Mon 24 Dec 07:26:23 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 2prx-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prx-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prx-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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 07:26:28 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/2prx-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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 202 and 0 Target number of residues in the AU: 202 Target solvent content: 0.6281 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.55 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: 28.816 4.001 Wilson plot Bfac: 65.55 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2404 reflections ( 99.50 % complete ) and 0 restraints for refining 2822 atoms. Observations/parameters ratio is 0.21 ------------------------------------------------------ Starting model: R = 0.3154 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3099 (Rfree = 0.000) for 2822 atoms. Found 13 (13 requested) and removed 101 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward NCS extension: 0 residues added, 2759 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.242 Round 2: 83 peptides, 16 chains. Longest chain 13 peptides. Score 0.297 Round 3: 91 peptides, 17 chains. Longest chain 13 peptides. Score 0.320 Round 4: 97 peptides, 17 chains. Longest chain 14 peptides. Score 0.356 Round 5: 98 peptides, 18 chains. Longest chain 13 peptides. Score 0.336 Taking the results from Round 4 Chains 17, Residues 80, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 5827 restraints for refining 2296 atoms. 5512 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2333 (Rfree = 0.000) for 2296 atoms. Found 10 (10 requested) and removed 45 (5 requested) atoms. Cycle 2: After refmac, R = 0.2125 (Rfree = 0.000) for 2240 atoms. Found 10 (10 requested) and removed 29 (5 requested) atoms. Cycle 3: After refmac, R = 0.2108 (Rfree = 0.000) for 2197 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. Cycle 4: After refmac, R = 0.1472 (Rfree = 0.000) for 2163 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.1893 (Rfree = 0.000) for 2144 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward NCS extension: 0 residues added, 2184 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 5 peptides. Score 0.203 Round 2: 98 peptides, 20 chains. Longest chain 9 peptides. Score 0.285 Round 3: 99 peptides, 17 chains. Longest chain 12 peptides. Score 0.368 Round 4: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.306 Round 5: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 3 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4723 restraints for refining 1939 atoms. 4412 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2028 (Rfree = 0.000) for 1939 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 7: After refmac, R = 0.1935 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 8: After refmac, R = 0.1697 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.1681 (Rfree = 0.000) for 1860 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 10: After refmac, R = 0.1648 (Rfree = 0.000) for 1851 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.97 Search for helices and strands: 0 residues in 0 chains, 1887 seeds are put forward NCS extension: 0 residues added, 1887 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 8 peptides. Score 0.224 Round 2: 91 peptides, 17 chains. Longest chain 10 peptides. Score 0.320 Round 3: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.398 Round 4: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.303 Round 5: 93 peptides, 15 chains. Longest chain 10 peptides. Score 0.384 Taking the results from Round 3 Chains 14, Residues 77, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4034 restraints for refining 1783 atoms. 3718 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1705 (Rfree = 0.000) for 1783 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 12: After refmac, R = 0.1619 (Rfree = 0.000) for 1760 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 13: After refmac, R = 0.1669 (Rfree = 0.000) for 1750 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 14: After refmac, R = 0.1719 (Rfree = 0.000) for 1743 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.1554 (Rfree = 0.000) for 1736 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward NCS extension: 0 residues added, 1800 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.222 Round 2: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.395 Round 3: 100 peptides, 18 chains. Longest chain 12 peptides. Score 0.348 Round 4: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.379 Round 5: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.360 Taking the results from Round 2 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4096 restraints for refining 1815 atoms. 3791 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1702 (Rfree = 0.000) for 1815 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 17: After refmac, R = 0.1625 (Rfree = 0.000) for 1802 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 18: After refmac, R = 0.1638 (Rfree = 0.000) for 1783 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.1559 (Rfree = 0.000) for 1771 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.1656 (Rfree = 0.000) for 1761 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 1798 seeds are put forward NCS extension: 0 residues added, 1798 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 6 peptides. Score 0.250 Round 2: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.306 Round 3: 104 peptides, 18 chains. Longest chain 9 peptides. Score 0.371 Round 4: 95 peptides, 18 chains. Longest chain 7 peptides. Score 0.318 Round 5: 104 peptides, 18 chains. Longest chain 9 peptides. Score 0.371 Taking the results from Round 5 Chains 18, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4097 restraints for refining 1816 atoms. 