1XVQ data. 2010-11-23/ 2011-01-25 Tests on model rebuilding starting with homologues of 1XVQ This data goes with the paper "Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization" by Frank DiMaio, Thomas C. Terwilliger, Randy J. Read, Alexander Wlodawer, Gustav Oberdorfer, Eugene Valkov, Assaf Alon, Deborah Fass, Herbert L. Axelrod, Debanu Das, Sergey M. Vorobiev, Hideo Iwai, P. Raj Pokkuluri & David Baker (Nature 2011, in press) For this set of tests the raw data for 1XVQ is provided, along with a set of aligned templates, the results of using DEN refinement in CNS on those aligned templates, and the results of running Rosetta modeling on the templates. Additionally a script for running autobuild on each template is provided. In the root directory you'll find the final deposited PDB, the data, the sequence and a shell script to be run from within the directory for a particular template (i.e. .../autobuild.csh). Inside each directory there's the PDB file for the template, then (with the same name inside each directory) there's the file resulting from modelling against that template with an hhpred alignment, superimposing on the target PDB and doing a rigid-body refinement in Phaser (1XVQ_rnp.1.pdb) plus the result of refining that model with DEN refinement in CNS (refine_den_1xvq.pdb). You can see from the Rfree values in the REMARK cards of the refine_den_1xvq.pdb files which ones worked in DEN refinement. The results of Rosetta modeling followed by refinement are also in these directories (1xvq_1FOH_rosetta_refine_001.pdb). Listing of directory after untarring: .: total 788 drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1FOH/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1HD2/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1JFU/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1N8J/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1XXU/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1Y25/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 1ZZO/ -rw-r--r-- 1 terwill lanl 558656 Oct 19 00:56 1xvq.mtz -rw-r--r-- 1 terwill lanl 144261 Oct 19 00:56 1xvq.pdb -rw-r--r-- 1 terwill lanl 207 Oct 19 00:56 1xvq.seq drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 2A4V/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 2BMX/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 2CX4/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 2HYX/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 2K6V/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 2YWN/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3CMI/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3DRN/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3EWL/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3FW2/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3GL3/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3HCZ/ drwxr-xr-x 2 terwill lanl 4096 Jan 25 18:58 3HDC/ -rwxr-xr-x 1 terwill lanl 150 Oct 19 10:38 autobuild.csh* -rw-r--r-- 1 terwill lanl 5818 Jan 25 08:33 readme.txt ./1FOH: total 2140 -rw-r--r-- 1 terwill lanl 1902204 Oct 19 03:37 1FOH.pdb -rw-r--r-- 1 terwill lanl 88090 Oct 19 05:38 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_1FOH_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 94199 Nov 1 05:22 refine_den_1xvq.pdb ./1HD2: total 520 -rw-r--r-- 1 terwill lanl 263412 Oct 19 03:37 1HD2.pdb -rw-r--r-- 1 terwill lanl 84930 Oct 19 05:38 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 84460 Jan 25 18:58 1xvq_1HD2_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 90960 Nov 1 05:36 refine_den_1xvq.pdb ./1JFU: total 572 -rw-r--r-- 1 terwill lanl 296055 Oct 19 03:37 1JFU.pdb -rw-r--r-- 1 terwill lanl 88089 Oct 19 05:38 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_1JFU_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 94205 Nov 1 05:51 refine_den_1xvq.pdb ./1N8J: total 2760 -rw-r--r-- 1 terwill lanl 2566485 Oct 19 03:37 1N8J.pdb -rw-r--r-- 1 terwill lanl 85325 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 76402 Jan 25 18:58 1xvq_1N8J_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 91371 Nov 1 06:06 refine_den_1xvq.pdb ./1XXU: total 704 -rw-r--r-- 1 terwill lanl 85957 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 434808 Oct 19 03:37 1XXU.