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Hi Kenneth, This looks like an off-by-one bug in the restraint generation. Typical sources are weird LINKs, wrong atom names and bad luck. I suggest you make sure you have the very latest Refmac and dictionary and try setting up a new refinement instead of recycling an old job. If that doesn't work, we may need a closer look at your input model. Cheers, Robbie > Date: Thu, 27 Oct 2011 20:48:49 -0500 > From: [log in to unmask] > Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0 > To: [log in to unmask] > > 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