Dear Ed,
Not in my case. I still do *restrained* refinement.
I use:
refi type REST -
resi MLKF -
meth CGMAT -
bref MIXED
ncyc 10
blim 0.1 200.0
With both: weight MATRIX 50 or weight AUTO it gives the same problem.
I have also tested the latest refmac5 version (Refmac_5.6.0119) and latest
dictionaries (refmac_dictionary_v5.31), but it still produce the same error,
directly from the first cycle.
I can give more details and files off-list if requested.
Cheers,
Pierre
________________________________________
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Ed Pozharski
[epozh...@umaryland.edu]
Date d'envoi : vendredi 28 octobre 2011 16:00
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
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> Dear Kenneth A. Satyshur,
>
> what is your weight set to? If it is set to 'auto', try setting it to a
> specific value and lower that value until the explosion stops.
>
> If this happens at low matrix values (at 1.24A it should be way above 5
> or 10 for a well refined structure), your resolution might not be 1.24A,
> i.e., you may have integrated noise (check I/sigI over resolution shells).
>
> Tim
>
> P.S.: I wonder what power somebody might have to _force_ you use a
> specific software version...
>
>
> On 10/28/2011 03:48 AM, Kenneth A. Satyshur wrote:
> > Has anyone had problems with Refmac 5.6? I tried refining our stucture at
> > 1.24 A,
> > aniso with H in riding position and it just exploded! I get error in
> > distances such as
> >
> > Standard External All
> > Bonds: 3270 0 3270
> > Angles: 4923 0 4923
> > Chirals: 214 0 214
> > Planes: 368 0 368
> > Torsions: 957 0 957
> > ---------------------------------------
> >
> > Number of reflections in file 90428
> > Number of reflections read 90428
> >
> >
> > CGMAT cycle number = 1
> >
> > **** Bond distance outliers
> > ****
> >
> > Bond distance deviations from the ideal >10.000Sigma will be monitored
> >
> > A 5 PRO C A - A 5 PRO HB1 A mod.= 3.344 id.= 1.329 dev= -2.015
> > sig.= 0.014
> > A 5 PRO C B - A 5 PRO HB1 B mod.= 2.997 id.= 1.329 dev= -1.668
> > sig.= 0.014
> > A 5 PRO HB1 A - A 5 PRO HG1 A mod.= 2.292 id.= 1.458 dev= -0.834
> > sig.= 0.021
> > A 5 PRO HB1 A - A 6 LEU HD23A mod.= 7.407 id.= 0.860 dev= -6.547
> > sig.= 0.020
> > A 5 PRO HB1 B - A 5 PRO HG1 B mod.= 2.247 id.= 1.458 dev= -0.789
> > sig.= 0.021
> > A 5 PRO HB1 B - A 6 LEU HD23B mod.= 6.529 id.= 0.860 dev= -5.669
> > sig.= 0.020
> > A 5 PRO HG1 A - A 5 PRO HD1 A mod.= 2.267 id.= 0.980 dev= -1.287
> > sig.= 0.020
> > A 5 PRO HG1 A - A 6 LEU N A mod.= 4.860 id.= 1.530 dev= -3.330
> > sig.= 0.020
> > A 5 PRO HG1 A - A 6 LEU HD21A mod.= 6.129 id.= 1.525 dev= -4.604
> > sig.= 0.021
> > A 5 PRO HG1 B - A 5 PRO HD1 B mod.= 2.236 id.= 0.980 dev= -1.256
> > sig.= 0.020
> > A 5 PRO HG1 B - A 6 LEU N B mod.= 4.922 id.= 1.530 dev= -3.392
> > sig.= 0.020
> > A 5 PRO HG1 B - A 6 LEU HD21B mod.= 6.664 id.= 1.525 dev= -5.139
> > sig.= 0.021
> > A 6 LEU N A - A 6 LEU CA A mod.= 1.467 id.= 0.970 dev= -0.497
> > sig.= 0.020
> > A 6 LEU N A - A 6 LEU HA A mod.= 2.005 id.= 0.970 dev= -1.035
> > sig.= 0.020
> > A 6 LEU N A - A 6 LEU CB A mod.= 2.497 id.= 1.530 dev= -0.967
> > sig.= 0.020
> > A 6 LEU N B - A 6 LEU CA B mod.= 1.469 id.= 0.970 dev= -0.499
> > sig.= 0.020
> > A 6 LEU N B - A 6 LEU HA B mod.= 2.032 id.= 0.970 dev= -1.062
> > sig.= 0.020
> > A 6 LEU N B - A 6 LEU CB B mod.= 2.446 id.= 1.530 dev= -0.916
> > sig.= 0.020
> > A 6 LEU CB A - A 6 LEU HB2 A mod.= 0.969 id.= 1.521 dev= 0.552
> > sig.= 0.020
> > A
> >
> > Rfree goes form 17 to 28 and R from 15 to 25.
> > Coot map looks like a bunch of busted insect parts.
> >
> >
> > I use the exact same input using ccp4 6.1.13 and Refmac 5.5 and all is
> > good. I am forced to use the
> > old ccp4 and refmac to publish. Rf 17 R 15.
> > thanks
> >
> > --
> > Kenneth A. Satyshur, M.S.,Ph.D.
> > Associate Scientist
> > University of Wisconsin
> > Madison, Wisconsin 53706
> > 608-215-5207
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
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