Mon 24 Dec 01:07:32 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 1zko-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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/1zko-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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 01:07:37 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/1zko-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.2-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 179 and 0 Target number of residues in the AU: 179 Target solvent content: 0.6031 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-3.2-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2176 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: 47.500 3.200 Wilson plot Bfac: 53.76 4004 reflections ( 92.28 % complete ) and 0 restraints for refining 2410 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3498 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3321 (Rfree = 0.000) for 2410 atoms. Found 21 (21 requested) and removed 42 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.48 Search for helices and strands: 0 residues in 0 chains, 2412 seeds are put forward NCS extension: 0 residues added, 2412 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 9 peptides. Score 0.245 Round 2: 114 peptides, 21 chains. Longest chain 12 peptides. Score 0.383 Round 3: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.440 Round 4: 125 peptides, 22 chains. Longest chain 13 peptides. Score 0.426 Round 5: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 3 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4566 restraints for refining 1986 atoms. 4179 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3149 (Rfree = 0.000) for 1986 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 2: After refmac, R = 0.3035 (Rfree = 0.000) for 1973 atoms. Found 9 (17 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2855 (Rfree = 0.000) for 1964 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.2868 (Rfree = 0.000) for 1953 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2656 (Rfree = 0.000) for 1949 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.48 Search for helices and strands: 0 residues in 0 chains, 1988 seeds are put forward NCS extension: 0 residues added, 1988 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 12 peptides. Score 0.325 Round 2: 119 peptides, 21 chains. Longest chain 14 peptides. Score 0.415 Round 3: 123 peptides, 21 chains. Longest chain 13 peptides. Score 0.440 Round 4: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.501 Round 5: 126 peptides, 23 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 4 Chains 20, Residues 109, Estimated correctness of the model 11.7 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4259 restraints for refining 1889 atoms. 3819 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2812 (Rfree = 0.000) for 1889 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 7: After refmac, R = 0.2753 (Rfree = 0.000) for 1877 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. Cycle 8: After refmac, R = 0.2603 (Rfree = 0.000) for 1866 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2416 (Rfree = 0.000) for 1857 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2348 (Rfree = 0.000) for 1848 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 3.43 Search for helices and strands: 0 residues in 0 chains, 1895 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 1915 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 10 peptides. Score 0.294 Round 2: 110 peptides, 18 chains. Longest chain 17 peptides. Score 0.439 Round 3: 126 peptides, 22 chains. Longest chain 11 peptides. Score 0.432 Round 4: 128 peptides, 22 chains. Longest chain 14 peptides. Score 0.444 Round 5: 125 peptides, 20 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 5 Chains 20, Residues 105, Estimated correctness of the model 4.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4325 restraints for refining 1896 atoms. 3925 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2471 (Rfree = 0.000) for 1896 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 12: After refmac, R = 0.2328 (Rfree = 0.000) for 1889 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.2504 (Rfree = 0.000) for 1884 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2277 (Rfree = 0.000) for 1872 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2280 (Rfree = 0.000) for 1865 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 3.43 Search for helices and strands: 0 residues in 0 chains, 1901 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1923 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.344 Round 2: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.367 Round 3: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.348 Round 4: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.454 Round 5: 122 peptides, 21 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 4 Chains 20, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4181 restraints for refining 1860 atoms. 3797 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 1860 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2342 (Rfree = 0.000) for 1861 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.2294 (Rfree = 0.000) for 1856 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2503 (Rfree = 0.000) for 1850 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2298 (Rfree = 0.000) for 1845 atoms. Found 8 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.98 3.41 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: 118 peptides, 22 chains. Longest chain 16 peptides. Score 0.381 Round 2: 130 peptides, 20 chains. Longest chain 15 peptides. Score 0.507 Round 3: 122 peptides, 22 chains. Longest chain 13 peptides. Score 0.407 Round 4: 122 peptides, 22 chains. Longest chain 14 peptides. Score 0.407 Round 5: 120 peptides, 21 chains. Longest chain 15 peptides. Score 0.421 Taking the results from Round 2 Chains 20, Residues 110, Estimated correctness of the model 13.