1rqw arp warp log: Difference between revisions

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(New page: <HTML> <BODY> <pre> The parameter file is: ARP_run_warp.par <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> The ARP/wARP job will run on the EMBL Hamburg 16-processor cluster Entering arp_...)
 
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<HTML>
<BODY>
<pre>
The parameter file is: ARP_run_warp.par
The parameter file is: ARP_run_warp.par
 
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
The ARP/wARP job will run on the EMBL Hamburg 16-processor cluster
The ARP/wARP job will run on the EMBL Hamburg 16-processor cluster
 
Entering arp_warp.sh from the CCP4I interface
Entering arp_warp.sh from the CCP4I interface
<!--SUMMARY_END--></FONT></B>
<!--SUMMARY_END--></FONT></B>
 
ARP/wARP will run in the subdirectory: ARP_run_arp_warp
ARP/wARP will run in the subdirectory: ARP_run_arp_warp
 
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Building free atoms model.
Building free atoms model.
<!--SUMMARY_END--></FONT></B>
<!--SUMMARY_END--></FONT></B>
 
  Initial map calculated, amplitude weighted by extra weight ...
  Initial map calculated, amplitude weighted by extra weight ...
  ... and extended to AU
  ... and extended to AU
  Now building 1 initial model(s)
  Now building 1 initial model(s)
  Had to go as low as 0.30 sigma, to complete atoms search.
  Had to go as low as 0.30 sigma, to complete atoms search.
 
 
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
   ARP will be iterated with REFMAC 5.
   ARP will be iterated with REFMAC 5.
Line 27: Line 25:
   Atoms will be removed if below 1.0 sigmas in 2mFoDFc map.
   Atoms will be removed if below 1.0 sigmas in 2mFoDFc map.
   Atoms will be added if above 3.2 sigmas in mFoDFc map.
   Atoms will be added if above 3.2 sigmas in mFoDFc map.
 
   Refmac Refinement Parameters
   Refmac Refinement Parameters
     1 REFMAC cycle(s) with  0.99 0.99  fractional shifts damping in each ARP cycle.
     1 REFMAC cycle(s) with  0.99 0.99  fractional shifts damping in each ARP cycle.
Line 33: Line 31:
     FreeR will not be used.
     FreeR will not be used.
     Anisotropic scaling with bulk solvent correction
     Anisotropic scaling with bulk solvent correction
 
   Autobuilding Parameters
   Autobuilding Parameters
     Autobuilding will take place every 5 ARP cycles.
     Autobuilding will take place every 5 ARP cycles.
Line 45: Line 43:
| Nature Struct. Biol., 6:458-463, 1999.                                        |
| Nature Struct. Biol., 6:458-463, 1999.                                        |
=================================================================================
=================================================================================
 
