Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ouw-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ouw-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-hancs/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 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.6367 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-3.2-parrot-hancs.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-3.2-parrot-hancs.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 3.200 Wilson plot Bfac: 69.09 4672 reflections ( 99.85 % complete ) and 0 restraints for refining 2447 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3445 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3286 (Rfree = 0.000) for 2447 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2518 seeds are put forward NCS extension: 0 residues added, 2518 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.243 Round 2: 108 peptides, 20 chains. Longest chain 8 peptides. Score 0.370 Round 3: 139 peptides, 25 chains. Longest chain 14 peptides. Score 0.432 Round 4: 144 peptides, 24 chains. Longest chain 14 peptides. Score 0.486 Round 5: 143 peptides, 22 chains. Longest chain 13 peptides. Score 0.528 Taking the results from Round 5 Chains 22, Residues 121, Estimated correctness of the model 20.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4603 restraints for refining 2015 atoms. 4103 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2861 (Rfree = 0.000) for 2015 atoms. Found 18 (18 requested) and removed 45 (9 requested) atoms. Cycle 2: After refmac, R = 0.2862 (Rfree = 0.000) for 1969 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 3: After refmac, R = 0.2535 (Rfree = 0.000) for 1942 atoms. Found 10 (17 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2502 (Rfree = 0.000) for 1931 atoms. Found 7 (17 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.2758 (Rfree = 0.000) for 1921 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.63 Search for helices and strands: 0 residues in 0 chains, 2008 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2025 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.243 Round 2: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.291 Round 3: 115 peptides, 21 chains. Longest chain 13 peptides. Score 0.388 Round 4: 123 peptides, 24 chains. Longest chain 8 peptides. Score 0.358 Round 5: 122 peptides, 22 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Chains 22, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4500 restraints for refining 1931 atoms. 4122 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3284 (Rfree = 0.000) for 1931 atoms. Found 17 (17 requested) and removed 40 (8 requested) atoms. Cycle 7: After refmac, R = 0.2816 (Rfree = 0.000) for 1902 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2810 (Rfree = 0.000) for 1898 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2871 (Rfree = 0.000) for 1891 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.3012 (Rfree = 0.000) for 1891 atoms. Found 15 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.61 Search for helices and strands: 0 residues in 0 chains, 1985 seeds are put forward NCS extension: 0 residues added, 1985 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 11 peptides. Score 0.311 Round 2: 119 peptides, 22 chains. Longest chain 10 peptides. Score 0.386 Round 3: 119 peptides, 20 chains. Longest chain 13 peptides. Score 0.440 Round 4: 113 peptides, 20 chains. Longest chain 14 peptides. Score 0.402 Round 5: 122 peptides, 20 chains. Longest chain 16 peptides. Score 0.458 Taking the results from Round 5 Chains 20, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4117 restraints for refining 1847 atoms. 3729 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2862 (Rfree = 0.000) for 1847 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 12: After refmac, R = 0.2848 (Rfree = 0.000) for 1842 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 13: After refmac, R = 0.2778 (Rfree = 0.000) for 1846 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 14: After refmac, R = 0.2426 (Rfree = 0.000) for 1844 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2395 (Rfree = 0.000) for 1837 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.64 Search for helices and strands: 0 residues in 0 chains, 1926 seeds are put forward NCS extension: 0 residues added, 1926 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 10 peptides. Score 0.314 Round 2: 121 peptides, 18 chains. Longest chain 18 peptides. Score 0.503 Round 3: 122 peptides, 20 chains. Longest chain 15 peptides. Score 0.458 Round 4: 130 peptides, 21 chains. Longest chain 15 peptides. Score 0.480 Round 5: 117 peptides, 19 chains. Longest chain 9 peptides. Score 0.454 Taking the results from Round 2 Chains 18, Residues 103, Estimated correctness of the model 12.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4048 restraints for refining 1839 atoms. 3654 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2625 (Rfree = 0.000) for 1839 atoms. Found 12 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2695 (Rfree = 0.000) for 1836 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2688 (Rfree = 0.000) for 1840 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2681 (Rfree = 0.000) for 1843 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.2695 (Rfree = 0.000) for 1843 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 1914 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 1945 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 9 peptides. Score 0.272 Round 2: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Round 3: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.409 Round 4: 102 peptides, 17 chains. Longest chain 9 peptides. Score 0.415 Round 5: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.454 Taking the results from Round 5 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4326 restraints for refining 1915 atoms. 