Mon 24 Dec 07:29:54 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 2p1a-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-4.0-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/2p1a-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-4.0-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 07:29:59 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/2p1a-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-4.0-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 183 and 0 Target number of residues in the AU: 183 Target solvent content: 0.6774 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-4.0-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: 19 Cell parameters: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.60 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: 29.570 4.001 Wilson plot Bfac: 98.76 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2832 reflections ( 99.33 % complete ) and 0 restraints for refining 2730 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3666 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3647 (Rfree = 0.000) for 2730 atoms. Found 12 (12 requested) and removed 40 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.00 4.22 Search for helices and strands: 0 residues in 0 chains, 2788 seeds are put forward NCS extension: 0 residues added, 2788 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.198 Round 2: 75 peptides, 15 chains. Longest chain 10 peptides. Score 0.270 Round 3: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.311 Round 4: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.297 Round 5: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.338 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 5729 restraints for refining 2225 atoms. 5434 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2606 (Rfree = 0.000) for 2225 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 2: After refmac, R = 0.2747 (Rfree = 0.000) for 2165 atoms. Found 8 (10 requested) and removed 24 (5 requested) atoms. Cycle 3: After refmac, R = 0.2581 (Rfree = 0.000) for 2116 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 4: After refmac, R = 0.2336 (Rfree = 0.000) for 2085 atoms. Found 7 (9 requested) and removed 17 (4 requested) atoms. Cycle 5: After refmac, R = 0.2622 (Rfree = 0.000) for 2050 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.88 4.09 Search for helices and strands: 0 residues in 0 chains, 2156 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2168 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.249 Round 2: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.297 Round 3: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.349 Round 4: 99 peptides, 14 chains. Longest chain 12 peptides. Score 0.434 Round 5: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 4 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4578 restraints for refining 1956 atoms. 4252 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2617 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 7: After refmac, R = 0.2291 (Rfree = 0.000) for 1919 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 8: After refmac, R = 0.2025 (Rfree = 0.000) for 1898 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2015 (Rfree = 0.000) for 1893 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.2108 (Rfree = 0.000) for 1878 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.96 4.18 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2023 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.280 Round 2: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.400 Round 3: 119 peptides, 17 chains. Longest chain 14 peptides. Score 0.466 Round 4: 112 peptides, 16 chains. Longest chain 13 peptides. Score 0.454 Round 5: 106 peptides, 15 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 3 Chains 17, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4385 restraints for refining 1952 atoms. 3994 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2252 (Rfree = 0.000) for 1952 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 12: After refmac, R = 0.2302 (Rfree = 0.000) for 1920 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2131 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.1939 (Rfree = 0.000) for 1888 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 15: After refmac, R = 0.2078 (Rfree = 0.000) for 1870 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 1979 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1996 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.270 Round 2: 103 peptides, 14 chains. Longest chain 13 peptides. Score 0.454 Round 3: 108 peptides, 15 chains. Longest chain 12 peptides. Score 0.456 Round 4: 102 peptides, 17 chains. Longest chain 14 peptides. Score 0.378 Round 5: 102 peptides, 15 chains. Longest chain 11 peptides. Score 0.426 Taking the results from Round 3 Chains 15, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4287 restraints for refining 1914 atoms. 3930 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2337 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 33 (4 requested) atoms. Cycle 17: After refmac, R = 0.2346 (Rfree = 0.000) for 1876 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 18: After refmac, R = 0.1994 (Rfree = 0.000) for 1865 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 19: After refmac, R = 0.2049 (Rfree = 0.000) for 1848 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.2073 (Rfree = 0.000) for 1837 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 4.07 Search for helices and strands: 0 residues in 0 chains, 1950 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1967 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.258 Round 2: 101 peptides, 16 chains. Longest chain 17 peptides. Score 0.396 Round 3: 110 peptides, 17 chains. Longest chain 20 peptides. Score 0.421 Round 4: 109 peptides, 19 chains. Longest chain 14 peptides. Score 0.368 Round 5: 107 peptides, 17 chains. Longest chain 17 peptides. Score 0.405 Taking the results from Round 3 Chains 19, Residues 93, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 3948 restraints for refining 1906 atoms. 