Sun 23 Dec 22:23:10 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 2gjg-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-4.0-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/2gjg-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-4.0-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 ============================================================ Sun 23 Dec 22:23:20 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/2gjg-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-4.0-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 166 and 0 Target number of residues in the AU: 166 Target solvent content: 0.6428 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.47 Input MTZ file: 2gjg-4.0-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: 5 Cell parameters: 89.350 48.920 57.630 90.000 93.310 90.000 Input sequence file: 2gjg-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.70 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: 28.767 4.000 Wilson plot Bfac: 72.60 2169 reflections ( 98.73 % complete ) and 0 restraints for refining 2197 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3080 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3031 (Rfree = 0.000) for 2197 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.76 Search for helices and strands: 0 residues in 0 chains, 2220 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 10 peptides. Score 0.275 Round 2: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.397 Round 3: 133 peptides, 23 chains. Longest chain 11 peptides. Score 0.443 Round 4: 128 peptides, 19 chains. Longest chain 14 peptides. Score 0.513 Round 5: 133 peptides, 19 chains. Longest chain 16 peptides. Score 0.539 Taking the results from Round 5 Chains 19, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4128 restraints for refining 1790 atoms. 3691 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2441 (Rfree = 0.000) for 1790 atoms. Found 3 (8 requested) and removed 29 (4 requested) atoms. Cycle 2: After refmac, R = 0.2302 (Rfree = 0.000) for 1738 atoms. Found 7 (8 requested) and removed 18 (4 requested) atoms. Cycle 3: After refmac, R = 0.2018 (Rfree = 0.000) for 1711 atoms. Found 3 (8 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.1891 (Rfree = 0.000) for 1685 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.1963 (Rfree = 0.000) for 1665 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.66 Search for helices and strands: 0 residues in 0 chains, 1711 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.331 Round 2: 128 peptides, 20 chains. Longest chain 18 peptides. Score 0.488 Round 3: 124 peptides, 19 chains. Longest chain 14 peptides. Score 0.490 Round 4: 127 peptides, 19 chains. Longest chain 15 peptides. Score 0.507 Round 5: 125 peptides, 18 chains. Longest chain 12 peptides. Score 0.520 Taking the results from Round 5 Chains 18, Residues 107, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4035 restraints for refining 1790 atoms. 3604 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2140 (Rfree = 0.000) for 1790 atoms. Found 3 (8 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.2049 (Rfree = 0.000) for 1756 atoms. Found 7 (8 requested) and removed 17 (4 requested) atoms. Cycle 8: After refmac, R = 0.1779 (Rfree = 0.000) for 1733 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.1676 (Rfree = 0.000) for 1717 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.1656 (Rfree = 0.000) for 1711 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.72 Search for helices and strands: 0 residues in 0 chains, 1774 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 7 peptides. Score 0.304 Round 2: 126 peptides, 23 chains. Longest chain 9 peptides. Score 0.400 Round 3: 119 peptides, 20 chains. Longest chain 14 peptides. Score 0.436 Round 4: 111 peptides, 17 chains. Longest chain 12 peptides. Score 0.466 Round 5: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 4 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4135 restraints for refining 1789 atoms. 3776 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1831 (Rfree = 0.000) for 1789 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 12: After refmac, R = 0.1690 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.1895 (Rfree = 0.000) for 1760 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 14: After refmac, R = 0.1567 (Rfree = 0.000) for 1747 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 15: After refmac, R = 0.1734 (Rfree = 0.000) for 1741 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.62 Search for helices and strands: 0 residues in 0 chains, 1782 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.286 Round 2: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.340 Round 3: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.405 Round 4: 113 peptides, 18 chains. Longest chain 8 peptides. Score 0.452 Round 5: 101 peptides, 16 chains. Longest chain 9 peptides. Score 0.432 Taking the results from Round 4 Chains 18, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4073 restraints for refining 1791 atoms. 3711 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1962 (Rfree = 0.000) for 1791 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.1794 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 18: After refmac, R = 0.1192 (Rfree = 0.000) for 1764 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.1030 (Rfree = 0.000) for 1761 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1009 (Rfree = 0.000) for 1754 atoms. Found 0 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.58 Search for helices and strands: 0 residues in 0 chains, 1796 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 6 peptides. Score 0.277 Round 2: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.320 Round 3: 103 peptides, 20 chains. Longest chain 7 peptides. Score 0.333 Round 4: 108 peptides, 22 chains. Longest chain 8 peptides. Score 0.310 Round 5: 129 peptides, 22 chains. Longest chain 9 peptides. Score 0.444 Taking the results from Round 5 Chains 22, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4103 restraints for refining 1791 atoms. 