null Mon 24 Dec 07:59:55 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 2o8q-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-4.0-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/2o8q-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-4.0-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 07:59:59 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/2o8q-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-4.0-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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.6541 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-4.0-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.90 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: 29.026 4.000 Wilson plot Bfac: 80.46 3635 reflections ( 98.22 % complete ) and 0 restraints for refining 2361 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3133 (Rfree = 0.000) for 2361 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.07 Search for helices and strands: 0 residues in 0 chains, 2378 seeds are put forward NCS extension: 0 residues added, 2378 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.308 Round 2: 146 peptides, 24 chains. Longest chain 13 peptides. Score 0.400 Round 3: 165 peptides, 24 chains. Longest chain 16 peptides. Score 0.474 Round 4: 160 peptides, 23 chains. Longest chain 20 peptides. Score 0.472 Round 5: 159 peptides, 21 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 5 Chains 22, Residues 138, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4304 restraints for refining 1936 atoms. 3717 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2574 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2629 (Rfree = 0.000) for 1917 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2629 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 4: After refmac, R = 0.2421 (Rfree = 0.000) for 1892 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2596 (Rfree = 0.000) for 1886 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.03 Search for helices and strands: 0 residues in 0 chains, 1908 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1922 seeds are put forward Round 1: 165 peptides, 26 chains. Longest chain 14 peptides. Score 0.440 Round 2: 162 peptides, 22 chains. Longest chain 21 peptides. Score 0.496 Round 3: 157 peptides, 19 chains. Longest chain 17 peptides. Score 0.527 Round 4: 183 peptides, 19 chains. Longest chain 28 peptides. Score 0.612 Round 5: 173 peptides, 21 chains. Longest chain 22 peptides. Score 0.550 Taking the results from Round 4 Chains 19, Residues 164, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4049 restraints for refining 1936 atoms. 3364 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2715 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 7: After refmac, R = 0.2690 (Rfree = 0.000) for 1898 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2472 (Rfree = 0.000) for 1884 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 9: After refmac, R = 0.2537 (Rfree = 0.000) for 1866 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2231 (Rfree = 0.000) for 1856 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.03 Search for helices and strands: 0 residues in 0 chains, 1888 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 1918 seeds are put forward Round 1: 161 peptides, 27 chains. Longest chain 12 peptides. Score 0.407 Round 2: 154 peptides, 20 chains. Longest chain 16 peptides. Score 0.500 Round 3: 154 peptides, 19 chains. Longest chain 19 peptides. Score 0.517 Round 4: 164 peptides, 18 chains. Longest chain 25 peptides. Score 0.567 Round 5: 165 peptides, 19 chains. Longest chain 16 peptides. Score 0.555 Taking the results from Round 4 Chains 19, Residues 146, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4027 restraints for refining 1936 atoms. 3371 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2759 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.2593 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2707 (Rfree = 0.000) for 1880 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 14: After refmac, R = 0.2520 (Rfree = 0.000) for 1863 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 15: After refmac, R = 0.2511 (Rfree = 0.000) for 1851 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.01 Search for helices and strands: 0 residues in 0 chains, 1880 seeds are put forward NCS extension: 0 residues added, 1880 seeds are put forward Round 1: 147 peptides, 24 chains. Longest chain 11 peptides. Score 0.404 Round 2: 161 peptides, 23 chains. Longest chain 14 peptides. Score 0.476 Round 3: 155 peptides, 22 chains. Longest chain 15 peptides. Score 0.470 Round 4: 166 peptides, 22 chains. Longest chain 22 peptides. Score 0.510 Round 5: 169 peptides, 22 chains. Longest chain 21 peptides. Score 0.521 Taking the results from Round 5 Chains 22, Residues 147, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4162 restraints for refining 1936 atoms. 3571 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2624 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 17: After refmac, R = 0.2576 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 18: After refmac, R = 0.2269 (Rfree = 0.000) for 1895 atoms. Found 6 (9 requested) and removed 15 (4 requested) atoms. Cycle 19: After refmac, R = 0.2459 (Rfree = 0.000) for 1880 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 20: After refmac, R = 0.2467 (Rfree = 0.000) for 1870 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.09 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 40 residues added (5 deleted due to clashes), 1937 seeds are put forward Round 1: 139 peptides, 25 chains. Longest chain 11 peptides. Score 0.352 Round 2: 151 peptides, 23 chains. Longest chain 17 peptides. Score 0.437 Round 3: 159 peptides, 25 chains. Longest chain 15 peptides. Score 0.434 Round 4: 156 peptides, 20 chains. Longest chain 20 peptides. Score 0.507 Round 5: 157 peptides, 22 chains. Longest chain 12 peptides. Score 0.478 Taking the results from Round 4 Chains 20, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4400 restraints for refining 1936 atoms. 