Mon 24 Dec 07:57:40 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 2ouw-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ouw-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-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/2ouw-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-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 07:57:44 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/2ouw-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-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 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-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: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.2-parrot-noncs.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 2446 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3484 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3235 (Rfree = 0.000) for 2446 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.81 Search for helices and strands: 0 residues in 0 chains, 2510 seeds are put forward NCS extension: 0 residues added, 2510 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.311 Round 2: 127 peptides, 23 chains. Longest chain 10 peptides. Score 0.410 Round 3: 138 peptides, 22 chains. Longest chain 12 peptides. Score 0.501 Round 4: 137 peptides, 23 chains. Longest chain 10 peptides. Score 0.471 Round 5: 151 peptides, 25 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 5 Chains 25, Residues 126, Estimated correctness of the model 12.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4525 restraints for refining 2016 atoms. 4010 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2939 (Rfree = 0.000) for 2016 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 2: After refmac, R = 0.2874 (Rfree = 0.000) for 1977 atoms. Found 15 (17 requested) and removed 29 (8 requested) atoms. Cycle 3: After refmac, R = 0.2780 (Rfree = 0.000) for 1952 atoms. Found 11 (17 requested) and removed 28 (8 requested) atoms. Cycle 4: After refmac, R = 0.2531 (Rfree = 0.000) for 1931 atoms. Found 8 (17 requested) and removed 22 (8 requested) atoms. Cycle 5: After refmac, R = 0.2628 (Rfree = 0.000) for 1911 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 2011 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2014 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 7 peptides. Score 0.228 Round 2: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.362 Round 3: 110 peptides, 22 chains. Longest chain 9 peptides. Score 0.327 Round 4: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.427 Round 5: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4733 restraints for refining 1982 atoms. 4377 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2606 (Rfree = 0.000) for 1982 atoms. Found 12 (17 requested) and removed 21 (8 requested) atoms. Cycle 7: After refmac, R = 0.2829 (Rfree = 0.000) for 1967 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 8: After refmac, R = 0.2747 (Rfree = 0.000) for 1950 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 9: After refmac, R = 0.2350 (Rfree = 0.000) for 1946 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 10: After refmac, R = 0.2276 (Rfree = 0.000) for 1936 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 5 residues added (0 deleted due to clashes), 2031 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 7 peptides. Score 0.221 Round 2: 109 peptides, 22 chains. Longest chain 9 peptides. Score 0.320 Round 3: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.327 Round 4: 113 peptides, 21 chains. Longest chain 8 peptides. Score 0.375 Round 5: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.358 Taking the results from Round 4 Chains 21, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4582 restraints for refining 1972 atoms. 4235 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3138 (Rfree = 0.000) for 1972 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 12: After refmac, R = 0.2726 (Rfree = 0.000) for 1948 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 13: After refmac, R = 0.2686 (Rfree = 0.000) for 1938 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2632 (Rfree = 0.000) for 1938 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 15: After refmac, R = 0.2702 (Rfree = 0.000) for 1935 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward NCS extension: 0 residues added, 2016 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 6 peptides. Score 0.191 Round 2: 92 peptides, 18 chains. Longest chain 10 peptides. Score 0.318 Round 3: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.334 Round 4: 100 peptides, 17 chains. Longest chain 10 peptides. Score 0.402 Round 5: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 5 Chains 16, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4487 restraints for refining 1927 atoms. 4175 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2576 (Rfree = 0.000) for 1927 atoms. Found 16 (17 requested) and removed 22 (8 requested) atoms. Cycle 17: After refmac, R = 0.2705 (Rfree = 0.000) for 1915 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2744 (Rfree = 0.000) for 1915 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 19: After refmac, R = 0.2689 (Rfree = 0.000) for 1916 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 20: After refmac, R = 0.2345 (Rfree = 0.000) for 1908 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 1992 seeds are put forward NCS extension: 0 residues added, 1992 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.247 Round 2: 97 peptides, 19 chains. Longest chain 10 peptides. Score 0.324 Round 3: 91 peptides, 15 chains. Longest chain 13 peptides. Score 0.400 Round 4: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.355 Round 5: 95 peptides, 18 chains. Longest chain 7 peptides. Score 0.339 Taking the results from Round 3 Chains 15, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4570 restraints for refining 1943 atoms. 