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1rqw arp warp log: Difference between revisions
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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 ... | ||
| Line 20: | Line 20: | ||
<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. | ||
75 ARP refinement cycles will be run in total. | 75 ARP refinement cycles will be run in total. | ||
| Line 37: | Line 37: | ||
The Depth first search (NEW) autobuilding algorithm will be used. | The Depth first search (NEW) autobuilding algorithm will be used. | ||
================================================================================= | ================================================================================= | ||
| Please cite the correct publication for the ARP/wARP application you are using| | | Please cite the correct publication for the ARP/wARP application you are using| | ||
| Perrakis A, Morris R and Lamzin VS | | | Perrakis A, Morris R and Lamzin VS | | ||
| Automated protein model building combined with iterative structure refinement.| | | Automated protein model building combined with iterative structure refinement.| | ||
| 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. | ||
Observations/parameters ratio is 3.17 | Observations/parameters ratio is 3.17 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Starting model: R = 0.379 (Rfree = 0.000). | Starting model: R = 0.379 (Rfree = 0.000). | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 0: After refmac, R = 0.332 (Rfree = 0.000). | Cycle 0: After refmac, R = 0.332 (Rfree = 0.000). | ||
Found 25 (25 requested) and removed 12 (12 requested) atoms. | Found 25 (25 requested) and removed 12 (12 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 0 Atomic shape factors 1.74 1.63 | Building Cycle 0 Atomic shape factors 1.74 1.63 | ||
Round 1: 27 peptides in 5 chains. The longest chain comprises 7 peptides. | Round 1: 27 peptides in 5 chains. The longest chain comprises 7 peptides. | ||
| Line 60: | Line 60: | ||
Round 5: 28 peptides in 4 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 | Taking the results from Round 4 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 3, Residues 20, Connectivity Index 0.71 | Chains 3, Residues 20, Connectivity Index 0.71 | ||
0 of these (0 residues) have been docked in sequence. | 0 of these (0 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 77 restraints for refining 1731 atoms. | 23179 reflections ( 95.69 % complete ) and 77 restraints for refining 1731 atoms. | ||
Observations/parameters ratio is 3.35 | Observations/parameters ratio is 3.35 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 1: After refmac, R = 0.316 (Rfree = 0.000). | Cycle 1: After refmac, R = 0.316 (Rfree = 0.000). | ||
Found 38 (38 requested) and removed 19 (19 requested) atoms. | Found 38 (38 requested) and removed 19 (19 requested) atoms. | ||
| Line 78: | Line 78: | ||
Cycle 5: After refmac, R = 0.253 (Rfree = 0.000). | Cycle 5: After refmac, R = 0.253 (Rfree = 0.000). | ||
Found 25 (25 requested) and removed 12 (12 requested) atoms. | Found 25 (25 requested) and removed 12 (12 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 1 Atomic shape factors 1.71 1.60 | Building Cycle 1 Atomic shape factors 1.71 1.60 | ||
Round 1: 58 peptides in 10 chains. The longest chain comprises 9 peptides. | Round 1: 58 peptides in 10 chains. The longest chain comprises 9 peptides. | ||
| Line 85: | Line 85: | ||
Round 4: 69 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 | Taking the results from Round 4 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 7, Residues 48, Connectivity Index 0.71 | Chains 7, Residues 48, Connectivity Index 0.71 | ||
2 of these (15 residues) have been docked in sequence. | 2 of these (15 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 243 restraints for refining 1731 atoms. | 23179 reflections ( 95.69 % complete ) and 243 restraints for refining 1731 atoms. | ||
Observations/parameters ratio is 3.35 | Observations/parameters ratio is 3.35 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 6: After refmac, R = 0.290 (Rfree = 0.000). | Cycle 6: After refmac, R = 0.290 (Rfree = 0.000). | ||
Found 38 (38 requested) and removed 19 (19 requested) atoms. | Found 38 (38 requested) and removed 19 (19 requested) atoms. | ||
| Line 103: | Line 103: | ||
