Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
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: satys...@wisc.edu Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0 To: CCP4BB@JISCMAIL.AC.UK 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
[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
Hi Kenneth, I am experiencing exactly the same problem, in similar conditions: refinement with H at 0.84 A resolution. From a bunch of tests made yesterday, I have found that it is linked to incompatibilities between cif dictionaries definitions and H names in the input PDB. For me, one simple solution to that problem, was to remove all H atoms from my input pdb and let refmac rebuild them (MAKE HYDR ALL). I hope the trick will work for you. By the way, I am facing an other problem: Clashes in inter residues H-bonds between H and acceptor atoms. What is the correct way to define these. The HYDBND pdb definition doesn't seems to work. Do I need to use LINK definitions ? Is there a way to do that automatically ? Cheers, Pierre De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Robbie Joosten [robbie_joos...@hotmail.com] Date d'envoi : vendredi 28 octobre 2011 09:42 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 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: satys...@wisc.edu Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0 To: CCP4BB@JISCMAIL.AC.UK 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
Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
Hi All I think that is the reason. In version of refmac (with new dictio uses new pdb v3 hydrogen naming and there are a lot of differences. regards Garib On 28 Oct 2011, at 10:00, LEGRAND Pierre wrote: Hi Kenneth, I am experiencing exactly the same problem, in similar conditions: refinement with H at 0.84 A resolution. From a bunch of tests made yesterday, I have found that it is linked to incompatibilities between cif dictionaries definitions and H names in the input PDB. For me, one simple solution to that problem, was to remove all H atoms from my input pdb and let refmac rebuild them (MAKE HYDR ALL). I hope the trick will work for you. By the way, I am facing an other problem: Clashes in inter residues H-bonds between H and acceptor atoms. What is the correct way to define these. The HYDBND pdb definition doesn't seems to work. Do I need to use LINK definitions ? Is there a way to do that automatically ? Cheers, Pierre De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Robbie Joosten [robbie_joos...@hotmail.com] Date d'envoi : vendredi 28 octobre 2011 09:42 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 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: satys...@wisc.edu Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0 To: CCP4BB@JISCMAIL.AC.UK 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 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
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-
[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
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-
Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
-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-
Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
Hi my two cents ... At I would use full anisotropic refinement only with relaxed weights on B values. Weight 50 seems to me very very loose (but I haven't seen the log file). I would use weight auto and then look at the refmac log file. The Log file tells you what is the weight matrix being used. For the next refmac run - use half of THAT weight matrix from the weight auto run before ! cheers Stefan On Fri, 28 Oct 2011 15:22:49 + LEGRAND Pierre pierre.legr...@synchrotron-soleil.fr 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
[ccp4bb] Fwd: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
-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 t...@shelx.uni-ac.gwdg.de Reply-To: Tim Gruene t...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK 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-
Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
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
[ccp4bb] RE : [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
Thanks all for your suggestions, Here's a little summary of my recent tests. I am currently using WEIGHT AUTO and BREF MIXED with a pdb file that contains ANISOU definition for all atoms except hydrogens. Final results for BREF MIXED refinement : InitialFinal R factor0.0880 0.0867 R free0.0932 0.0925 Rms BondLength0.0174 0.0189 Rms BondAngle2.8613 2.8740 Rms ChirVolume0.1076 0.1146 Final results for BREF ANISO refinement: InitialFinal R factor0.0880 0.0874 R free0.0932 0.0956 Rms BondLength0.0174 0.0189 Rms BondAngle2.8613 2.8683 Rms ChirVolume0.1076 0.1151 In the WEIGHT AUTO run refmac5 uses: Weight matrix137.7641 Final results for WEIGHT MATRIX 60 refinement: InitialFinal R factor0.0880 0.0872 R free0.0932 0.0922 Rms BondLength0.0174 0.0181 Rms BondAngle2.8613 2.8632 Rms ChirVolume0.1076 0.1134 I have just sent Garib different data files so that he can reproduce the problem one can have with H naming/dictionaries definitions. When it happens, from the same initial pdb with WEIGHT AUTO and BREF MIXED but a differente cif definition (from the latest refmac_dictionary_v5.31) here what it gives: InitialFinal R factor0.0880 0.1820 R free0.0932 0.1869 Rms BondLength2.8573 2.3884 Rms BondAngle 35.7010 34.7547 Rms ChirVolume 10.5335 4.2429 I hope it helps to clarify the situation, Cheers, Pierre De : Garib Murshudov [garib.murshu...@gmail.com] de la part de Garib N Murshudov [ga...@mrc-lmb.cam.ac.uk] Date d'envoi : vendredi 28 octobre 2011 17:49 À : LEGRAND Pierre Cc : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0 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.UKmailto: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
[ccp4bb] refmac 5.6 ccp4 6.2.0
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 attachment: satyshur.vcf