1rqw arp warp log: Difference between revisions

1rqw arp warp log (view source)

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 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_warp.sh from the CCP4I interface
 <!--SUMMARY_END--></FONT></B>
 ARP/wARP will run in the subdirectory: ARP_run_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 0.30 sigma, to complete atoms search.
 <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
    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 added if above 3.2 sigmas in mFoDFc map.
    Refmac Refinement Parameters
 REFMAC cycle(s) with  0.99 0.99  fractional shifts damping in each ARP cycle.
@@ Line 33: / Line 31: @@
      FreeR will not be used.
      Anisotropic scaling with bulk solvent correction
    Autobuilding Parameters
      Autobuilding will take place every 5 ARP cycles.
@@ Line 45: / Line 43: @@
 | Nature Struct. Biol., 6:458-463, 1999.                                        |
 =================================================================================
 <!--SUMMARY_END--></FONT></B>
 reflections ( 95.69 % complete ), for refining 1829 atoms.
@@ Line 172: / Line 170: @@
    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
+<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
+  Chains 6, Residues 191, Connectivity Index 0.94
+of these (149 residues) have been docked in sequence.
+<!--SUMMARY_END--></FONT></B>
+------------------------------------------------------
+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
+of these (199 residues) have been docked in sequence.
+<!--SUMMARY_END--></FONT></B>
+------------------------------------------------------
+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
+of these (203 residues) have been docked in sequence.