Cycle 10: After refmac, R = 0.244 (Rfree = 0.000). | Cycle 10: After refmac, R = 0.244 (Rfree = 0.000). | ||
Found 24 (24 requested) and removed 12 (12 requested) atoms. | Found 24 (24 requested) and removed 12 (12 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 2 Atomic shape factors 1.71 1.60 | Building Cycle 2 Atomic shape factors 1.71 1.60 | ||
Round 1: 75 peptides in 13 chains. The longest chain comprises 9 peptides. | Round 1: 75 peptides in 13 chains. The longest chain comprises 9 peptides. | ||
| Line 110: | Line 110: | ||
Round 4: 95 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 | Taking the results from Round 4 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 9, Residues 78, Connectivity Index 0.77 | Chains 9, Residues 78, Connectivity Index 0.77 | ||
1 of these (8 residues) have been docked in sequence. | 1 of these (8 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 338 restraints for refining 1731 atoms. | 23179 reflections ( 95.69 % complete ) and 338 restraints for refining 1731 atoms. | ||
Observations/parameters ratio is 3.35 | Observations/parameters ratio is 3.35 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 11: After refmac, R = 0.274 (Rfree = 0.000). | Cycle 11: After refmac, R = 0.274 (Rfree = 0.000). | ||
Found 38 (38 requested) and removed 16 (19 requested) atoms. | Found 38 (38 requested) and removed 16 (19 requested) atoms. | ||
| Line 128: | Line 128: | ||
Cycle 15: After refmac, R = 0.239 (Rfree = 0.000). | Cycle 15: After refmac, R = 0.239 (Rfree = 0.000). | ||
Found 24 (24 requested) and removed 12 (12 requested) atoms. | Found 24 (24 requested) and removed 12 (12 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 3 Atomic shape factors 1.71 1.60 | Building Cycle 3 Atomic shape factors 1.71 1.60 | ||
Round 1: 95 peptides in 9 chains. The longest chain comprises 16 peptides. | Round 1: 95 peptides in 9 chains. The longest chain comprises 16 peptides. | ||
| Line 134: | Line 134: | ||
Round 3: 107 peptides in 9 chains. The longest chain comprises 20 peptides. | Round 3: 107 peptides in 9 chains. The longest chain comprises 20 peptides. | ||
Taking the results from Round 2 | Taking the results from Round 2 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 7, Residues 93, Connectivity Index 0.83 | Chains 7, Residues 93, Connectivity Index 0.83 | ||
3 of these (59 residues) have been docked in sequence. | 3 of these (59 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 577 restraints for refining 1823 atoms. | 23179 reflections ( 95.69 % complete ) and 577 restraints for refining 1823 atoms. | ||
Observations/parameters ratio is 3.18 | Observations/parameters ratio is 3.18 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 16: After refmac, R = 0.285 (Rfree = 0.000). | Cycle 16: After refmac, R = 0.285 (Rfree = 0.000). | ||
Found 24 (24 requested) and removed 12 (12 requested) atoms. | Found 24 (24 requested) and removed 12 (12 requested) atoms. | ||
| Line 152: | Line 152: | ||
Cycle 20: After refmac, R = 0.237 (Rfree = 0.000). | Cycle 20: After refmac, R = 0.237 (Rfree = 0.000). | ||
Found 25 (25 requested) and removed 9 (16 requested) atoms. | Found 25 (25 requested) and removed 9 (16 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 4 Atomic shape factors 1.71 1.60 | Building Cycle 4 Atomic shape factors 1.71 1.60 | ||
Round 1: 147 peptides in 13 chains. The longest chain comprises 26 peptides. | Round 1: 147 peptides in 13 chains. The longest chain comprises 26 peptides. | ||
| Line 160: | Line 160: | ||
Round 5: 159 peptides in 9 chains. The longest chain comprises 42 peptides. | Round 5: 159 peptides in 9 chains. The longest chain comprises 42 peptides. | ||
Taking the results from Round 4 | Taking the results from Round 4 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 9, Residues 172, Connectivity Index 0.89 | Chains 9, Residues 172, Connectivity Index 0.89 | ||
4 of these (116 residues) have been docked in sequence. | 4 of these (116 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 1104 restraints for refining 1890 atoms. | 23179 reflections ( 95.69 % complete ) and 1104 restraints for refining 1890 atoms. | ||
Observations/parameters ratio is 3.07 | Observations/parameters ratio is 3.07 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
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. | ||