3771 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1598 (Rfree = 0.000) for 1816 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 22: After refmac, R = 0.1410 (Rfree = 0.000) for 1794 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 23: After refmac, R = 0.1615 (Rfree = 0.000) for 1789 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.1503 (Rfree = 0.000) for 1778 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 25: After refmac, R = 0.1311 (Rfree = 0.000) for 1771 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 0 residues added, 1816 seeds are put forward Round 1: 94 peptides, 22 chains. Longest chain 5 peptides. Score 0.207 Round 2: 106 peptides, 19 chains. Longest chain 13 peptides. Score 0.358 Round 3: 112 peptides, 20 chains. Longest chain 16 peptides. Score 0.368 Round 4: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.329 Round 5: 105 peptides, 19 chains. Longest chain 12 peptides. Score 0.352 Taking the results from Round 3 Chains 21, Residues 92, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4105 restraints for refining 1851 atoms. 3725 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1670 (Rfree = 0.000) for 1851 atoms. Found 8 (8 requested) and removed 32 (4 requested) atoms. Cycle 27: After refmac, R = 0.1600 (Rfree = 0.000) for 1821 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 28: After refmac, R = 0.1433 (Rfree = 0.000) for 1810 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 29: After refmac, R = 0.1403 (Rfree = 0.000) for 1802 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 30: After refmac, R = 0.1405 (Rfree = 0.000) for 1793 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.92 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward NCS extension: 0 residues added, 1829 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 7 peptides. Score 0.281 Round 2: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.338 Round 3: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.368 Round 4: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.324 Round 5: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.366 Taking the results from Round 3 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4388 restraints for refining 1890 atoms. 4059 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1519 (Rfree = 0.000) for 1890 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 32: After refmac, R = 0.1544 (Rfree = 0.000) for 1862 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 33: After refmac, R = 0.1109 (Rfree = 0.000) for 1846 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.0977 (Rfree = 0.000) for 1845 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.0964 (Rfree = 0.000) for 1844 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 1876 seeds are put forward NCS extension: 0 residues added, 1876 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 6 peptides. Score 0.229 Round 2: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.346 Round 3: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.336 Round 4: 95 peptides, 15 chains. Longest chain 11 peptides. Score 0.395 Round 5: 100 peptides, 16 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 5 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4540 restraints for refining 1941 atoms. 4203 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1680 (Rfree = 0.000) for 1941 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 37: After refmac, R = 0.1559 (Rfree = 0.000) for 1921 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 38: After refmac, R = 0.1602 (Rfree = 0.000) for 1907 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 39: After refmac, R = 0.1669 (Rfree = 0.000) for 1903 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 40: After refmac, R = 0.1642 (Rfree = 0.000) for 1894 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.91 Search for helices and strands: 0 residues in 0 chains, 1931 seeds are put forward NCS extension: 0 residues added, 1931 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.237 Round 2: 82 peptides, 16 chains. Longest chain 10 peptides. Score 0.291 Round 3: 89 peptides, 15 chains. Longest chain 12 peptides. Score 0.361 Round 4: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.336 Round 5: 90 peptides, 14 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 14, Residues 76, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4490 restraints for refining 1948 atoms. 4161 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1774 (Rfree = 0.000) for 1948 atoms. Found 9 (9 requested) and removed 25 (4 requested) atoms. Cycle 42: After refmac, R = 0.1717 (Rfree = 0.000) for 1930 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 43: After refmac, R = 0.1719 (Rfree = 0.000) for 1915 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 44: After refmac, R = 0.1689 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 45: After refmac, R = 0.1791 (Rfree = 0.000) for 1885 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 1922 seeds are put forward NCS extension: 7 residues added (1 deleted due to clashes), 1929 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 11 peptides. Score 0.297 Round 2: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.384 Round 3: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.284 Round 4: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.326 Round 5: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.346 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 71, 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 2prx-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2404 reflections ( 99.50 % complete ) and 4311 restraints for refining 1874 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1680 (Rfree = 0.000) for 1874 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1737 (Rfree = 0.000) for 1867 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1456 (Rfree = 0.000) for 1859 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1729 (Rfree = 0.000) for 1851 atoms. TimeTaking 26.37