Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2etj-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 155 and 0 Target number of residues in the AU: 155 Target solvent content: 0.6454 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 250 Adjusted target solvent content: 0.43 Input MTZ file: 2etj-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 144 Cell parameters: 51.821 51.821 76.293 90.000 90.000 120.000 Input sequence file: 2etj-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2000 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 24.534 3.603 Wilson plot Bfac: 74.13 2633 reflections ( 99.66 % complete ) and 0 restraints for refining 2212 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3374 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3307 (Rfree = 0.000) for 2212 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 2245 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.216 Round 2: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.386 Round 3: 87 peptides, 14 chains. Longest chain 12 peptides. Score 0.409 Round 4: 89 peptides, 16 chains. Longest chain 11 peptides. Score 0.362 Round 5: 98 peptides, 15 chains. Longest chain 12 peptides. Score 0.453 Taking the results from Round 5 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4424 restraints for refining 1813 atoms. 4107 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2426 (Rfree = 0.000) for 1813 atoms. Found 6 (11 requested) and removed 20 (5 requested) atoms. Cycle 2: After refmac, R = 0.2380 (Rfree = 0.000) for 1771 atoms. Found 9 (11 requested) and removed 21 (5 requested) atoms. Cycle 3: After refmac, R = 0.2330 (Rfree = 0.000) for 1742 atoms. Found 9 (11 requested) and removed 20 (5 requested) atoms. Cycle 4: After refmac, R = 0.2106 (Rfree = 0.000) for 1727 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.1700 (Rfree = 0.000) for 1716 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.70 Search for helices and strands: 0 residues in 0 chains, 1767 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 12 peptides. Score 0.287 Round 2: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.374 Round 3: 104 peptides, 18 chains. Longest chain 14 peptides. Score 0.407 Round 4: 93 peptides, 16 chains. Longest chain 13 peptides. Score 0.390 Round 5: 93 peptides, 17 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 3 Chains 19, Residues 86, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4051 restraints for refining 1695 atoms. 3692 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1938 (Rfree = 0.000) for 1695 atoms. Found 4 (10 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.1850 (Rfree = 0.000) for 1673 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1792 (Rfree = 0.000) for 1669 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.1759 (Rfree = 0.000) for 1664 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1734 (Rfree = 0.000) for 1661 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.73 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.315 Round 2: 107 peptides, 18 chains. Longest chain 18 peptides. Score 0.426 Round 3: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.461 Round 4: 121 peptides, 17 chains. Longest chain 19 peptides. Score 0.538 Round 5: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.424 Taking the results from Round 4 Chains 18, Residues 104, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 3916 restraints for refining 1741 atoms. 3471 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2099 (Rfree = 0.000) for 1741 atoms. Found 7 (11 requested) and removed 20 (5 requested) atoms. Cycle 12: After refmac, R = 0.1950 (Rfree = 0.000) for 1721 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.1843 (Rfree = 0.000) for 1709 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.1794 (Rfree = 0.000) for 1700 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.1733 (Rfree = 0.000) for 1694 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 1751 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 7 peptides. Score 0.320 Round 2: 95 peptides, 15 chains. Longest chain 10 peptides. Score 0.433 Round 3: 100 peptides, 16 chains. Longest chain 14 peptides. Score 0.437 Round 4: 98 peptides, 14 chains. Longest chain 11 peptides. Score 0.481 Round 5: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.437 Taking the results from Round 4 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4149 restraints for refining 1750 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1893 (Rfree = 0.000) for 1750 atoms. Found 7 (11 requested) and removed 20 (5 requested) atoms. Cycle 17: After refmac, R = 0.1720 (Rfree = 0.000) for 1735 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1656 (Rfree = 0.000) for 1726 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.1767 (Rfree = 0.000) for 1723 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1821 (Rfree = 0.000) for 1715 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 1765 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.317 Round 2: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.404 Round 3: 107 peptides, 18 chains. Longest chain 14 peptides. Score 0.426 Round 4: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.395 Round 5: 103 peptides, 18 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 3 Chains 18, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4251 restraints for refining 1784 atoms. 