Sun 23 Dec 22:23:13 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 2oc6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-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/2oc6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-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 22:23:22 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/2oc6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6646 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-3.8-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.90 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 60.653 3.802 Wilson plot Bfac: 87.20 2794 reflections ( 99.61 % complete ) and 0 restraints for refining 2194 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3613 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3265 (Rfree = 0.000) for 2194 atoms. Found 9 (12 requested) and removed 94 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 2131 seeds are put forward NCS extension: 0 residues added, 2131 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.213 Round 2: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.282 Round 3: 89 peptides, 17 chains. Longest chain 7 peptides. Score 0.314 Round 4: 92 peptides, 15 chains. Longest chain 14 peptides. Score 0.387 Round 5: 91 peptides, 17 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 4 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4242 restraints for refining 1794 atoms. 3949 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2627 (Rfree = 0.000) for 1794 atoms. Found 8 (9 requested) and removed 23 (4 requested) atoms. Cycle 2: After refmac, R = 0.2361 (Rfree = 0.000) for 1772 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2337 (Rfree = 0.000) for 1766 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2260 (Rfree = 0.000) for 1760 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2347 (Rfree = 0.000) for 1751 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 1801 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 1812 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 12 peptides. Score 0.335 Round 2: 120 peptides, 21 chains. Longest chain 14 peptides. Score 0.398 Round 3: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.427 Round 4: 118 peptides, 20 chains. Longest chain 16 peptides. Score 0.411 Round 5: 114 peptides, 18 chains. Longest chain 12 peptides. Score 0.438 Taking the results from Round 5 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4293 restraints for refining 1793 atoms. 3927 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2574 (Rfree = 0.000) for 1793 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 7: After refmac, R = 0.2225 (Rfree = 0.000) for 1772 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 1764 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2074 (Rfree = 0.000) for 1763 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2062 (Rfree = 0.000) for 1757 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 1826 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 7 peptides. Score 0.315 Round 2: 98 peptides, 17 chains. Longest chain 9 peptides. Score 0.370 Round 3: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.451 Round 4: 109 peptides, 17 chains. Longest chain 13 peptides. Score 0.434 Round 5: 114 peptides, 17 chains. Longest chain 11 peptides. Score 0.462 Taking the results from Round 5 Chains 17, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4182 restraints for refining 1794 atoms. 3811 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 1794 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2051 (Rfree = 0.000) for 1768 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 13: After refmac, R = 0.1933 (Rfree = 0.000) for 1765 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.1916 (Rfree = 0.000) for 1758 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.1842 (Rfree = 0.000) for 1757 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1806 seeds are put forward NCS extension: 0 residues added, 1806 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 12 peptides. Score 0.269 Round 2: 105 peptides, 19 chains. Longest chain 9 peptides. Score 0.360 Round 3: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.423 Round 4: 111 peptides, 19 chains. Longest chain 10 peptides. Score 0.396 Round 5: 101 peptides, 17 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 3 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4183 restraints for refining 1783 atoms. 3840 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2142 (Rfree = 0.000) for 1783 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2088 (Rfree = 0.000) for 1774 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2030 (Rfree = 0.000) for 1771 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2011 (Rfree = 0.000) for 1766 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.1981 (Rfree = 0.000) for 1765 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward NCS extension: 0 residues added, 1805 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 7 peptides. Score 0.258 Round 2: 99 peptides, 17 chains. Longest chain 13 peptides. Score 0.376 Round 3: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.322 Round 4: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.331 Round 5: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 2 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4319 restraints for refining 1792 atoms. 4008 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2058 (Rfree = 0.000) for 1792 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.1947 (Rfree = 0.000) for 1785 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2036 (Rfree = 0.000) for 1782 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.1897 (Rfree = 0.000) for 1779 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1862 (Rfree = 0.000) for 1775 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1838 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.240 Round 2: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.371 Round 3: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.301 Round 4: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.337 Round 5: 95 peptides, 16 chains. Longest chain 15 peptides. Score 0.378 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4358 restraints for refining 1794 atoms. 4058 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2230 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 27: After refmac, R = 0.2075 (Rfree = 0.000) for 1793 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2028 (Rfree = 0.000) for 1792 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.1978 (Rfree = 0.000) for 1790 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1965 (Rfree = 0.000) for 1787 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 0 residues added, 1832 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 6 peptides. Score 0.250 Round 2: 99 peptides, 18 chains. Longest chain 8 peptides. Score 0.350 Round 3: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.325 Round 4: 102 peptides, 17 chains. Longest chain 9 peptides. Score 0.394 Round 5: 98 peptides, 17 chains. Longest chain 8 peptides. Score 0.370 Taking the results from Round 4 Chains 17, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4191 restraints for refining 1794 atoms. 3868 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1985 (Rfree = 0.000) for 1794 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.1924 (Rfree = 0.000) for 1785 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.1868 (Rfree = 0.000) for 1783 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.1873 (Rfree = 0.000) for 1779 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1870 (Rfree = 0.000) for 1773 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 1815 seeds are put forward NCS extension: 0 residues added, 1815 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 7 peptides. Score 0.230 Round 2: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.354 Round 3: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.340 Round 4: 110 peptides, 17 chains. Longest chain 13 peptides. Score 0.440 Round 5: 102 peptides, 19 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 4 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4205 restraints for refining 1794 atoms. 3850 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2078 (Rfree = 0.000) for 1794 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.1980 (Rfree = 0.000) for 1788 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.1839 (Rfree = 0.000) for 1787 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1670 (Rfree = 0.000) for 1779 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1653 (Rfree = 0.000) for 1777 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1831 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1849 seeds are put forward Round 1: 85 peptides, 20 chains. Longest chain 5 peptides. Score 0.202 Round 2: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.317 Round 3: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.281 Round 4: 86 peptides, 17 chains. Longest chain 10 peptides. Score 0.294 Round 5: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 2 Chains 15, Residues 66, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4285 restraints for refining 1794 atoms. 4008 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1888 (Rfree = 0.000) for 1794 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.1824 (Rfree = 0.000) for 1787 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.1809 (Rfree = 0.000) for 1783 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1781 (Rfree = 0.000) for 1781 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1769 (Rfree = 0.000) for 1776 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 1831 seeds are put forward NCS extension: 0 residues added, 1831 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 9 peptides. Score 0.252 Round 2: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.337 Round 3: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.294 Round 4: 74 peptides, 13 chains. Longest chain 8 peptides. Score 0.329 Round 5: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 69, 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 2oc6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2794 reflections ( 99.61 % complete ) and 4331 restraints for refining 1794 atoms. 4070 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1902 (Rfree = 0.000) for 1794 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1687 (Rfree = 0.000) for 1784 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1649 (Rfree = 0.000) for 1780 atoms. Found 0 (9 requested) and removed 3 (4 requested) atoms. Cycle 49: After refmac, R = 0.1651 (Rfree = 0.000) for 1776 atoms. TimeTaking 29.48