<!--SUMMARY_END--></FONT></B>
<!--SUMMARY_END--></FONT></B>
   23179 reflections ( 95.69 % complete ), for refining 1829 atoms.
   23179 reflections ( 95.69 % complete ), for refining 1829 atoms.
Line 172: Line 170:
   Cycle 21:  After refmac, R = 0.295 (Rfree = 0.000).
   Cycle 21:  After refmac, R = 0.295 (Rfree = 0.000).
             Found 25 (25 requested) and removed  19 (19 requested) atoms.
             Found 25 (25 requested) and removed  19 (19 requested) atoms.
  Cycle 22:  After refmac, R = 0.256 (Rfree = 0.000).
            Found 25 (25 requested) and removed  20 (20 requested) atoms.
  Cycle 23:  After refmac, R = 0.236 (Rfree = 0.000).
            Found 25 (25 requested) and removed  21 (21 requested) atoms.
  Cycle 24:  After refmac, R = 0.226 (Rfree = 0.000).
            Found 26 (26 requested) and removed  23 (23 requested) atoms.
  Cycle 25:  After refmac, R = 0.218 (Rfree = 0.000).
            Found 26 (26 requested) and removed  16 (23 requested) atoms.
------------------------------------------------------
Building Cycle 5    Atomic shape factors  1.71  1.60
  Round 1: 189 peptides in 8 chains. The longest chain comprises 56 peptides.
  Round 2: 193 peptides in 5 chains. The longest chain comprises 59 peptides.
  Round 3: 197 peptides in 6 chains. The longest chain comprises 83 peptides.
  Taking the results from Round 3
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 6, Residues 191, Connectivity Index 0.94
  3 of these (149 residues) have been docked in sequence.
<!--SUMMARY_END--></FONT></B>
------------------------------------------------------
  23179 reflections ( 95.69 % complete ) and  1345 restraints for refining 1886 atoms.
  Observations/parameters ratio is 3.07
------------------------------------------------------
  Cycle 26:  After refmac, R = 0.235 (Rfree = 0.000).
            Found 25 (25 requested) and removed  18 (18 requested) atoms.
  Cycle 27:  After refmac, R = 0.210 (Rfree = 0.000).
            Found 25 (25 requested) and removed  19 (19 requested) atoms.
  Cycle 28:  After refmac, R = 0.195 (Rfree = 0.000).
            Found 25 (25 requested) and removed  19 (21 requested) atoms.
  Cycle 29:  After refmac, R = 0.184 (Rfree = 0.000).
            Found 26 (26 requested) and removed  8 (23 requested) atoms.
  Cycle 30:  After refmac, R = 0.176 (Rfree = 0.000).
            Found 26 (26 requested) and removed  12 (26 requested) atoms.
------------------------------------------------------
Building Cycle 6    Atomic shape factors  1.71  1.60
  Round 1: 200 peptides in 5 chains. The longest chain comprises 81 peptides.
  Round 2: 202 peptides in 3 chains. The longest chain comprises 83 peptides.
  Round 3: 202 peptides in 5 chains. The longest chain comprises 83 peptides.
  Taking the results from Round 2
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 3, Residues 199, Connectivity Index 0.95
  3 of these (199 residues) have been docked in sequence.
<!--SUMMARY_END--></FONT></B>
------------------------------------------------------
  23179 reflections ( 95.69 % complete ) and  1545 restraints for refining 1885 atoms.
  Observations/parameters ratio is 3.07
------------------------------------------------------
  Cycle 31:  After refmac, R = 0.206 (Rfree = 0.000).
            Found 25 (25 requested) and removed  18 (18 requested) atoms.
  Cycle 32:  After refmac, R = 0.184 (Rfree = 0.000).
            Found 25 (25 requested) and removed  14 (19 requested) atoms.
  Cycle 33:  After refmac, R = 0.174 (Rfree = 0.000).
            Found 26 (26 requested) and removed  12 (22 requested) atoms.
  Cycle 34:  After refmac, R = 0.167 (Rfree = 0.000).
            Found 26 (26 requested) and removed  6 (25 requested) atoms.
  Cycle 35:  After refmac, R = 0.162 (Rfree = 0.000).
            Found 13 (13 requested) and removed  8 (28 requested) atoms.
------------------------------------------------------
Building Cycle 7    Atomic shape factors  1.71  1.60
  Round 1: 202 peptides in 5 chains. The longest chain comprises 81 peptides.
  Round 2: 205 peptides in 2 chains. The longest chain comprises 123 peptides.
  Round 3: 202 peptides in 3 chains. The longest chain comprises 93 peptides.
  Taking the results from Round 2
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
  Chains 2, Residues 203, Connectivity Index 0.97
  2 of these (203 residues) have been docked in sequence.

Revision as of 22:38, 1 May 2008

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 0.30 sigma, to complete atoms search.




 ARP will be iterated with REFMAC 5.
 75 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.
   Side chain docking will be performed from autobuilding cycle number 0
   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. |

=====================================================================

  23179 reflections ( 95.69 % complete ), for refining 1829 atoms.
  Observations/parameters ratio is 3.17

Starting model:  R = 0.379 (Rfree = 0.000). 

 Cycle 0:   After refmac, R = 0.332 (Rfree = 0.000).
            Found 25 (25 requested) and removed  12 (12 requested) atoms.

Building Cycle 0    Atomic shape factors  1.74  1.63
  Round 1: 27 peptides in 5 chains. The longest chain comprises 7 peptides.
  Round 2: 30 peptides in 5 chains. The longest chain comprises 8 peptides.
  Round 3: 28 peptides in 4 chains. The longest chain comprises 9 peptides.
  Round 4: 32 peptides in 5 chains. The longest chain comprises 9 peptides.
  Round 5: 28 peptides in 4 chains. The longest chain comprises 9 peptides.
  Taking the results from Round 4


 Chains 3, Residues 20, Connectivity Index 0.71
 0 of these (0 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  77 restraints for refining 1731 atoms.
  Observations/parameters ratio is 3.35

 Cycle 1:   After refmac, R = 0.316 (Rfree = 0.000).
            Found 38 (38 requested) and removed  19 (19 requested) atoms.
 Cycle 2:   After refmac, R = 0.287 (Rfree = 0.000).
            Found 34 (34 requested) and removed  17 (17 requested) atoms.
 Cycle 3:   After refmac, R = 0.271 (Rfree = 0.000).
            Found 31 (31 requested) and removed  15 (15 requested) atoms.
 Cycle 4:   After refmac, R = 0.261 (Rfree = 0.000).
            Found 28 (28 requested) and removed  14 (14 requested) atoms.
 Cycle 5:   After refmac, R = 0.253 (Rfree = 0.000).
            Found 25 (25 requested) and removed  12 (12 requested) atoms.

