#CCP4I VERSION CCP4Interface 1.4.4.2
#CCP4I SCRIPT LOG arp_warp
#CCP4I DATE 23 Nov 2006  20:34:43
#CCP4I USER phzwart
#CCP4I PROJECT betty
#CCP4I JOB_ID 13
#CCP4I SCRATCH /tmp/phzwart
#CCP4I HOSTNAME rosie.lbl.gov
#CCP4I PID 10073

The parameter file is: /net/cci-filer1/vol1/home/phzwart/Banu/Betty/latest_data/acorn/13_arp_warp.par

<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->

Entering arp_warp.sh from the CCP4I interface
<!--SUMMARY_END--></FONT></B>

The working directory is: /net/cci-filer1/vol1/home/phzwart/Banu/Betty/latest_data/acorn
ARP/wARP will run in the subdirectory: 13_arp_warp

<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Building free atoms model.
<!--SUMMARY_END--></FONT></B>

 Initial map calculated, amplitude weighted by extra weight ...
 ... and extended to AU
 Now building 1 initial model(s)
 Had to go as low as 0.35 sigma, to complete atoms search.


<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  ARP will be iterated with REFMAC 5.
  50 ARP refinement cycles will be run in total.
  Atoms will be removed if below 1.0 sigmas in 2mFoDFc map.
  Atoms will be added if above 3.2 sigmas in mFoDFc map.

  Refmac Refinement Parameters
    1 REFMAC cycle(s) with  0.99 0.99  fractional shifts damping in each ARP cycle.
    Weight for restraints is set to AUTO 
    FreeR will not be used.
    Anisotropic scaling with bulk solvent correction

  Autobuilding Parameters
    Autobuilding will take place every 5 ARP cycles.
    The Depth first search (NEW) autobuilding algorithm will be used.
    In place of autobuilding cycle nr.3 random shifts of 0.5 will be applied.
 
=================================================================================
| Please cite the correct publication for the ARP/wARP application you are using|
| Perrakis A, Morris R and Lamzin VS                                            |
| Automated protein model building combined with iterative structure refinement.|
| Nature Struct. Biol., 6:458-463, 1999.                                        |
=================================================================================