3913 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1736 (Rfree = 0.000) for 1784 atoms. Found 8 (11 requested) and removed 13 (5 requested) atoms. Cycle 22: After refmac, R = 0.1588 (Rfree = 0.000) for 1776 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.1582 (Rfree = 0.000) for 1767 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1549 (Rfree = 0.000) for 1761 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1619 (Rfree = 0.000) for 1757 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 11 peptides. Score 0.296 Round 2: 96 peptides, 18 chains. Longest chain 13 peptides. Score 0.352 Round 3: 101 peptides, 17 chains. Longest chain 10 peptides. Score 0.415 Round 4: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.443 Round 5: 98 peptides, 14 chains. Longest chain 18 peptides. Score 0.481 Taking the results from Round 5 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4327 restraints for refining 1788 atoms. 4005 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1676 (Rfree = 0.000) for 1788 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 27: After refmac, R = 0.1519 (Rfree = 0.000) for 1775 atoms. Found 0 (11 requested) and removed 9 (5 requested) atoms. Cycle 28: After refmac, R = 0.1466 (Rfree = 0.000) for 1763 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.1481 (Rfree = 0.000) for 1755 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1500 (Rfree = 0.000) for 1746 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 1791 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.258 Round 2: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.413 Round 3: 85 peptides, 13 chains. Longest chain 15 peptides. Score 0.426 Round 4: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.413 Round 5: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 3 Chains 13, Residues 72, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4261 restraints for refining 1771 atoms. 3955 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1647 (Rfree = 0.000) for 1771 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 32: After refmac, R = 0.1398 (Rfree = 0.000) for 1761 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.1332 (Rfree = 0.000) for 1747 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1254 (Rfree = 0.000) for 1742 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1434 (Rfree = 0.000) for 1735 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.226 Round 2: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.323 Round 3: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.311 Round 4: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.296 Round 5: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.370 Taking the results from Round 5 Chains 16, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2633 reflections ( 99.66 % complete ) and 4176 restraints for refining 1743 atoms. 3896 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1666 (Rfree = 0.000) for 1743 atoms. Found 9 (11 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1842 (Rfree = 0.000) for 1733 atoms. Found 8 (11 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.1721 (Rfree = 0.000) for 1723 atoms. Found 6 (11 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.1694 (Rfree = 0.000) for 1717 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1547 (Rfree = 0.000) for 1714 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 1785 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.211 Round 2: 84 peptides, 17 chains. Longest chain 10 peptides. Score 0.295 Round 3: 69 peptides, 13 chains. Longest chain 11 peptides. Score 0.310 Round 4: 85 peptides, 16 chains. Longest chain 14 peptides. Score 0.334 Round 5: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.290 Taking the results from Round 4 Chains 16, Residues 69, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2633 reflections ( 99.66 % complete ) and 4254 restraints for refining 1789 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1525 (Rfree = 0.000) for 1789 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.1507 (Rfree = 0.000) for 1782 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.1186 (Rfree = 0.000) for 1775 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.1085 (Rfree = 0.000) for 1770 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1113 (Rfree = 0.000) for 1764 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.70 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.217 Round 2: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.299 Round 3: 62 peptides, 10 chains. Longest chain 11 peptides. Score 0.357 Round 4: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.362 Round 5: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2etj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2633 reflections ( 99.66 % complete ) and 4126 restraints for refining 1741 atoms. 3909 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1650 (Rfree = 0.000) for 1741 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1796 (Rfree = 0.000) for 1734 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2551 (Rfree = 0.000) for 1727 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1651 (Rfree = 0.000) for 1721 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:07:08 GMT 2018 Job finished. TimeTaking 39.18