Building Cycle 1    Atomic shape factors  1.71  1.60
  Round 1: 58 peptides in 10 chains. The longest chain comprises 9 peptides.
  Round 2: 64 peptides in 10 chains. The longest chain comprises 9 peptides.
  Round 3: 68 peptides in 10 chains. The longest chain comprises 9 peptides.
  Round 4: 69 peptides in 10 chains. The longest chain comprises 9 peptides.
  Taking the results from Round 4


 Chains 7, Residues 48, Connectivity Index 0.71
 2 of these (15 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  243 restraints for refining 1731 atoms.
  Observations/parameters ratio is 3.35

 Cycle 6:   After refmac, R = 0.290 (Rfree = 0.000).
            Found 38 (38 requested) and removed  19 (19 requested) atoms.
 Cycle 7:   After refmac, R = 0.271 (Rfree = 0.000).
            Found 34 (34 requested) and removed  15 (17 requested) atoms.
 Cycle 8:   After refmac, R = 0.254 (Rfree = 0.000).
            Found 30 (30 requested) and removed  11 (15 requested) atoms.
 Cycle 9:   After refmac, R = 0.249 (Rfree = 0.000).
            Found 27 (27 requested) and removed  12 (13 requested) atoms.
 Cycle 10:  After refmac, R = 0.244 (Rfree = 0.000).
            Found 24 (24 requested) and removed  12 (12 requested) atoms.

Building Cycle 2    Atomic shape factors  1.71  1.60
  Round 1: 75 peptides in 13 chains. The longest chain comprises 9 peptides.
  Round 2: 86 peptides in 13 chains. The longest chain comprises 10 peptides.
  Round 3: 93 peptides in 11 chains. The longest chain comprises 16 peptides.
  Round 4: 95 peptides in 11 chains. The longest chain comprises 16 peptides.
  Taking the results from Round 4


 Chains 9, Residues 78, Connectivity Index 0.77
 1 of these (8 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  338 restraints for refining 1731 atoms.
  Observations/parameters ratio is 3.35

 Cycle 11:  After refmac, R = 0.274 (Rfree = 0.000).
            Found 38 (38 requested) and removed  16 (19 requested) atoms.
 Cycle 12:  After refmac, R = 0.259 (Rfree = 0.000).
            Found 34 (34 requested) and removed  4 (17 requested) atoms.
 Cycle 13:  After refmac, R = 0.249 (Rfree = 0.000).
            Found 28 (28 requested) and removed  7 (14 requested) atoms.
 Cycle 14:  After refmac, R = 0.243 (Rfree = 0.000).
            Found 24 (24 requested) and removed  12 (12 requested) atoms.
 Cycle 15:  After refmac, R = 0.239 (Rfree = 0.000).
            Found 24 (24 requested) and removed  12 (12 requested) atoms.

Building Cycle 3    Atomic shape factors  1.71  1.60
  Round 1: 95 peptides in 9 chains. The longest chain comprises 16 peptides.
  Round 2: 105 peptides in 8 chains. The longest chain comprises 26 peptides.
  Round 3: 107 peptides in 9 chains. The longest chain comprises 20 peptides.
  Taking the results from Round 2


 Chains 7, Residues 93, Connectivity Index 0.83
 3 of these (59 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  577 restraints for refining 1823 atoms.
  Observations/parameters ratio is 3.18

 Cycle 16:  After refmac, R = 0.285 (Rfree = 0.000).
            Found 24 (24 requested) and removed  12 (12 requested) atoms.
 Cycle 17:  After refmac, R = 0.267 (Rfree = 0.000).
            Found 25 (25 requested) and removed  12 (12 requested) atoms.
 Cycle 18:  After refmac, R = 0.253 (Rfree = 0.000).
            Found 25 (25 requested) and removed  12 (12 requested) atoms.
 Cycle 19:  After refmac, R = 0.244 (Rfree = 0.000).
            Found 25 (25 requested) and removed  10 (13 requested) atoms.
 Cycle 20:  After refmac, R = 0.237 (Rfree = 0.000).
            Found 25 (25 requested) and removed  9 (16 requested) atoms.

