Mon 24 Dec 07:55:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oc6-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:55:13 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/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.4-parrot-noncs/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 179 and 0 Target number of residues in the AU: 179 Target solvent content: 0.6509 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: 2oc6-3.4-parrot-noncs.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: 2oc6-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 78.19 3890 reflections ( 99.64 % complete ) and 0 restraints for refining 2217 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3683 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3160 (Rfree = 0.000) for 2217 atoms. Found 12 (16 requested) and removed 36 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 2240 seeds are put forward NCS extension: 0 residues added, 2240 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 9 peptides. Score 0.262 Round 2: 132 peptides, 25 chains. Longest chain 8 peptides. Score 0.369 Round 3: 133 peptides, 24 chains. Longest chain 10 peptides. Score 0.399 Round 4: 142 peptides, 24 chains. Longest chain 10 peptides. Score 0.449 Round 5: 139 peptides, 22 chains. Longest chain 11 peptides. Score 0.478 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4069 restraints for refining 1803 atoms. 3623 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2524 (Rfree = 0.000) for 1803 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 2: After refmac, R = 0.2384 (Rfree = 0.000) for 1776 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2279 (Rfree = 0.000) for 1770 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.1997 (Rfree = 0.000) for 1766 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.1973 (Rfree = 0.000) for 1759 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1835 seeds are put forward Round 1: 133 peptides, 24 chains. Longest chain 12 peptides. Score 0.399 Round 2: 132 peptides, 24 chains. Longest chain 12 peptides. Score 0.393 Round 3: 133 peptides, 24 chains. Longest chain 12 peptides. Score 0.399 Round 4: 132 peptides, 21 chains. Longest chain 10 peptides. Score 0.464 Round 5: 136 peptides, 23 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 4 Chains 21, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4158 restraints for refining 1803 atoms. 3735 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2337 (Rfree = 0.000) for 1803 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. Cycle 7: After refmac, R = 0.2257 (Rfree = 0.000) for 1793 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2293 (Rfree = 0.000) for 1789 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 1788 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.1915 (Rfree = 0.000) for 1782 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1855 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1861 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 10 peptides. Score 0.304 Round 2: 148 peptides, 25 chains. Longest chain 13 peptides. Score 0.458 Round 3: 135 peptides, 23 chains. Longest chain 11 peptides. Score 0.434 Round 4: 146 peptides, 27 chains. Longest chain 12 peptides. Score 0.401 Round 5: 142 peptides, 22 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 5 Chains 23, Residues 120, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 3815 restraints for refining 1804 atoms. 3317 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2208 (Rfree = 0.000) for 1804 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 1795 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2020 (Rfree = 0.000) for 1789 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1901 (Rfree = 0.000) for 1784 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1731 (Rfree = 0.000) for 1780 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1867 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1882 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 10 peptides. Score 0.306 Round 2: 137 peptides, 25 chains. Longest chain 8 peptides. Score 0.398 Round 3: 136 peptides, 22 chains. Longest chain 13 peptides. Score 0.463 Round 4: 130 peptides, 20 chains. Longest chain 16 peptides. Score 0.477 Round 5: 132 peptides, 20 chains. Longest chain 10 peptides. Score 0.487 Taking the results from Round 5 Chains 20, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 3957 restraints for refining 1803 atoms. 3529 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2338 (Rfree = 0.000) for 1803 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 17: After refmac, R = 0.2093 (Rfree = 0.000) for 1799 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2030 (Rfree = 0.000) for 1797 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1799 (Rfree = 0.000) for 1791 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1736 (Rfree = 0.000) for 1787 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1860 seeds are put forward NCS extension: 0 residues added, 1860 seeds are put forward Round 1: 111 peptides, 24 chains. Longest chain 7 peptides. Score 0.266 Round 2: 134 peptides, 23 chains. Longest chain 15 peptides. Score 0.429 Round 3: 132 peptides, 22 chains. Longest chain 15 peptides. Score 0.441 Round 4: 129 peptides, 21 chains. Longest chain 10 peptides. Score 0.448 Round 5: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.447 Taking the results from Round 4 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4121 restraints for refining 1804 atoms. 