3529 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2239 (Rfree = 0.000) for 1906 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.2103 (Rfree = 0.000) for 1883 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.2126 (Rfree = 0.000) for 1872 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 24: After refmac, R = 0.2197 (Rfree = 0.000) for 1859 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.2163 (Rfree = 0.000) for 1852 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 4.06 Search for helices and strands: 0 residues in 0 chains, 1948 seeds are put forward NCS extension: 0 residues added, 1948 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 10 peptides. Score 0.287 Round 2: 111 peptides, 21 chains. Longest chain 12 peptides. Score 0.332 Round 3: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.381 Round 4: 114 peptides, 18 chains. Longest chain 13 peptides. Score 0.418 Round 5: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 4 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4456 restraints for refining 1948 atoms. 4090 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2261 (Rfree = 0.000) for 1948 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2310 (Rfree = 0.000) for 1929 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 28: After refmac, R = 0.2203 (Rfree = 0.000) for 1909 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 29: After refmac, R = 0.2101 (Rfree = 0.000) for 1891 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 30: After refmac, R = 0.2103 (Rfree = 0.000) for 1884 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 4.01 Search for helices and strands: 0 residues in 0 chains, 1982 seeds are put forward NCS extension: 0 residues added, 1982 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.221 Round 2: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.309 Round 3: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.279 Round 4: 91 peptides, 18 chains. Longest chain 7 peptides. Score 0.290 Round 5: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.321 Taking the results from Round 5 Chains 17, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4762 restraints for refining 2016 atoms. 4479 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2195 (Rfree = 0.000) for 2016 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 32: After refmac, R = 0.2315 (Rfree = 0.000) for 1988 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 33: After refmac, R = 0.2259 (Rfree = 0.000) for 1978 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.2322 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 35: After refmac, R = 0.2338 (Rfree = 0.000) for 1947 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 0 residues added, 2038 seeds are put forward Round 1: 70 peptides, 17 chains. Longest chain 5 peptides. Score 0.181 Round 2: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.281 Round 3: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.319 Round 4: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.297 Round 5: 84 peptides, 17 chains. Longest chain 10 peptides. Score 0.273 Taking the results from Round 3 Chains 15, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4266 restraints for refining 1865 atoms. 4009 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2119 (Rfree = 0.000) for 1865 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 37: After refmac, R = 0.2011 (Rfree = 0.000) for 1838 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 38: After refmac, R = 0.2172 (Rfree = 0.000) for 1828 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.2168 (Rfree = 0.000) for 1815 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.2140 (Rfree = 0.000) for 1804 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.87 4.08 Search for helices and strands: 0 residues in 0 chains, 1891 seeds are put forward NCS extension: 0 residues added, 1891 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.219 Round 2: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.235 Round 3: 78 peptides, 16 chains. Longest chain 6 peptides. Score 0.262 Round 4: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.307 Round 5: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.328 Taking the results from Round 5 Chains 14, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4098 restraints for refining 1821 atoms. 3848 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2120 (Rfree = 0.000) for 1821 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 42: After refmac, R = 0.2096 (Rfree = 0.000) for 1803 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 43: After refmac, R = 0.2109 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2268 (Rfree = 0.000) for 1778 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 45: After refmac, R = 0.2194 (Rfree = 0.000) for 1759 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 4.05 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 0 residues added, 1838 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 8 peptides. Score 0.219 Round 2: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.274 Round 3: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.301 Round 4: 86 peptides, 14 chains. Longest chain 10 peptides. Score 0.363 Round 5: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 72, 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 2p1a-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2832 reflections ( 99.33 % complete ) and 3932 restraints for refining 1780 atoms. 3658 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2091 (Rfree = 0.000) for 1780 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2345 (Rfree = 0.000) for 1767 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 1756 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2283 (Rfree = 0.000) for 1750 atoms. TimeTaking 27.5