Mon 24 Dec 00:10:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prx-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-4.0-parrot-mrncs ############### 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 00:10:54 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/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-4.0-parrot-mrncs/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-mrncs.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-mrncs.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 2820 atoms. Observations/parameters ratio is 0.21 ------------------------------------------------------ Starting model: R = 0.3163 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2913 (Rfree = 0.000) for 2820 atoms. Found 12 (13 requested) and removed 93 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 0 residues added, 2753 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 5 peptides. Score 0.197 Round 2: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.248 Round 3: 99 peptides, 21 chains. Longest chain 9 peptides. Score 0.265 Round 4: 104 peptides, 22 chains. Longest chain 9 peptides. Score 0.270 Round 5: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.295 Taking the results from Round 5 Chains 22, Residues 86, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 5495 restraints for refining 2284 atoms. 5113 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2528 (Rfree = 0.000) for 2284 atoms. Found 10 (10 requested) and removed 44 (5 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2286 (Rfree = 0.000) for 2216 atoms. Found 9 (10 requested) and removed 28 (5 requested) atoms. Cycle 3: After refmac, R = 0.2094 (Rfree = 0.000) for 2179 atoms. Found 10 (10 requested) and removed 27 (5 requested) atoms. Cycle 4: After refmac, R = 0.2032 (Rfree = 0.000) for 2133 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 5: After refmac, R = 0.1957 (Rfree = 0.000) for 2103 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 0 residues added, 2139 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.211 Round 2: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.262 Round 3: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.302 Round 4: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Round 5: 91 peptides, 18 chains. Longest chain 10 peptides. Score 0.294 Taking the results from Round 3 Chains 21, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4548 restraints for refining 1880 atoms. 4233 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1903 (Rfree = 0.000) for 1880 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.1911 (Rfree = 0.000) for 1846 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.1369 (Rfree = 0.000) for 1836 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.1193 (Rfree = 0.000) for 1826 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1188 (Rfree = 0.000) for 1819 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.93 Search for helices and strands: 0 residues in 0 chains, 1869 seeds are put forward NCS extension: 0 residues added, 1869 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 11 peptides. Score 0.297 Round 2: 99 peptides, 18 chains. Longest chain 8 peptides. Score 0.342 Round 3: 95 peptides, 16 chains. Longest chain 16 peptides. Score 0.370 Round 4: 94 peptides, 15 chains. Longest chain 16 peptides. Score 0.390 Round 5: 98 peptides, 15 chains. Longest chain 13 peptides. Score 0.412 Taking the results from Round 5 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4381 restraints for refining 1883 atoms. 4057 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1890 (Rfree = 0.000) for 1883 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 12: After refmac, R = 0.1653 (Rfree = 0.000) for 1863 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 13: After refmac, R = 0.1738 (Rfree = 0.000) for 1849 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.1661 (Rfree = 0.000) for 1842 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.1549 (Rfree = 0.000) for 1836 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.89 Search for helices and strands: 0 residues in 0 chains, 1902 seeds are put forward NCS extension: 0 residues added, 1902 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.252 Round 2: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.346 Round 3: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.291 Round 4: 105 peptides, 19 chains. Longest chain 8 peptides. Score 0.352 Round 5: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.339 Taking the results from Round 4 Chains 19, Residues 86, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4498 restraints for refining 1908 atoms. 4128 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2265 (Rfree = 0.000) for 1908 atoms. Found 9 (9 requested) and removed 25 (4 requested) atoms. Cycle 17: After refmac, R = 0.1739 (Rfree = 0.000) for 1864 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 18: After refmac, R = 0.1739 (Rfree = 0.000) for 1847 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.1708 (Rfree = 0.000) for 1835 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.1536 (Rfree = 0.000) for 1830 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 1889 seeds are put forward NCS extension: 0 residues added, 1889 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.249 Round 2: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.315 Round 3: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.278 Round 4: 103 peptides, 19 chains. Longest chain 12 peptides. Score 0.341 Round 5: 104 peptides, 21 chains. Longest chain 12 peptides. Score 0.296 Taking the results from Round 4 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4379 restraints for refining 1877 atoms. 4062 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1766 (Rfree = 0.000) for 1877 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 22: After refmac, R = 0.1811 (Rfree = 0.000) for 1869 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.1620 (Rfree = 0.000) for 1856 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.1160 (Rfree = 0.000) for 1855 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.1219 (Rfree = 0.000) for 1847 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 1912 seeds are put forward NCS extension: 0 residues added, 1912 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 7 peptides. Score 0.220 Round 2: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.333 Round 3: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.369 Round 4: 113 peptides, 20 chains. Longest chain 9 peptides. Score 0.373 Round 5: 108 peptides, 18 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 5 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4508 restraints for refining 1908 atoms. 4166 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1760 (Rfree = 0.000) for 1908 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 27: After refmac, R = 0.1683 (Rfree = 0.000) for 1881 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.1230 (Rfree = 0.000) for 1872 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.1120 (Rfree = 0.000) for 1869 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1176 (Rfree = 0.000) for 1862 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 1914 seeds are put forward NCS extension: 0 residues added, 1914 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.265 Round 2: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.327 Round 3: 98 peptides, 18 chains. Longest chain 14 peptides. Score 0.336 Round 4: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.388 Round 5: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 4 Chains 18, Residues 89, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4448 restraints for refining 1922 atoms. 4084 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1707 (Rfree = 0.000) for 1922 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.1647 (Rfree = 0.000) for 1909 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.1775 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 34: After refmac, R = 0.1570 (Rfree = 0.000) for 1892 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 35: After refmac, R = 0.1591 (Rfree = 0.000) for 1883 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 1913 seeds are put forward NCS extension: 0 residues added, 1913 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.256 Round 2: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.338 Round 3: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.358 Round 4: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.411 Round 5: 117 peptides, 20 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 4 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4362 restraints for refining 1917 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1771 (Rfree = 0.000) for 1917 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1765 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1579 (Rfree = 0.000) for 1888 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 39: After refmac, R = 0.1633 (Rfree = 0.000) for 1882 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1796 (Rfree = 0.000) for 1879 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.91 Search for helices and strands: 0 residues in 0 chains, 1933 seeds are put forward NCS extension: 0 residues added, 1933 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.222 Round 2: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.302 Round 3: 97 peptides, 17 chains. Longest chain 12 peptides. Score 0.356 Round 4: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 5: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.324 Taking the results from Round 3 Chains 17, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2404 reflections ( 99.50 % complete ) and 4291 restraints for refining 1890 atoms. 3988 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1560 (Rfree = 0.000) for 1890 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.1787 (Rfree = 0.000) for 1884 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 43: After refmac, R = 0.1517 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1705 (Rfree = 0.000) for 1867 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.1026 (Rfree = 0.000) for 1861 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 0 residues added, 1897 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.231 Round 2: 75 peptides, 13 chains. Longest chain 12 peptides. Score 0.329 Round 3: 80 peptides, 15 chains. Longest chain 9 peptides. Score 0.305 Round 4: 72 peptides, 12 chains. Longest chain 14 peptides. Score 0.338 Round 5: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 60, 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 4528 restraints for refining 1899 atoms. 4300 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1850 (Rfree = 0.000) for 1899 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1841 (Rfree = 0.000) for 1892 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1586 (Rfree = 0.000) for 1882 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1699 (Rfree = 0.000) for 1876 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 26.62