Mon 24 Dec 07:51:35 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 2ooj-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ooj-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.8-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/2ooj-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.8-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 07:51:40 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/2ooj-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ooj-3.8-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6323 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-3.8-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: 19 Cell parameters: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.65 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: 53.043 3.800 Wilson plot Bfac: 66.95 2963 reflections ( 98.87 % complete ) and 0 restraints for refining 2489 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3695 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2895 (Rfree = 0.000) for 2489 atoms. Found 5 (13 requested) and removed 27 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 2488 seeds are put forward NCS extension: 0 residues added, 2488 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 8 peptides. Score 0.230 Round 2: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.266 Round 3: 99 peptides, 20 chains. Longest chain 10 peptides. Score 0.297 Round 4: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.309 Round 5: 103 peptides, 19 chains. Longest chain 12 peptides. Score 0.348 Taking the results from Round 5 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4930 restraints for refining 2041 atoms. 4613 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2787 (Rfree = 0.000) for 2041 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 2: After refmac, R = 0.2625 (Rfree = 0.000) for 2026 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2555 (Rfree = 0.000) for 2018 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2510 (Rfree = 0.000) for 2009 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2466 (Rfree = 0.000) for 1999 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward NCS extension: 0 residues added, 2025 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 9 peptides. Score 0.233 Round 2: 96 peptides, 20 chains. Longest chain 8 peptides. Score 0.277 Round 3: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.317 Round 4: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Round 5: 111 peptides, 20 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 4 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4953 restraints for refining 1962 atoms. 4653 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2581 (Rfree = 0.000) for 1962 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 7: After refmac, R = 0.2404 (Rfree = 0.000) for 1943 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2365 (Rfree = 0.000) for 1934 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2340 (Rfree = 0.000) for 1926 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2294 (Rfree = 0.000) for 1918 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1956 seeds are put forward NCS extension: 0 residues added, 1956 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 9 peptides. Score 0.288 Round 2: 108 peptides, 19 chains. Longest chain 13 peptides. Score 0.379 Round 3: 114 peptides, 18 chains. Longest chain 13 peptides. Score 0.439 Round 4: 115 peptides, 20 chains. Longest chain 15 peptides. Score 0.395 Round 5: 127 peptides, 22 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 3 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2963 reflections ( 98.87 % complete ) and 4675 restraints for refining 1935 atoms. 4309 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2620 (Rfree = 0.000) for 1935 atoms. Found 6 (10 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2498 (Rfree = 0.000) for 1925 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2441 (Rfree = 0.000) for 1919 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2406 (Rfree = 0.000) for 1913 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2385 (Rfree = 0.000) for 1909 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1947 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1966 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.322 Round 2: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.352 Round 3: 99 peptides, 17 chains. Longest chain 18 peptides. Score 0.377 Round 4: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.362 Round 5: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4906 restraints for refining 1996 atoms. 4579 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2717 (Rfree = 0.000) for 1996 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.2601 (Rfree = 0.000) for 1992 atoms. Found 1 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2588 (Rfree = 0.000) for 1982 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2584 (Rfree = 0.000) for 1975 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2562 (Rfree = 0.000) for 1971 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 2003 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2018 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.317 Round 2: 100 peptides, 17 chains. Longest chain 12 peptides. Score 0.383 Round 3: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.393 Round 4: 102 peptides, 16 chains. Longest chain 12 peptides. Score 0.420 Round 5: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 4 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4959 restraints for refining 2036 atoms. 4586 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2708 (Rfree = 0.000) for 2036 atoms. Found 6 (11 requested) and removed 14 (5 requested) atoms. Cycle 22: After refmac, R = 0.2573 (Rfree = 0.000) for 2024 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 23: After refmac, R = 0.2601 (Rfree = 0.000) for 2016 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2474 (Rfree = 0.000) for 2004 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2458 (Rfree = 0.000) for 1997 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2040 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 7 peptides. Score 0.276 Round 2: 87 peptides, 15 chains. Longest chain 8 peptides. Score 0.356 Round 3: 88 peptides, 15 chains. Longest chain 19 peptides. Score 0.363 Round 4: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.360 Round 5: 107 peptides, 17 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 5 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5093 restraints for refining 2039 atoms. 4750 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2641 (Rfree = 0.000) for 2039 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.2524 (Rfree = 0.000) for 2028 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2494 (Rfree = 0.000) for 2021 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2457 (Rfree = 0.000) for 2013 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2439 (Rfree = 0.000) for 2010 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 2046 seeds are put forward NCS extension: 0 residues added, 2046 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 6 peptides. Score 0.253 Round 2: 93 peptides, 17 chains. Longest chain 8 peptides. Score 0.340 Round 3: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.409 Round 4: 99 peptides, 16 chains. Longest chain 8 peptides. Score 0.403 Round 5: 106 peptides, 15 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 5 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4916 restraints for refining 2041 atoms. 4520 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2703 (Rfree = 0.000) for 2041 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2636 (Rfree = 0.000) for 2038 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2604 (Rfree = 0.000) for 2029 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2597 (Rfree = 0.000) for 2021 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2583 (Rfree = 0.000) for 2019 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2075 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.259 Round 2: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.325 Round 3: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.364 Round 4: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.385 Round 5: 83 peptides, 13 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 5 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 5198 restraints for refining 2041 atoms. 4913 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2681 (Rfree = 0.000) for 2041 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.2559 (Rfree = 0.000) for 2039 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2512 (Rfree = 0.000) for 2032 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2485 (Rfree = 0.000) for 2028 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2469 (Rfree = 0.000) for 2021 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 0 residues added, 2044 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 10 peptides. Score 0.284 Round 2: 100 peptides, 18 chains. Longest chain 16 peptides. Score 0.356 Round 3: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.362 Round 4: 114 peptides, 15 chains. Longest chain 21 peptides. Score 0.510 Round 5: 112 peptides, 20 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 4 Chains 16, Residues 99, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2963 reflections ( 98.87 % complete ) and 4826 restraints for refining 2041 atoms. 4408 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2650 (Rfree = 0.000) for 2041 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 42: After refmac, R = 0.2531 (Rfree = 0.000) for 2036 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2481 (Rfree = 0.000) for 2032 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2481 (Rfree = 0.000) for 2025 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2469 (Rfree = 0.000) for 2019 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 2059 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2071 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 9 peptides. Score 0.254 Round 2: 98 peptides, 15 chains. Longest chain 22 peptides. Score 0.423 Round 3: 97 peptides, 17 chains. Longest chain 18 peptides. Score 0.364 Round 4: 94 peptides, 14 chains. Longest chain 21 peptides. Score 0.426 Round 5: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 80, 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 2ooj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2963 reflections ( 98.87 % complete ) and 5083 restraints for refining 2040 atoms. 4777 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2539 (Rfree = 0.000) for 2040 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2490 (Rfree = 0.000) for 2028 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2463 (Rfree = 0.000) for 2023 atoms. Found 0 (11 requested) and removed 3 (5 requested) atoms. Cycle 49: After refmac, R = 0.2436 (Rfree = 0.000) for 2020 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Writing output files ... TimeTaking 28.08