4281 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2639 (Rfree = 0.000) for 1943 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 22: After refmac, R = 0.2940 (Rfree = 0.000) for 1936 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 23: After refmac, R = 0.2586 (Rfree = 0.000) for 1931 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.2306 (Rfree = 0.000) for 1931 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2240 (Rfree = 0.000) for 1926 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 1999 seeds are put forward NCS extension: 0 residues added, 1999 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.238 Round 2: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.397 Round 3: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.302 Round 4: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.331 Round 5: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 2 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4517 restraints for refining 1938 atoms. 4217 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2685 (Rfree = 0.000) for 1938 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2436 (Rfree = 0.000) for 1937 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2346 (Rfree = 0.000) for 1930 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2336 (Rfree = 0.000) for 1923 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2358 (Rfree = 0.000) for 1916 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 0 residues added, 1997 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 5 peptides. Score 0.221 Round 2: 100 peptides, 21 chains. Longest chain 9 peptides. Score 0.286 Round 3: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.284 Round 4: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.391 Round 5: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.412 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4484 restraints for refining 1954 atoms. 4137 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2753 (Rfree = 0.000) for 1954 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 32: After refmac, R = 0.2704 (Rfree = 0.000) for 1952 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.3049 (Rfree = 0.000) for 1956 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 34: After refmac, R = 0.3243 (Rfree = 0.000) for 1954 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 35: After refmac, R = 0.2795 (Rfree = 0.000) for 1952 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 0 residues added, 2054 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 7 peptides. Score 0.244 Round 2: 99 peptides, 19 chains. Longest chain 11 peptides. Score 0.338 Round 3: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.393 Round 4: 105 peptides, 20 chains. Longest chain 12 peptides. Score 0.350 Round 5: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 5 Chains 19, Residues 89, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4443 restraints for refining 1966 atoms. 4082 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2640 (Rfree = 0.000) for 1966 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.2631 (Rfree = 0.000) for 1962 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.3221 (Rfree = 0.000) for 1961 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 39: After refmac, R = 0.2774 (Rfree = 0.000) for 1953 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.3279 (Rfree = 0.000) for 1954 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.59 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: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.224 Round 2: 93 peptides, 19 chains. Longest chain 10 peptides. Score 0.295 Round 3: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.281 Round 4: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Round 5: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 5 Chains 16, Residues 74, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4296 restraints for refining 1942 atoms. 3995 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2837 (Rfree = 0.000) for 1942 atoms. Found 12 (17 requested) and removed 19 (8 requested) atoms. Cycle 42: After refmac, R = 0.2798 (Rfree = 0.000) for 1934 atoms. Found 16 (17 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2780 (Rfree = 0.000) for 1934 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 44: After refmac, R = 0.2727 (Rfree = 0.000) for 1934 atoms. Found 14 (17 requested) and removed 14 (8 requested) atoms. Cycle 45: After refmac, R = 0.2678 (Rfree = 0.000) for 1927 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.63 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 0 residues added, 1996 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 6 peptides. Score 0.239 Round 2: 84 peptides, 17 chains. Longest chain 7 peptides. Score 0.291 Round 3: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 4: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.293 Round 5: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.324 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 78, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2ouw-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (78 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4672 reflections ( 99.85 % complete ) and 3991 restraints for refining 1847 atoms. 3678 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2860 (Rfree = 0.000) for 1847 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.3053 (Rfree = 0.000) for 1835 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.3491 (Rfree = 0.000) for 1825 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2659 (Rfree = 0.000) for 1814 atoms. TimeTaking 32.22