Mon 24 Dec 00:18:53 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 2ouw-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.6-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/2ouw-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.6-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 00:18:57 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/2ouw-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.6-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 158 and 0 Target number of residues in the AU: 158 Target solvent content: 0.6521 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-3.6-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.70 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: 108.355 3.601 Wilson plot Bfac: 79.25 3346 reflections ( 99.79 % complete ) and 0 restraints for refining 2434 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3711 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3383 (Rfree = 0.000) for 2434 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 2481 seeds are put forward NCS extension: 0 residues added, 2481 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 6 peptides. Score 0.220 Round 2: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.321 Round 3: 116 peptides, 22 chains. Longest chain 8 peptides. Score 0.367 Round 4: 124 peptides, 20 chains. Longest chain 11 peptides. Score 0.470 Round 5: 125 peptides, 20 chains. Longest chain 11 peptides. Score 0.476 Taking the results from Round 5 Chains 20, Residues 105, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4635 restraints for refining 2001 atoms. 4205 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3210 (Rfree = 0.000) for 2001 atoms. Found 11 (12 requested) and removed 18 (6 requested) atoms. Cycle 2: After refmac, R = 0.3183 (Rfree = 0.000) for 1956 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 3: After refmac, R = 0.2867 (Rfree = 0.000) for 1943 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2963 (Rfree = 0.000) for 1924 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.2897 (Rfree = 0.000) for 1909 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 1987 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 1998 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 7 peptides. Score 0.281 Round 2: 112 peptides, 21 chains. Longest chain 8 peptides. Score 0.368 Round 3: 115 peptides, 20 chains. Longest chain 11 peptides. Score 0.415 Round 4: 114 peptides, 20 chains. Longest chain 8 peptides. Score 0.409 Round 5: 117 peptides, 20 chains. Longest chain 9 peptides. Score 0.428 Taking the results from Round 5 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4166 restraints for refining 1823 atoms. 3798 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2793 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.2705 (Rfree = 0.000) for 1795 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 1784 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2060 (Rfree = 0.000) for 1776 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2226 (Rfree = 0.000) for 1774 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 1871 seeds are put forward NCS extension: 0 residues added, 1871 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 6 peptides. Score 0.264 Round 2: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.424 Round 3: 123 peptides, 22 chains. Longest chain 9 peptides. Score 0.412 Round 4: 121 peptides, 21 chains. Longest chain 10 peptides. Score 0.426 Round 5: 124 peptides, 20 chains. Longest chain 11 peptides. Score 0.470 Taking the results from Round 5 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4118 restraints for refining 1854 atoms. 3689 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2597 (Rfree = 0.000) for 1854 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.2305 (Rfree = 0.000) for 1833 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2552 (Rfree = 0.000) for 1827 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 14: After refmac, R = 0.2508 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2584 (Rfree = 0.000) for 1821 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward NCS extension: 0 residues added, 1923 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 11 peptides. Score 0.294 Round 2: 117 peptides, 20 chains. Longest chain 12 peptides. Score 0.428 Round 3: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.470 Round 4: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.378 Round 5: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.446 Taking the results from Round 3 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 3908 restraints for refining 1837 atoms. 3520 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2519 (Rfree = 0.000) for 1837 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 17: After refmac, R = 0.2502 (Rfree = 0.000) for 1815 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2384 (Rfree = 0.000) for 1811 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 19: After refmac, R = 0.2424 (Rfree = 0.000) for 1808 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.1973 (Rfree = 0.000) for 1808 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.97 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: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.266 Round 2: 101 peptides, 18 chains. Longest chain 11 peptides. Score 0.380 Round 3: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.431 Round 4: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.438 Round 5: 113 peptides, 19 chains. Longest chain 10 peptides. Score 0.429 Taking the results from Round 4 Chains 18, Residues 92, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4338 restraints for refining 1904 atoms. 3960 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2619 (Rfree = 0.000) for 1904 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.2785 (Rfree = 0.000) for 1880 atoms. Found 12 (12 requested) and removed 43 (6 requested) atoms. Cycle 23: After refmac, R = 0.2877 (Rfree = 0.000) for 1845 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 24: After refmac, R = 0.2872 (Rfree = 0.000) for 1821 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 25: After refmac, R = 0.2766 (Rfree = 0.000) for 1810 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 1905 seeds are put forward NCS extension: 0 residues added, 1905 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 7 peptides. Score 0.225 Round 2: 89 peptides, 18 chains. Longest chain 7 peptides. Score 0.297 Round 3: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.329 Round 4: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.304 Round 5: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.339 Taking the results from Round 5 Chains 18, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4275 restraints for refining 1866 atoms. 3985 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2852 (Rfree = 0.000) for 1866 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.2940 (Rfree = 0.000) for 1852 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 28: After refmac, R = 0.2771 (Rfree = 0.000) for 1837 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.3012 (Rfree = 0.000) for 1835 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 30: After refmac, R = 0.2870 (Rfree = 0.000) for 1830 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 1899 seeds are put forward NCS extension: 0 residues added, 1899 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.258 Round 2: 61 peptides, 11 chains. Longest chain 12 peptides. Score 0.311 Round 3: 55 peptides, 9 chains. Longest chain 12 peptides. Score 0.334 Round 4: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.315 Round 5: 62 peptides, 10 chains. Longest chain 11 peptides. Score 0.352 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4066 restraints for refining 1771 atoms. 3868 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2908 (Rfree = 0.000) for 1771 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 32: After refmac, R = 0.2598 (Rfree = 0.000) for 1752 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 33: After refmac, R = 0.2245 (Rfree = 0.000) for 1737 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.2150 (Rfree = 0.000) for 1734 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2177 (Rfree = 0.000) for 1733 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward NCS extension: 0 residues added, 1819 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 7 peptides. Score 0.209 Round 2: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.245 Round 3: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.294 Round 4: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.343 Round 5: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.336 Taking the results from Round 4 Chains 16, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 3961 restraints for refining 1795 atoms. 3693 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2429 (Rfree = 0.000) for 1795 atoms. Found 6 (11 requested) and removed 17 (5 requested) atoms. Cycle 37: After refmac, R = 0.2523 (Rfree = 0.000) for 1779 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.2532 (Rfree = 0.000) for 1776 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2562 (Rfree = 0.000) for 1776 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.2378 (Rfree = 0.000) for 1775 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.81 Search for helices and strands: 0 residues in 0 chains, 1841 seeds are put forward NCS extension: 0 residues added, 1841 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.249 Round 2: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.340 Round 3: 72 peptides, 15 chains. Longest chain 9 peptides. Score 0.264 Round 4: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.294 Round 5: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Chains 13, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3346 reflections ( 99.79 % complete ) and 4182 restraints for refining 1820 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2679 (Rfree = 0.000) for 1820 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 42: After refmac, R = 0.2643 (Rfree = 0.000) for 1812 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 43: After refmac, R = 0.2605 (Rfree = 0.000) for 1805 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2644 (Rfree = 0.000) for 1802 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 45: After refmac, R = 0.2630 (Rfree = 0.000) for 1799 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 1871 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1874 seeds are put forward Round 1: 76 peptides, 18 chains. Longest chain 5 peptides. Score 0.199 Round 2: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.247 Round 3: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.322 Round 4: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.320 Round 5: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.296 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 68, 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 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3346 reflections ( 99.79 % complete ) and 4320 restraints for refining 1869 atoms. 4064 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2720 (Rfree = 0.000) for 1869 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2675 (Rfree = 0.000) for 1862 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2692 (Rfree = 0.000) for 1853 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2552 (Rfree = 0.000) for 1846 atoms. TimeTaking 35.12