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-----