3697 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1722 (Rfree = 0.000) for 1791 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 22: After refmac, R = 0.1508 (Rfree = 0.000) for 1774 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.1345 (Rfree = 0.000) for 1772 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.1501 (Rfree = 0.000) for 1767 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.1518 (Rfree = 0.000) for 1765 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.66 Search for helices and strands: 0 residues in 0 chains, 1787 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.248 Round 2: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.374 Round 3: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.374 Round 4: 104 peptides, 17 chains. Longest chain 18 peptides. Score 0.423 Round 5: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.442 Taking the results from Round 5 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4116 restraints for refining 1791 atoms. 3738 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1924 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 27: After refmac, R = 0.1781 (Rfree = 0.000) for 1776 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 28: After refmac, R = 0.1712 (Rfree = 0.000) for 1761 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.1608 (Rfree = 0.000) for 1754 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.1396 (Rfree = 0.000) for 1750 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.62 Search for helices and strands: 0 residues in 0 chains, 1799 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.207 Round 2: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.285 Round 3: 75 peptides, 14 chains. Longest chain 8 peptides. Score 0.316 Round 4: 76 peptides, 15 chains. Longest chain 7 peptides. Score 0.292 Round 5: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.326 Taking the results from Round 5 Chains 13, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4358 restraints for refining 1791 atoms. 4135 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2016 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.1915 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.1769 (Rfree = 0.000) for 1767 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1315 (Rfree = 0.000) for 1760 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.1096 (Rfree = 0.000) for 1759 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.64 Search for helices and strands: 0 residues in 0 chains, 1797 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 6 peptides. Score 0.200 Round 2: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.266 Round 3: 67 peptides, 14 chains. Longest chain 6 peptides. Score 0.257 Round 4: 58 peptides, 10 chains. Longest chain 12 peptides. Score 0.320 Round 5: 62 peptides, 11 chains. Longest chain 13 peptides. Score 0.317 Taking the results from Round 4 Chains 10, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4298 restraints for refining 1789 atoms. 4116 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1642 (Rfree = 0.000) for 1789 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.1895 (Rfree = 0.000) for 1781 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.1692 (Rfree = 0.000) for 1779 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.2040 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.1676 (Rfree = 0.000) for 1769 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.66 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 7 peptides. Score 0.214 Round 2: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.273 Round 3: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.302 Round 4: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.324 Round 5: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.321 Taking the results from Round 4 Chains 17, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2169 reflections ( 98.73 % complete ) and 4087 restraints for refining 1777 atoms. 3816 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1693 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 42: After refmac, R = 0.1854 (Rfree = 0.000) for 1757 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.1629 (Rfree = 0.000) for 1749 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 44: After refmac, R = 0.1709 (Rfree = 0.000) for 1737 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.1496 (Rfree = 0.000) for 1732 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 1765 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 8 peptides. Score 0.211 Round 2: 68 peptides, 14 chains. Longest chain 10 peptides. Score 0.264 Round 3: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.294 Round 4: 63 peptides, 13 chains. Longest chain 9 peptides. Score 0.258 Round 5: 68 peptides, 13 chains. Longest chain 9 peptides. Score 0.296 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 55, 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 2gjg-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2169 reflections ( 98.73 % complete ) and 4096 restraints for refining 1733 atoms. 3889 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1787 (Rfree = 0.000) for 1733 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1554 (Rfree = 0.000) for 1724 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1368 (Rfree = 0.000) for 1717 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1492 (Rfree = 0.000) for 1710 atoms. TimeTaking 30.07