Building Cycle 4    Atomic shape factors  1.71  1.60
  Round 1: 147 peptides in 13 chains. The longest chain comprises 26 peptides.
  Round 2: 166 peptides in 12 chains. The longest chain comprises 27 peptides.
  Round 3: 170 peptides in 10 chains. The longest chain comprises 27 peptides.
  Round 4: 181 peptides in 9 chains. The longest chain comprises 55 peptides.
  Round 5: 159 peptides in 9 chains. The longest chain comprises 42 peptides.
  Taking the results from Round 4


 Chains 9, Residues 172, Connectivity Index 0.89
 4 of these (116 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  1104 restraints for refining 1890 atoms.
  Observations/parameters ratio is 3.07

 Cycle 21:  After refmac, R = 0.295 (Rfree = 0.000).
            Found 25 (25 requested) and removed  19 (19 requested) atoms.
 Cycle 22:  After refmac, R = 0.256 (Rfree = 0.000).
            Found 25 (25 requested) and removed  20 (20 requested) atoms.
 Cycle 23:  After refmac, R = 0.236 (Rfree = 0.000).
            Found 25 (25 requested) and removed  21 (21 requested) atoms.
 Cycle 24:  After refmac, R = 0.226 (Rfree = 0.000).
            Found 26 (26 requested) and removed  23 (23 requested) atoms.
 Cycle 25:  After refmac, R = 0.218 (Rfree = 0.000).
            Found 26 (26 requested) and removed  16 (23 requested) atoms.

Building Cycle 5    Atomic shape factors  1.71  1.60
  Round 1: 189 peptides in 8 chains. The longest chain comprises 56 peptides.
  Round 2: 193 peptides in 5 chains. The longest chain comprises 59 peptides.
  Round 3: 197 peptides in 6 chains. The longest chain comprises 83 peptides.
  Taking the results from Round 3


 Chains 6, Residues 191, Connectivity Index 0.94
 3 of these (149 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  1345 restraints for refining 1886 atoms.
  Observations/parameters ratio is 3.07

 Cycle 26:  After refmac, R = 0.235 (Rfree = 0.000).
            Found 25 (25 requested) and removed  18 (18 requested) atoms.
 Cycle 27:  After refmac, R = 0.210 (Rfree = 0.000).
            Found 25 (25 requested) and removed  19 (19 requested) atoms.
 Cycle 28:  After refmac, R = 0.195 (Rfree = 0.000).
            Found 25 (25 requested) and removed  19 (21 requested) atoms.
 Cycle 29:  After refmac, R = 0.184 (Rfree = 0.000).
            Found 26 (26 requested) and removed  8 (23 requested) atoms.
 Cycle 30:  After refmac, R = 0.176 (Rfree = 0.000).
            Found 26 (26 requested) and removed  12 (26 requested) atoms.

Building Cycle 6    Atomic shape factors  1.71  1.60
  Round 1: 200 peptides in 5 chains. The longest chain comprises 81 peptides.
  Round 2: 202 peptides in 3 chains. The longest chain comprises 83 peptides.
  Round 3: 202 peptides in 5 chains. The longest chain comprises 83 peptides.
  Taking the results from Round 2


 Chains 3, Residues 199, Connectivity Index 0.95
 3 of these (199 residues) have been docked in sequence.


  23179 reflections ( 95.69 % complete ) and  1545 restraints for refining 1885 atoms.
  Observations/parameters ratio is 3.07

 Cycle 31:  After refmac, R = 0.206 (Rfree = 0.000).
            Found 25 (25 requested) and removed  18 (18 requested) atoms.
 Cycle 32:  After refmac, R = 0.184 (Rfree = 0.000).
            Found 25 (25 requested) and removed  14 (19 requested) atoms.
 Cycle 33:  After refmac, R = 0.174 (Rfree = 0.000).
            Found 26 (26 requested) and removed  12 (22 requested) atoms.
 Cycle 34:  After refmac, R = 0.167 (Rfree = 0.000).
            Found 26 (26 requested) and removed  6 (25 requested) atoms.
 Cycle 35:  After refmac, R = 0.162 (Rfree = 0.000).
            Found 13 (13 requested) and removed  8 (28 requested) atoms.

Building Cycle 7    Atomic shape factors  1.71  1.60
  Round 1: 202 peptides in 5 chains. The longest chain comprises 81 peptides.
  Round 2: 205 peptides in 2 chains. The longest chain comprises 123 peptides.
  Round 3: 202 peptides in 3 chains. The longest chain comprises 93 peptides.
  Taking the results from Round 2


 Chains 2, Residues 203, Connectivity Index 0.97
 2 of these (203 residues) have been docked in sequence.
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