<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ), for refining 362 atoms.
   Observations/parameters ratio is 1.30
------------------------------------------------------
 Starting model:  R = 0.444 (Rfree = 0.000). 
------------------------------------------------------
  Cycle 0:   After refmac, R = 0.364 (Rfree = 0.000).
             Found 2 (2 requested) and removed  1 (1 requested) atoms.
------------------------------------------------------
 Building Cycle 0    Atomic shape factors  2.38  2.61
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 328 atoms.
   Observations/parameters ratio is 1.43
------------------------------------------------------
  Cycle 1:   After refmac, R = 0.306 (Rfree = 0.000).
             Found 7 (7 requested) and removed  3 (3 requested) atoms.
  Cycle 2:   After refmac, R = 0.268 (Rfree = 0.000).
             Found 6 (7 requested) and removed  3 (3 requested) atoms.
  Cycle 3:   After refmac, R = 0.264 (Rfree = 0.000).
             Found 5 (6 requested) and removed  3 (3 requested) atoms.
  Cycle 4:   After refmac, R = 0.248 (Rfree = 0.000).
             Found 6 (6 requested) and removed  3 (3 requested) atoms.
  Cycle 5:   After refmac, R = 0.220 (Rfree = 0.000).
             Found 5 (5 requested) and removed  2 (2 requested) atoms.
------------------------------------------------------
 Building Cycle 1    Atomic shape factors  2.44  2.68
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 328 atoms.
   Observations/parameters ratio is 1.43
------------------------------------------------------
  Cycle 6:   After refmac, R = 0.222 (Rfree = 0.000).
             Found 2 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 7:   After refmac, R = 0.229 (Rfree = 0.000).
             Found 4 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 8:   After refmac, R = 0.227 (Rfree = 0.000).
             Found 3 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 9:   After refmac, R = 0.218 (Rfree = 0.000).
             Found 3 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 10:  After refmac, R = 0.225 (Rfree = 0.000).
             Found 3 (9 requested) and removed  4 (4 requested) atoms.
------------------------------------------------------
 Building Cycle 2    Atomic shape factors  2.44  2.68
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 322 atoms.
   Observations/parameters ratio is 1.46
------------------------------------------------------
  Cycle 11:  After refmac, R = 0.223 (Rfree = 0.000).
             Found 6 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 12:  After refmac, R = 0.208 (Rfree = 0.000).
             Found 5 (9 requested) and removed  4 (4 requested) atoms.
  Cycle 13:  After refmac, R = 0.206 (Rfree = 0.000).
             Found 3 (9 requested) and removed  4 (4 requested) atoms.
  Cycle 14:  After refmac, R = 0.215 (Rfree = 0.000).
             Found 5 (9 requested) and removed  4 (4 requested) atoms.
  Cycle 15:  After refmac, R = 0.200 (Rfree = 0.000).
             Found 4 (8 requested) and removed  4 (4 requested) atoms.
------------------------------------------------------
  Will skip this building and will shake the model instead ...
  First randomisation, xyz shifts of 0.5
   B factor cutoff 58 and B factor reset between 14.5 and 29.0
------------------------------------------------------
   1882 reflections ( 99.52 % complete ) and   restraints for refining 123 atoms.
   Observations/parameters ratio is 3.83
------------------------------------------------------
  Cycle 16:  After refmac, R = 0.495 (Rfree = 0.000).
             Found 9 (48 requested) and removed  23 (24 requested) atoms.
  Cycle 17:  After refmac, R = 0.450 (Rfree = 0.000).
             Found 8 (51 requested) and removed  3 (25 requested) atoms.
  Cycle 18:  After refmac, R = 0.413 (Rfree = 0.000).
             Found 8 (50 requested) and removed  7 (25 requested) atoms.
  Cycle 19:  After refmac, R = 0.391 (Rfree = 0.000).
             Found 6 (50 requested) and removed  1 (25 requested) atoms.
  Cycle 20:  After refmac, R = 0.541 (Rfree = 0.000).
             Found 0 (50 requested) and removed  4 (25 requested) atoms.
------------------------------------------------------
 Building Cycle 4    Atomic shape factors  -1.88  -2.06
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 116 atoms.
   Observations/parameters ratio is 4.06
------------------------------------------------------
  Cycle 21:  After refmac, R = 0.518 (Rfree = 0.000).
             Found 5 (49 requested) and removed  11 (24 requested) atoms.
  Cycle 22:  After refmac, R = 0.494 (Rfree = 0.000).
             Found 2 (51 requested) and removed  2 (25 requested) atoms.
  Cycle 23:  After refmac, R = 0.472 (Rfree = 0.000).
             Found 4 (51 requested) and removed  4 (25 requested) atoms.
  Cycle 24:  After refmac, R = 0.466 (Rfree = 0.000).
             Found 6 (51 requested) and removed  2 (25 requested) atoms.
  Cycle 25:  After refmac, R = 0.402 (Rfree = 0.000).
             Found 2 (50 requested) and removed  2 (25 requested) atoms.
------------------------------------------------------
 Building Cycle 5    Atomic shape factors  2.35  2.58
