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<title>Automatic building using ARP/wARP (version 7.0)</title>
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<center><H1>Automatic building using ARP/wARP (version 7.0) in wARP_38.2pc</H1></center>
<center><H3><U><FONT COLOR="#C08000">Expert</FONT></U> user: <font color="#AA2244">derek</font> Project ID: <font color="#AA2244">MAD.7</font></H3></center>
<TABLE>
<TR>
<TD><B>Reference:</B></TD>
<TD>A. Perrakis, R. J. Morris, and V. S. Lamzin.</TD>
</TR>
<TR>
<TD></TD>
<TD>Automated protein model building combined with iterative structure refinement</TD>
</TR>
<TR>
<TD></TD>
<TD>Nature Struct. Biol., <B>6</B>:458-463, 1999.</TD>
</TR>
</TABLE>
<hr noshade size=4>
<table>
<tr>
<td>MTZ file</td><td> : </td>
<td>eden_flat_38.2pc.mtz</td>
</tr>
<tr>
<td>$warpbin</td><td> : </td>
<td>/usr/local/xtal/arp_warp_7.0/bin/bin-i386-Darwin</td>
</tr>
<tr>
<td>Cell</td><td> : </td>
<td>78.4730 91.8050 86.9940 90.0000 112.2880 90.0000</td>
</tr>
<tr>
<td>Spacegroup</td><td> : </td>
<td>P21 (4)</td>
</tr>
<tr>
<td>Protein size (asymmetric unit)</td><td> : </td>
<td>1302 residues</td>
</tr>
<tr>
<td>Resolution</td><td> : </td>
<td>39.120 2.500</td>
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</table>
<A HREF="wARP_38.2pc/">(directory index)</A>
<A HREF="wARP_38.2pc/20101119_133055/temp_tracing/arp_out.pdb">(current PDB)</A>
<H3>1. Running "auto_tracing.sh"</H3>
<HR noshade size=2><PRE>
<! /usr/local/xtal/arp_warp_7.0/bin/bin-i386-Darwin/auto_tracing.sh jobId 20101119_133055 datafile /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/eden_flat_38.2pc.mtz residues 1302 workdir /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc fp FPsha sigfp SIGFPsha freelabin FreeR_flag fbest FBshasol phibest PHIBshasol fom " " cgr 1 buildingcycles 4 restrref 5 phaselabin "HLA=HLA HLB=HLB HLC=HLC HLD=HLD" >
Fri Nov 19 13:30:56 CET 2010
Working directory /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc
Job ID is set to 20101119_133055
X-ray data file /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/eden_flat_38.2pc.mtz
Tracing mode WARPNTRACEPHASES
Creating directory /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc/20101119_133055
Accepted label: fp=FPsha
Accepted label: sigfp=SIGFPsha
Accepted label: fbest=FBshasol
Accepted label: freelabin=FreeR_flag
mtz labels taken: FPsha SIGFPsha FBshasol FreeR_flag
Parameter file /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc/20101119_133055/arp_warp_tracing.par
Job launched in /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc/20101119_133055
==================================================================================
| Please cite at least one of the publications below for |
| the ARP/wARP application you are using: |
| |
| Perrakis, A., Morris, R.M. & Lamzin, V.S. (1999) Automated protein |
| model building combined with iterative structure refinement. |
| Nature Struct. Biol. 6, 458-463 |
| |
| Morris, R.J., Perrakis, A. & Lamzin, V.S. (2003) ARP/wARP and automatic |
| interpretation of protein electron density maps. |
| In Meth. Enz. (Carter, C. & Sweet, B. eds.) 374, 229-244 |
| |
| Cohen, S.X., Morris, R.J., Fernandez, F.J., Ben Jelloul, M., Kakaris, M., |
| Parthasarathy, V., Lamzin, V.S., Kleywegt, G.J. & Perrakis, A. (2004) |
| Towards complete validated models in the next generation of ARP/wARP. |
| Acta Cryst. D60, 2222-2229 |
| |
| Morris, R.J., Perrakis, A. & Lamzin, V.S. (2002) ARP/wARP model-building |
| algorithms. I. The main chain. Acta Cryst. D58, 968-975 |
| |
| |
| Use of Refmac is an essential part of model building with ARP/wARP. |
| Please acknowledge the use of Refmac by citing the following publication: |
| |
| Murshudov, G.N., Vagin, A.A. & Dodson, E.J. (1997) Refinement of |
| macromolecular structures by the maximum-likelihood method. |
| Acta Crystallogr. D53, 240-255 |
==================================================================================
The parameter file is: /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc/20101119_133055/arp_warp_tracing.par
Entering warp_tracing.sh from the command line
The working directory is: /Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc/20101119_133055
ARP/wARP will run in the subdirectory: temp_tracing
Building free atoms model
Initial map will be calculated with pre-weighted amplitudes ...
CAD: Error in label assignments in LKYSET
QUITTING ... ARP/wARP module stopped with an error message:
CAD
*** Look for error message in the file:
/Users/sharp/sharp-2.6/users/derek/None.sharp/logfiles/MAD.7/wARP_38.2pc/20101119_133055/eden_flat_38.2pc_warp_build.log
QUITTING ... ARP/wARP module stopped with an error message:
MAIN_SCRIPT
*** Look for error message in the file:
main_log_file
QUITTING ... ARP/wARP module stopped with an error message:
/usr/local/xtal/arp_warp_7.0/bin/bin-i386-Darwin/warp_tracing.sh
*** Look for error message in the file:
MAIN_LOG_FILE
</PRE> <A HREF="wARP_38.2pc/20101119_133055/eden_flat_38.2pc_warp_build.log">Look for error message in this file!</A>
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<P><HR NOSHADE><P><B>ERROR in /Users/sharp/sharp-2.6/bin/sharp/arpwarp.pl</B>
<P>Command arguments: <TT>derek /Users/sharp/sharp-2.6</TT>
<P>
The following return values are set:
<UL>
<LI>Child error = 0
</UL>
<P>
<B>Error message : </B> <FONT COLOR="#CC00EE">error from running auto_tracing.sh - please check ARP/wARP log file!</FONT>
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