3876 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2822 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 22: After refmac, R = 0.2683 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.2459 (Rfree = 0.000) for 1886 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2650 (Rfree = 0.000) for 1863 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 25: After refmac, R = 0.2599 (Rfree = 0.000) for 1850 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.05 Search for helices and strands: 0 residues in 0 chains, 1912 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1939 seeds are put forward Round 1: 138 peptides, 24 chains. Longest chain 12 peptides. Score 0.366 Round 2: 152 peptides, 26 chains. Longest chain 11 peptides. Score 0.389 Round 3: 158 peptides, 27 chains. Longest chain 12 peptides. Score 0.395 Round 4: 158 peptides, 26 chains. Longest chain 11 peptides. Score 0.413 Round 5: 153 peptides, 24 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 5 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4346 restraints for refining 1934 atoms. 3831 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2880 (Rfree = 0.000) for 1934 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.2744 (Rfree = 0.000) for 1902 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2659 (Rfree = 0.000) for 1875 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2587 (Rfree = 0.000) for 1862 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.2405 (Rfree = 0.000) for 1844 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.10 Search for helices and strands: 0 residues in 0 chains, 1904 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1923 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 11 peptides. Score 0.291 Round 2: 135 peptides, 23 chains. Longest chain 13 peptides. Score 0.372 Round 3: 146 peptides, 23 chains. Longest chain 20 peptides. Score 0.418 Round 4: 141 peptides, 23 chains. Longest chain 12 peptides. Score 0.397 Round 5: 146 peptides, 22 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 5 Chains 22, Residues 124, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4342 restraints for refining 1933 atoms. 3843 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2599 (Rfree = 0.000) for 1933 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.2896 (Rfree = 0.000) for 1929 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 33: After refmac, R = 0.2603 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 34: After refmac, R = 0.2571 (Rfree = 0.000) for 1884 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 35: After refmac, R = 0.2360 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.08 Search for helices and strands: 0 residues in 0 chains, 1926 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1949 seeds are put forward Round 1: 127 peptides, 25 chains. Longest chain 8 peptides. Score 0.299 Round 2: 140 peptides, 24 chains. Longest chain 10 peptides. Score 0.375 Round 3: 143 peptides, 24 chains. Longest chain 11 peptides. Score 0.387 Round 4: 146 peptides, 22 chains. Longest chain 14 peptides. Score 0.435 Round 5: 152 peptides, 23 chains. Longest chain 12 peptides. Score 0.441 Taking the results from Round 5 Chains 24, Residues 129, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4336 restraints for refining 1935 atoms. 3826 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2759 (Rfree = 0.000) for 1935 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.2477 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 38: After refmac, R = 0.2565 (Rfree = 0.000) for 1903 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 39: After refmac, R = 0.2453 (Rfree = 0.000) for 1883 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2346 (Rfree = 0.000) for 1877 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1958 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.282 Round 2: 126 peptides, 20 chains. Longest chain 12 peptides. Score 0.390 Round 3: 142 peptides, 22 chains. Longest chain 17 peptides. Score 0.419 Round 4: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.414 Round 5: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 3 Chains 24, Residues 120, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4245 restraints for refining 1936 atoms. 3755 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2618 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.2651 (Rfree = 0.000) for 1918 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 43: After refmac, R = 0.2477 (Rfree = 0.000) for 1906 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 44: After refmac, R = 0.2549 (Rfree = 0.000) for 1895 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 45: After refmac, R = 0.2428 (Rfree = 0.000) for 1879 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.07 Search for helices and strands: 0 residues in 0 chains, 1918 seeds are put forward NCS extension: 0 residues added, 1918 seeds are put forward Round 1: 132 peptides, 25 chains. Longest chain 12 peptides. Score 0.321 Round 2: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.384 Round 3: 136 peptides, 22 chains. Longest chain 11 peptides. Score 0.395 Round 4: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.421 Round 5: 150 peptides, 23 chains. Longest chain 11 peptides. Score 0.433 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 127, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2o8q-4_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (127 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3635 reflections ( 98.22 % complete ) and 4324 restraints for refining 1936 atoms. 3813 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2475 (Rfree = 0.000) for 1936 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2668 (Rfree = 0.000) for 1916 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2511 (Rfree = 0.000) for 1899 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2554 (Rfree = 0.000) for 1891 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:27:58 GMT 2018 Job finished. TimeTaking 28.05 Used memory is bytes: 6739544