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 113 atoms.
   Observations/parameters ratio is 4.16
------------------------------------------------------
  Cycle 26:  After refmac, R = 0.419 (Rfree = 0.000).
             Found 3 (50 requested) and removed  1 (25 requested) atoms.
  Cycle 27:  After refmac, R = 0.403 (Rfree = 0.000).
             Found 1 (50 requested) and removed  0 (25 requested) atoms.
  Cycle 28:  After refmac, R = 0.380 (Rfree = 0.000).
             Found 1 (50 requested) and removed  0 (25 requested) atoms.
  Cycle 29:  After refmac, R = 0.392 (Rfree = 0.000).
             Found 2 (49 requested) and removed  1 (24 requested) atoms.
  Cycle 30:  After refmac, R = 0.366 (Rfree = 0.000).
             Found 3 (50 requested) and removed  2 (25 requested) atoms.
------------------------------------------------------
 Building Cycle 6    Atomic shape factors  2.35  2.58
   Round 1: 4 peptides in 1 chains. The longest chain comprises 4 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.50
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 118 atoms.
   Observations/parameters ratio is 3.99
------------------------------------------------------
  Cycle 31:  After refmac, R = 0.368 (Rfree = 0.000).
             Found 3 (49 requested) and removed  1 (24 requested) atoms.
  Cycle 32:  After refmac, R = 0.369 (Rfree = 0.000).
             Found 3 (49 requested) and removed  1 (24 requested) atoms.
  Cycle 33:  After refmac, R = 0.366 (Rfree = 0.000).
             Found 5 (49 requested) and removed  0 (24 requested) atoms.
  Cycle 34:  After refmac, R = 0.353 (Rfree = 0.000).
             Found 2 (48 requested) and removed  1 (24 requested) atoms.
  Cycle 35:  After refmac, R = 0.352 (Rfree = 0.000).
             Found 4 (48 requested) and removed  0 (24 requested) atoms.
------------------------------------------------------
 Building Cycle 7    Atomic shape factors  2.32  2.55
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 131 atoms.
   Observations/parameters ratio is 3.59
------------------------------------------------------
  Cycle 36:  After refmac, R = 0.356 (Rfree = 0.000).
             Found 2 (46 requested) and removed  1 (23 requested) atoms.
  Cycle 37:  After refmac, R = 0.341 (Rfree = 0.000).
             Found 2 (47 requested) and removed  0 (23 requested) atoms.
  Cycle 38:  After refmac, R = 0.336 (Rfree = 0.000).
             Found 1 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 39:  After refmac, R = 0.340 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 40:  After refmac, R = 0.338 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
------------------------------------------------------
 Building Cycle 8    Atomic shape factors  2.38  2.61
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
   1882 reflections ( 99.52 % complete ) and   restraints for refining 135 atoms.
   Observations/parameters ratio is 3.49
------------------------------------------------------
  Cycle 41:  After refmac, R = 0.339 (Rfree = 0.000).
             Found 0 (45 requested) and removed  0 (22 requested) atoms.
  Cycle 42:  After refmac, R = 0.339 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 43:  After refmac, R = 0.331 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 44:  After refmac, R = 0.338 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 45:  After refmac, R = 0.339 (Rfree = 0.000).
             Found 1 (46 requested) and removed  0 (23 requested) atoms.
------------------------------------------------------
 Building Cycle 9    Atomic shape factors  2.38  2.61
   Round 1: 0 peptides in 0 chains. The longest chain comprises 0 peptides.
   Taking the results from Round 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 0, Residues 0, Connectivity Index 0.00
<!--SUMMARY_END--></FONT></B>
 ---> Final restrained refinement block. No atom update.
   1882 reflections ( 99.52 % complete ) and   restraints for refining 135 atoms.
   Observations/parameters ratio is 3.49
------------------------------------------------------
  Cycle 46:  After refmac, R = 0.336 (Rfree = 0.000).
             Found 0 (45 requested) and removed  0 (22 requested) atoms.
  Cycle 47:  After refmac, R = 0.330 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 48:  After refmac, R = 0.336 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.
  Cycle 49:  After refmac, R = 0.339 (Rfree = 0.000).
             Found 0 (46 requested) and removed  0 (23 requested) atoms.

   Writing map files covering molecule ...
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Normal termination of warpNtrace
<!--SUMMARY_END--></FONT></B>
[1] 16949
<!--SUMMARY_END--></FONT></B>


#CCP4I TERMINATION STATUS 1 
#CCP4I TERMINATION TIME 23 Nov 2006  20:43:03
#CCP4I TERMINATION OUTPUT_FILES  /net/cci-filer1/vol1/home/phzwart/Banu/Betty/latest_data/acorn/13_arp_warp.par betty /net/cci-filer1/vol1/home/phzwart/Banu/Betty/latest_data/acorn/13_wilson.loggraph betty
#CCP4I MESSAGE Task completed successfully


#CCP4I TERMINATION STATUS 1 All done
#CCP4I TERMINATION TIME 23 Nov 2006  20:43:03
#CCP4I MESSAGE Task completed successfully