Dear Pierre Resolution seems to be good enough for full anisotropic refinement. Why don't you try this and see if it stabilises refinement.
regards Garib On 28 Oct 2011, at 16:22, LEGRAND Pierre 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----- Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
