The parameter file is: ARP_run_warp.par


The ARP/wARP job will run on the EMBL Hamburg 16-processor cluster

Entering arp_warp.sh from the CCP4I interface


ARP/wARP will run in the subdirectory: ARP_run_arp_warp


Building free atoms model.


 Initial map calculated, amplitude weighted by extra weight ...
 ... and extended to AU
 Now building 1 initial model(s)
 Had to go as low as 0.25 sigma, to complete atoms search.



  ARP will be iterated with REFMAC 5.
  15 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.
 
=================================================================================
| 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.                                        |
=================================================================================


   10578 reflections ( 100.00 % complete ), for refining 450 atoms.
   Observations/parameters ratio is 5.88
------------------------------------------------------
 Starting model:  R = 0.329 (Rfree = 0.000). 
------------------------------------------------------
  Cycle 0:   After refmac, R = 0.266 (Rfree = 0.000).
             Found 8 (8 requested) and removed  4 (4 requested) atoms.
------------------------------------------------------
 Building Cycle 0    Atomic shape factors  1.59  1.29
   Round 1: 44 peptides in 2 chains. The longest chain comprises 26 peptides.
   Round 2: 48 peptides in 2 chains. The longest chain comprises 28 peptides.
   Round 3: 48 peptides in 2 chains. The longest chain comprises 28 peptides.
   Taking the results from Round 3

  Chains 2, Residues 46, Connectivity Index 0.92

   10578 reflections ( 100.00 % complete ) and  309 restraints for refining 441 atoms.
   Observations/parameters ratio is 6.00
------------------------------------------------------
  Cycle 1:   After refmac, R = 0.288 (Rfree = 0.000).
             Found 8 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 2:   After refmac, R = 0.254 (Rfree = 0.000).
             Found 8 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 3:   After refmac, R = 0.235 (Rfree = 0.000).
             Found 8 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 4:   After refmac, R = 0.221 (Rfree = 0.000).
             Found 8 (8 requested) and removed  4 (4 requested) atoms.
  Cycle 5:   After refmac, R = 0.215 (Rfree = 0.000).
             Found 8 (8 requested) and removed  4 (4 requested) atoms.
------------------------------------------------------
 Building Cycle 1    Atomic shape factors  1.59  1.29
   Round 1: 46 peptides in 2 chains. The longest chain comprises 26 peptides.
   Round 2: 48 peptides in 2 chains. The longest chain comprises 28 peptides.
   Round 3: 48 peptides in 2 chains. The longest chain comprises 28 peptides.
   Taking the results from Round 3

  Chains 2, Residues 46, Connectivity Index 0.92

   10578 reflections ( 100.00 % complete ) and  310 restraints for refining 464 atoms.
   Observations/parameters ratio is 5.70
------------------------------------------------------
  Cycle 6:   After refmac, R = 0.231 (Rfree = 0.000).
             Found 9 (9 requested) and removed  6 (6 requested) atoms.
  Cycle 7:   After refmac, R = 0.213 (Rfree = 0.000).
             Found 9 (9 requested) and removed  6 (6 requested) atoms.
  Cycle 8:   After refmac, R = 0.205 (Rfree = 0.000).
             Found 9 (9 requested) and removed  7 (7 requested) atoms.
  Cycle 9:   After refmac, R = 0.204 (Rfree = 0.000).
             Found 9 (9 requested) and removed  7 (7 requested) atoms.
  Cycle 10:  After refmac, R = 0.195 (Rfree = 0.000).
             Found 9 (9 requested) and removed  7 (7 requested) atoms.
------------------------------------------------------
 Building Cycle 2    Atomic shape factors  1.59  1.29
   Round 1: 46 peptides in 2 chains. The longest chain comprises 26 peptides.
   Round 2: 48 peptides in 2 chains. The longest chain comprises 28 peptides.
   Round 3: 48 peptides in 2 chains. The longest chain comprises 28 peptides.
   Taking the results from Round 3

  Chains 2, Residues 46, Connectivity Index 0.92

 ---> Final restrained refinement block. No atom update.
   10578 reflections ( 100.00 % complete ) and  307 restraints for refining 482 atoms.
   Observations/parameters ratio is 5.49
------------------------------------------------------
  Cycle 11:  After refmac, R = 0.219 (Rfree = 0.000).
             Found 0 (4 requested) and removed  0 (9 requested) atoms.
  Cycle 12:  After refmac, R = 0.211 (Rfree = 0.000).
             Found 0 (4 requested) and removed  2 (9 requested) atoms.
  Cycle 13:  After refmac, R = 0.211 (Rfree = 0.000).
             Found 0 (9 requested) and removed  1 (9 requested) atoms.
  Cycle 14:  After refmac, R = 0.210 (Rfree = 0.000).
             Found 0 (9 requested) and removed  0 (9 requested) atoms.

   Writing map files covering molecule ...

 Normal termination of warpNtrace