-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 - -- - -- 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/ iD8DBQFOqsyaUxlJ7aRr7hoRAlSNAJ99GaOsMUiCpIOhWLd+lBVAqeX+LwCg4pLN 7T4lJXXTQX8LbeyFuGTrQIc= =QdmF -----END PGP SIGNATURE-----
