Hi my two cents ... At I would use full anisotropic refinement only with relaxed weights on B values. Weight "50" seems to me very very loose (but I haven't seen the log file). I would use weight auto and then look at the refmac log file. The Log file tells you what is the weight matrix being used. For the next refmac run -> use half of THAT weight matrix from the "weight auto" run before !
cheers Stefan On Fri, 28 Oct 2011 15:22:49 +0000 LEGRAND Pierre <pierre.legr...@synchrotron-soleil.fr> wrote: > 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: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > 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 > > > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.4.10 (GNU/Linux) > > Comment: Using GnuPG with Mozilla - > http://enigmail.mozdev.org/ > > > > > iD8DBQFOqluhUxlJ7aRr7hoRAjadAJ9Df2hbWjixDCdS3Z4DB7mm4ubRIACeOw6X > > 6JkjyzRUdxqjH/9b/oftBjE= > > =xRXE > > -----END PGP SIGNATURE----- Dr Stefan Gerhardt Albert-Ludwigs-Universität Freiburg Inst.f.Org.Chem.u.Biochem Albertstrasse 21 79104 Freiburg Tel. +49 761 2035970 Fax. +49 761 2036161
