Ran calculations including interesting NOEs predicted by 4tna; see ../italy2.results/33-36. Ran calculations omitting scary (not A-like, nonsequential) NOEs and then reincluding them; see ../italy2.results/scary. Ran calculations on each set of dihedral angles. The cheating sets always result in more tRNAPhe-like structures than the corresponding honest sets. The free and fixed sets come out about the same. Ran calculations with and without tcoupling=true in refine.inp (it was only omitted due to an error in the first place) and with an extra cooling step to get down to 0K. Neither made much difference; I'm now using the former (which I'd have used without thinking in the first place if I hadn't left it out by accident) but not the latter. See ../italy2.results/tcoup,cool Ran calculations with U12 ribose free; didn't make much difference. Increased NOE weighting by twofold relative to the manual. See ../italy2.results/noe-weighting Averaging: Determined that 3, 5, 8, 11, 14, 17, 18, 20, 22, 23, 24, 27 had converged. Ran average-dihedrals on those structures. Observed that A11 alpha, beta and gamma are in one distinct range in 8, 18, 27 and another in the rest. Ran average-dihedrals on 3, 5, 8, 11, 14, 17, 18, 20, 22, 23, 24, 27 and on 8, 18, 27. Will report average across all converged structures for all angles except A11 alpha, beta, gamma, for which I'll report averages for each subset. Ran average.inp once on all 12 and once on all but 8, 18, 27. The averaged structure is the same. Threw away the former.
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