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