3710 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2172 (Rfree = 0.000) for 1804 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.2002 (Rfree = 0.000) for 1800 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1808 (Rfree = 0.000) for 1796 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1800 (Rfree = 0.000) for 1789 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1911 (Rfree = 0.000) for 1784 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1874 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 14 peptides. Score 0.319 Round 2: 122 peptides, 21 chains. Longest chain 10 peptides. Score 0.409 Round 3: 129 peptides, 22 chains. Longest chain 12 peptides. Score 0.425 Round 4: 125 peptides, 19 chains. Longest chain 12 peptides. Score 0.474 Round 5: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.369 Taking the results from Round 4 Chains 19, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4141 restraints for refining 1804 atoms. 3736 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2238 (Rfree = 0.000) for 1804 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 27: After refmac, R = 0.2143 (Rfree = 0.000) for 1801 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.2023 (Rfree = 0.000) for 1790 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1973 (Rfree = 0.000) for 1789 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1920 (Rfree = 0.000) for 1783 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 1860 seeds are put forward NCS extension: 0 residues added, 1860 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 10 peptides. Score 0.268 Round 2: 113 peptides, 21 chains. Longest chain 9 peptides. Score 0.357 Round 3: 101 peptides, 18 chains. Longest chain 8 peptides. Score 0.362 Round 4: 100 peptides, 19 chains. Longest chain 8 peptides. Score 0.329 Round 5: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4201 restraints for refining 1804 atoms. 3867 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2217 (Rfree = 0.000) for 1804 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.2005 (Rfree = 0.000) for 1805 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.2008 (Rfree = 0.000) for 1802 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1936 (Rfree = 0.000) for 1804 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1636 (Rfree = 0.000) for 1802 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1856 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 1862 seeds are put forward Round 1: 102 peptides, 23 chains. Longest chain 7 peptides. Score 0.235 Round 2: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.280 Round 3: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.309 Round 4: 104 peptides, 19 chains. Longest chain 8 peptides. Score 0.354 Round 5: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.304 Taking the results from Round 4 Chains 19, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4216 restraints for refining 1804 atoms. 3895 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2181 (Rfree = 0.000) for 1804 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2099 (Rfree = 0.000) for 1808 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1979 (Rfree = 0.000) for 1813 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 1811 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1783 (Rfree = 0.000) for 1803 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 1863 seeds are put forward NCS extension: 0 residues added, 1863 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 17 peptides. Score 0.271 Round 2: 101 peptides, 21 chains. Longest chain 9 peptides. Score 0.282 Round 3: 106 peptides, 19 chains. Longest chain 15 peptides. Score 0.366 Round 4: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 5: 103 peptides, 18 chains. Longest chain 16 peptides. Score 0.374 Taking the results from Round 5 Chains 18, Residues 85, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3890 reflections ( 99.64 % complete ) and 4078 restraints for refining 1804 atoms. 3741 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2114 (Rfree = 0.000) for 1804 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.2121 (Rfree = 0.000) for 1801 atoms. Found 12 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 1803 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1684 (Rfree = 0.000) for 1805 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1594 (Rfree = 0.000) for 1801 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1859 seeds are put forward NCS extension: 0 residues added, 1859 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 11 peptides. Score 0.283 Round 2: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.315 Round 3: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.331 Round 4: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.328 Round 5: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 88, 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. 3890 reflections ( 99.64 % complete ) and 4176 restraints for refining 1804 atoms. 3843 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2244 (Rfree = 0.000) for 1804 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2109 (Rfree = 0.000) for 1791 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2158 (Rfree = 0.000) for 1781 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2085 (Rfree = 0.000) for 1770 atoms. TimeTaking 24.27