3953 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2864 (Rfree = 0.000) for 1915 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 22: After refmac, R = 0.2917 (Rfree = 0.000) for 1905 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2468 (Rfree = 0.000) for 1907 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2578 (Rfree = 0.000) for 1908 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2406 (Rfree = 0.000) for 1915 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 2003 seeds are put forward NCS extension: 0 residues added, 2003 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.309 Round 2: 114 peptides, 17 chains. Longest chain 18 peptides. Score 0.488 Round 3: 101 peptides, 16 chains. Longest chain 16 peptides. Score 0.436 Round 4: 109 peptides, 15 chains. Longest chain 16 peptides. Score 0.511 Round 5: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.397 Taking the results from Round 4 Chains 15, Residues 94, Estimated correctness of the model 14.9 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4672 reflections ( 99.85 % complete ) and 4414 restraints for refining 1947 atoms. 4030 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2567 (Rfree = 0.000) for 1947 atoms. Found 16 (17 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.2467 (Rfree = 0.000) for 1948 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.2468 (Rfree = 0.000) for 1940 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2351 (Rfree = 0.000) for 1938 atoms. Found 8 (17 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2434 (Rfree = 0.000) for 1936 atoms. Found 13 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2048 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.331 Round 2: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.408 Round 3: 106 peptides, 17 chains. Longest chain 17 peptides. Score 0.440 Round 4: 98 peptides, 14 chains. Longest chain 17 peptides. Score 0.472 Round 5: 100 peptides, 15 chains. Longest chain 17 peptides. Score 0.457 Taking the results from Round 4 Chains 14, Residues 84, Estimated correctness of the model 2.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4672 reflections ( 99.85 % complete ) and 4790 restraints for refining 2003 atoms. 4468 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2602 (Rfree = 0.000) for 2003 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2684 (Rfree = 0.000) for 2003 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2632 (Rfree = 0.000) for 2010 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.2686 (Rfree = 0.000) for 2015 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.2235 (Rfree = 0.000) for 2013 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.59 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2126 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.239 Round 2: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.316 Round 3: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.302 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.338 Round 5: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.336 Taking the results from Round 4 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4688 restraints for refining 1982 atoms. 4420 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2387 (Rfree = 0.000) for 1982 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 37: After refmac, R = 0.2365 (Rfree = 0.000) for 1982 atoms. Found 14 (17 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2156 (Rfree = 0.000) for 1983 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2175 (Rfree = 0.000) for 1981 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.2378 (Rfree = 0.000) for 1977 atoms. Found 16 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.63 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 0 residues added, 2048 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.272 Round 2: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.302 Round 3: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.360 Round 4: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.350 Round 5: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4751 restraints for refining 1984 atoms. 4514 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2473 (Rfree = 0.000) for 1984 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 42: After refmac, R = 0.2243 (Rfree = 0.000) for 1987 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2246 (Rfree = 0.000) for 1987 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.2159 (Rfree = 0.000) for 1985 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2206 (Rfree = 0.000) for 1982 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Round 2: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.264 Round 3: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.304 Round 4: 69 peptides, 12 chains. Longest chain 8 peptides. Score 0.338 Round 5: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.306 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 57, 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. 4672 reflections ( 99.85 % complete ) and 4689 restraints for refining 1982 atoms. 4473 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2617 (Rfree = 0.000) for 1982 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2676 (Rfree = 0.000) for 1973 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2310 (Rfree = 0.000) for 1963 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2241 (Rfree = 0.000) for 1954 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 51.63