| Line 178: | Line 178: | ||
Cycle 25: After refmac, R = 0.218 (Rfree = 0.000). | Cycle 25: After refmac, R = 0.218 (Rfree = 0.000). | ||
Found 26 (26 requested) and removed 16 (23 requested) atoms. | Found 26 (26 requested) and removed 16 (23 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 5 Atomic shape factors 1.71 1.60 | Building Cycle 5 Atomic shape factors 1.71 1.60 | ||
Round 1: 189 peptides in 8 chains. The longest chain comprises 56 peptides. | Round 1: 189 peptides in 8 chains. The longest chain comprises 56 peptides. | ||
| Line 184: | Line 184: | ||
Round 3: 197 peptides in 6 chains. The longest chain comprises 83 peptides. | Round 3: 197 peptides in 6 chains. The longest chain comprises 83 peptides. | ||
Taking the results from Round 3 | Taking the results from Round 3 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 6, Residues 191, Connectivity Index 0.94 | Chains 6, Residues 191, Connectivity Index 0.94 | ||
3 of these (149 residues) have been docked in sequence. | 3 of these (149 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 1345 restraints for refining 1886 atoms. | 23179 reflections ( 95.69 % complete ) and 1345 restraints for refining 1886 atoms. | ||
Observations/parameters ratio is 3.07 | Observations/parameters ratio is 3.07 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 26: After refmac, R = 0.235 (Rfree = 0.000). | Cycle 26: After refmac, R = 0.235 (Rfree = 0.000). | ||
Found 25 (25 requested) and removed 18 (18 requested) atoms. | Found 25 (25 requested) and removed 18 (18 requested) atoms. | ||
| Line 202: | Line 202: | ||
Cycle 30: After refmac, R = 0.176 (Rfree = 0.000). | Cycle 30: After refmac, R = 0.176 (Rfree = 0.000). | ||
Found 26 (26 requested) and removed 12 (26 requested) atoms. | Found 26 (26 requested) and removed 12 (26 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 6 Atomic shape factors 1.71 1.60 | Building Cycle 6 Atomic shape factors 1.71 1.60 | ||
Round 1: 200 peptides in 5 chains. The longest chain comprises 81 peptides. | Round 1: 200 peptides in 5 chains. The longest chain comprises 81 peptides. | ||
| Line 208: | Line 208: | ||
Round 3: 202 peptides in 5 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 | Taking the results from Round 2 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 3, Residues 199, Connectivity Index 0.95 | Chains 3, Residues 199, Connectivity Index 0.95 | ||
3 of these (199 residues) have been docked in sequence. | 3 of these (199 residues) have been docked in sequence. | ||
<!--SUMMARY_END--></FONT></B> | <!--SUMMARY_END--></FONT></B> | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
23179 reflections ( 95.69 % complete ) and 1545 restraints for refining 1885 atoms. | 23179 reflections ( 95.69 % complete ) and 1545 restraints for refining 1885 atoms. | ||
Observations/parameters ratio is 3.07 | Observations/parameters ratio is 3.07 | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Cycle 31: After refmac, R = 0.206 (Rfree = 0.000). | Cycle 31: After refmac, R = 0.206 (Rfree = 0.000). | ||
Found 25 (25 requested) and removed 18 (18 requested) atoms. | Found 25 (25 requested) and removed 18 (18 requested) atoms. | ||
| Line 226: | Line 226: | ||
Cycle 35: After refmac, R = 0.162 (Rfree = 0.000). | Cycle 35: After refmac, R = 0.162 (Rfree = 0.000). | ||
Found 13 (13 requested) and removed 8 (28 requested) atoms. | Found 13 (13 requested) and removed 8 (28 requested) atoms. | ||
------------------------------------------------------ | ------------------------------------------------------ | ||
Building Cycle 7 Atomic shape factors 1.71 1.60 | Building Cycle 7 Atomic shape factors 1.71 1.60 | ||
Round 1: 202 peptides in 5 chains. The longest chain comprises 81 peptides. | Round 1: 202 peptides in 5 chains. The longest chain comprises 81 peptides. | ||
| Line 232: | Line 232: | ||
Round 3: 202 peptides in 3 chains. The longest chain comprises 93 peptides. | Round 3: 202 peptides in 3 chains. The longest chain comprises 93 peptides. | ||
Taking the results from Round 2 | Taking the results from Round 2 | ||
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> | ||
Chains 2, Residues 203, Connectivity Index 0.97 | Chains 2, Residues 203, Connectivity Index 0.97 | ||
2 of these (203 residues) have been docked in sequence. | 2 of these (203 residues) have been docked in sequence. | ||