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_1XXU_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 92011 Nov 1 06:21 refine_den_1xvq.pdb ./1Y25: total 540 -rw-r--r-- 1 terwill lanl 87063 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 262521 Oct 19 03:37 1Y25.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_1Y25_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 93153 Nov 1 06:35 refine_den_1xvq.pdb ./1ZZO: total 396 -rw-r--r-- 1 terwill lanl 86668 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 120123 Oct 19 03:37 1ZZO.pdb -rw-r--r-- 1 terwill lanl 94730 Jan 25 18:58 1xvq_1ZZO_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 92742 Nov 1 06:49 refine_den_1xvq.pdb ./2A4V: total 416 -rw-r--r-- 1 terwill lanl 88089 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 96780 Jan 25 18:58 1xvq_2A4V_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 140697 Oct 19 03:37 2A4V.pdb -rw-r--r-- 1 terwill lanl 94200 Nov 1 07:04 refine_den_1xvq.pdb ./2BMX: total 680 -rw-r--r-- 1 terwill lanl 86668 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_2BMX_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 408888 Oct 19 03:37 2BMX.pdb -rw-r--r-- 1 terwill lanl 92747 Nov 1 07:18 refine_den_1xvq.pdb ./2CX4: total 1220 -rw-r--r-- 1 terwill lanl 86668 Oct 19 05:39 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_2CX4_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 962361 Oct 19 03:37 2CX4.pdb -rw-r--r-- 1 terwill lanl 92749 Nov 1 07:33 refine_den_1xvq.pdb ./2HYX: total 1200 -rw-r--r-- 1 terwill lanl 88089 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 94730 Jan 25 18:58 1xvq_2HYX_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 942354 Oct 19 03:37 2HYX.pdb -rw-r--r-- 1 terwill lanl 94200 Nov 1 07:47 refine_den_1xvq.pdb ./2K6V: total 7000 -rw-r--r-- 1 terwill lanl 88090 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_2K6V_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 6879978 Oct 19 03:37 2K6V.pdb -rw-r--r-- 1 terwill lanl 94200 Nov 1 08:02 refine_den_1xvq.pdb ./2YWN: total 416 -rw-r--r-- 1 terwill lanl 86984 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_2YWN_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 137619 Oct 19 03:37 2YWN.pdb -rw-r--r-- 1 terwill lanl 93072 Nov 1 08:15 refine_den_1xvq.pdb ./3CMI: total 400 -rw-r--r-- 1 terwill lanl 83034 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 94809 Jan 25 18:58 1xvq_3CMI_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 131949 Oct 19 03:37 3CMI.pdb -rw-r--r-- 1 terwill lanl 89016 Nov 1 08:30 refine_den_1xvq.pdb ./3DRN: total 536 -rw-r--r-- 1 terwill lanl 85325 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 100335 Jan 25 18:58 1xvq_3DRN_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 262683 Oct 19 03:37 3DRN.pdb -rw-r--r-- 1 terwill lanl 91372 Nov 1 08:45 refine_den_1xvq.pdb ./3EWL: total 508 -rw-r--r-- 1 terwill lanl 84297 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 87703 Jan 25 18:58 1xvq_3EWL_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 248427 Oct 19 03:37 3EWL.pdb -rw-r--r-- 1 terwill lanl 90312 Nov 1 08:58 refine_den_1xvq.pdb ./3FW2: total 800 -rw-r--r-- 1 terwill lanl 86194 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 94730 Jan 25 18:58 1xvq_3FW2_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 534276 Oct 19 03:37 3FW2.pdb -rw-r--r-- 1 terwill lanl 92257 Nov 1 09:13 refine_den_1xvq.pdb ./3GL3: total 688 -rw-r--r-- 1 terwill lanl 85957 Oct 19 05:40 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 94335 Jan 25 18:58 1xvq_3GL3_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 424845 Oct 19 03:37 3GL3.pdb -rw-r--r-- 1 terwill lanl 92014 Nov 1 09:27 refine_den_1xvq.pdb ./3HCZ: total 428 -rw-r--r-- 1 terwill lanl 86667 Oct 19 05:41 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 94730 Jan 25 18:58 1xvq_3HCZ_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 152928 Oct 19 03:37 3HCZ.pdb -rw-r--r-- 1 terwill lanl 92742 Nov 1 09:41 refine_den_1xvq.pdb ./3HDC: total 416 -rw-r--r-- 1 terwill lanl 86668 Oct 19 05:41 1XVQ_rnp.1.pdb -rw-r--r-- 1 terwill lanl 94730 Jan 25 18:58 1xvq_3HDC_rosetta_refine_001.pdb -rw-r--r-- 1 terwill lanl 140049 Oct 19 03:37 3HDC.pdb -rw-r--r-- 1 terwill lanl 92749 Nov 1 09:55 refine_den_1xvq.pdb