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4078 restraints for refining 1856 atoms. 3658 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2356 (Rfree = 0.000) for 1856 atoms. Found 13 (16 requested) and removed 8 (8 requested) atoms. Cycle 22: After refmac, R = 0.2329 (Rfree = 0.000) for 1857 atoms. Found 13 (16 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2173 (Rfree = 0.000) for 1855 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2094 (Rfree = 0.000) for 1855 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2103 (Rfree = 0.000) for 1847 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 1869 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1890 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.281 Round 2: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.371 Round 3: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.404 Round 4: 114 peptides, 20 chains. Longest chain 14 peptides. Score 0.410 Round 5: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 4 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4241 restraints for refining 1862 atoms. 3885 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2491 (Rfree = 0.000) for 1862 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2412 (Rfree = 0.000) for 1858 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2235 (Rfree = 0.000) for 1862 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2219 (Rfree = 0.000) for 1851 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2220 (Rfree = 0.000) for 1843 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.99 3.42 Search for helices and strands: 0 residues in 0 chains, 1880 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 1892 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 7 peptides. Score 0.288 Round 2: 99 peptides, 19 chains. Longest chain 12 peptides. Score 0.339 Round 3: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.375 Round 4: 113 peptides, 19 chains. Longest chain 13 peptides. Score 0.431 Round 5: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 4 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4271 restraints for refining 1900 atoms. 3885 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2560 (Rfree = 0.000) for 1900 atoms. Found 13 (17 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.2502 (Rfree = 0.000) for 1899 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.2541 (Rfree = 0.000) for 1890 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2469 (Rfree = 0.000) for 1889 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2340 (Rfree = 0.000) for 1889 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.47 Search for helices and strands: 0 residues in 0 chains, 1934 seeds are put forward NCS extension: 0 residues added, 1934 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 8 peptides. Score 0.207 Round 2: 92 peptides, 18 chains. Longest chain 13 peptides. Score 0.319 Round 3: 92 peptides, 18 chains. Longest chain 14 peptides. Score 0.319 Round 4: 106 peptides, 22 chains. Longest chain 10 peptides. Score 0.300 Round 5: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.280 Taking the results from Round 3 Chains 18, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4562 restraints for refining 1925 atoms. 4284 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2449 (Rfree = 0.000) for 1925 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2280 (Rfree = 0.000) for 1919 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2241 (Rfree = 0.000) for 1916 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2131 (Rfree = 0.000) for 1911 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2095 (Rfree = 0.000) for 1906 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 1932 seeds are put forward NCS extension: 0 residues added, 1932 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 7 peptides. Score 0.222 Round 2: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.340 Round 3: 111 peptides, 21 chains. Longest chain 8 peptides. Score 0.363 Round 4: 103 peptides, 19 chains. Longest chain 15 peptides. Score 0.366 Round 5: 104 peptides, 19 chains. Longest chain 8 peptides. Score 0.373 Taking the results from Round 5 Chains 19, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4004 reflections ( 92.28 % complete ) and 4534 restraints for refining 1951 atoms. 4213 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2394 (Rfree = 0.000) for 1951 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2267 (Rfree = 0.000) for 1951 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.2236 (Rfree = 0.000) for 1945 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2252 (Rfree = 0.000) for 1937 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2188 (Rfree = 0.000) for 1932 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 1958 seeds are put forward NCS extension: 0 residues added, 1958 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 9 peptides. Score 0.277 Round 2: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.397 Round 3: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.379 Round 4: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.370 Round 5: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.379 Taking the results from Round 2 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 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4004 reflections ( 92.28 % complete ) and 4567 restraints for refining 1950 atoms. 4293 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2255 (Rfree = 0.000) for 1950 atoms. Found 0 (17 requested) and removed 6 (8 requested) atoms. Cycle 47: After refmac, R = 0.2278 (Rfree = 0.000) for 1941 atoms. Found 0 (17 requested) and removed 5 (8 requested) atoms. Cycle 48: After refmac, R = 0.2357 (Rfree = 0.000) for 1934 atoms. Found 0 (17 requested) and removed 4 (8 requested) atoms. Cycle 49: After refmac, R = 0.2209 (Rfree = 0.000) for 1930 atoms. Found 0 (17 requested) and removed 3 (8 requested) atoms. Writing output files ... TimeTaking 28.9