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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Sorry, "should NOT appear in the list of deviations", of course! - -------- Original Message -------- Subject: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Date: Fri, 28 Oct 2011 17:39:06 +0200 From: Tim Gruene <[log in to unmask]> Reply-To: Tim Gruene <[log in to unmask]> To: [log in to unmask] Dear all, If those hydrogens are in riding position, their coordinates are calculated and should not be refined at all, isn't it? Hence they should appear in the list of deviations at all. Are the hydrogens present in the PDB file? Does it work to delete them all? Tim 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOqtB3UxlJ7aRr7hoRAq4bAKCQXz5E7KdEFw/Xvg6QhYlap42GhwCgnPJz 9g5GY7ZKW33r2Ejy06thT2M= =8E40 -----END PGP SIGNATURE-----