null Mon 24 Dec 00:35:33 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 2o8q-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-4.0-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/2o8q-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-4.0-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 00:35:38 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/2o8q-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-4.0-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 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-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-4.0-parrot-mrncs.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 2366 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3274 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3107 (Rfree = 0.000) for 2366 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.10 Search for helices and strands: 0 residues in 0 chains, 2384 seeds are put forward NCS extension: 0 residues added, 2384 seeds are put forward Round 1: 133 peptides, 27 chains. Longest chain 10 peptides. Score 0.288 Round 2: 154 peptides, 21 chains. Longest chain 16 peptides. Score 0.483 Round 3: 177 peptides, 26 chains. Longest chain 19 peptides. Score 0.486 Round 4: 173 peptides, 24 chains. Longest chain 25 peptides. Score 0.503 Round 5: 166 peptides, 23 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 4 Chains 26, Residues 149, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4163 restraints for refining 1934 atoms. 3524 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2496 (Rfree = 0.000) for 1934 atoms. Found 8 (9 requested) and removed 14 (4 requested) atoms. Cycle 2: After refmac, R = 0.2403 (Rfree = 0.000) for 1883 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.2247 (Rfree = 0.000) for 1861 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 4: After refmac, R = 0.1934 (Rfree = 0.000) for 1844 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2226 (Rfree = 0.000) for 1833 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 1886 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1908 seeds are put forward Round 1: 147 peptides, 24 chains. Longest chain 11 peptides. Score 0.404 Round 2: 165 peptides, 23 chains. Longest chain 15 peptides. Score 0.491 Round 3: 175 peptides, 24 chains. Longest chain 16 peptides. Score 0.510 Round 4: 159 peptides, 18 chains. Longest chain 19 peptides. Score 0.550 Round 5: 160 peptides, 20 chains. Longest chain 16 peptides. Score 0.522 Taking the results from Round 4 Chains 19, Residues 141, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4360 restraints for refining 1936 atoms. 3795 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2607 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2609 (Rfree = 0.000) for 1905 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2403 (Rfree = 0.000) for 1881 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 9: After refmac, R = 0.2435 (Rfree = 0.000) for 1859 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2392 (Rfree = 0.000) for 1847 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.05 Search for helices and strands: 0 residues in 0 chains, 1904 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1922 seeds are put forward Round 1: 149 peptides, 27 chains. Longest chain 11 peptides. Score 0.358 Round 2: 180 peptides, 25 chains. Longest chain 14 peptides. Score 0.512 Round 3: 168 peptides, 23 chains. Longest chain 15 peptides. Score 0.502 Round 4: 172 peptides, 21 chains. Longest chain 27 peptides. Score 0.547 Round 5: 167 peptides, 22 chains. Longest chain 20 peptides. Score 0.514 Taking the results from Round 4 Chains 23, Residues 151, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4160 restraints for refining 1936 atoms. 3537 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2618 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 12: After refmac, R = 0.2488 (Rfree = 0.000) for 1916 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2471 (Rfree = 0.000) for 1909 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2636 (Rfree = 0.000) for 1891 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.2433 (Rfree = 0.000) for 1879 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.05 Search for helices and strands: 0 residues in 0 chains, 1949 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 1986 seeds are put forward Round 1: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.411 Round 2: 155 peptides, 20 chains. Longest chain 18 peptides. Score 0.504 Round 3: 175 peptides, 25 chains. Longest chain 12 peptides. Score 0.494 Round 4: 169 peptides, 21 chains. Longest chain 18 peptides. Score 0.537 Round 5: 172 peptides, 21 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 5 Chains 21, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4361 restraints for refining 1936 atoms. 3778 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2609 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 17: After refmac, R = 0.2385 (Rfree = 0.000) for 1917 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 18: After refmac, R = 0.2453 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 19: After refmac, R = 0.2328 (Rfree = 0.000) for 1885 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2083 (Rfree = 0.000) for 1876 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.03 Search for helices and strands: 0 residues in 0 chains, 1926 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1951 seeds are put forward Round 1: 142 peptides, 25 chains. Longest chain 15 peptides. Score 0.365 Round 2: 155 peptides, 24 chains. Longest chain 13 peptides. Score 0.436 Round 3: 146 peptides, 18 chains. Longest chain 21 peptides. Score 0.504 Round 4: 156 peptides, 20 chains. Longest chain 16 peptides. Score 0.507 Round 5: 163 peptides, 20 chains. Longest chain 20 peptides. Score 0.532 Taking the results from Round 5 Chains 22, Residues 143, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4074 restraints for refining 1935 atoms. 3430 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2714 (Rfree = 0.000) for 1935 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.2451 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.2439 (Rfree = 0.000) for 1870 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2069 (Rfree = 0.000) for 1858 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2286 (Rfree = 0.000) for 1854 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.07 Search for helices and strands: 0 residues in 0 chains, 1896 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1912 seeds are put forward Round 1: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.373 Round 2: 160 peptides, 22 chains. Longest chain 20 peptides. Score 0.489 Round 3: 163 peptides, 22 chains. Longest chain 15 peptides. Score 0.500 Round 4: 169 peptides, 20 chains. Longest chain 19 peptides. Score 0.552 Round 5: 172 peptides, 20 chains. Longest chain 24 peptides. Score 0.562 Taking the results from Round 5 Chains 22, Residues 152, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4098 restraints for refining 1936 atoms. 3417 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2666 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 27: After refmac, R = 0.2567 (Rfree = 0.000) for 1896 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.2599 (Rfree = 0.000) for 1878 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2444 (Rfree = 0.000) for 1870 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.2521 (Rfree = 0.000) for 1862 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.01 Search for helices and strands: 0 residues in 0 chains, 1904 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1931 seeds are put forward Round 1: 145 peptides, 24 chains. Longest chain 13 peptides. Score 0.396 Round 2: 166 peptides, 21 chains. Longest chain 32 peptides. Score 0.527 Round 3: 164 peptides, 21 chains. Longest chain 19 peptides. Score 0.520 Round 4: 157 peptides, 21 chains. Longest chain 17 peptides. Score 0.494 Round 5: 169 peptides, 20 chains. Longest chain 17 peptides. Score 0.552 Taking the results from Round 5 Chains 21, Residues 149, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4149 restraints for refining 1936 atoms. 3535 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2777 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.2663 (Rfree = 0.000) for 1916 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.2424 (Rfree = 0.000) for 1898 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.2183 (Rfree = 0.000) for 1889 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.2399 (Rfree = 0.000) for 1891 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.05 Search for helices and strands: 0 residues in 0 chains, 1971 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1985 seeds are put forward Round 1: 119 peptides, 23 chains. Longest chain 11 peptides. Score 0.301 Round 2: 148 peptides, 25 chains. Longest chain 15 peptides. Score 0.390 Round 3: 153 peptides, 20 chains. Longest chain 26 peptides. Score 0.496 Round 4: 160 peptides, 23 chains. Longest chain 19 peptides. Score 0.472 Round 5: 158 peptides, 24 chains. Longest chain 13 peptides. Score 0.447 Taking the results from Round 3 Chains 22, Residues 133, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4079 restraints for refining 1936 atoms. 3476 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2790 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 37: After refmac, R = 0.2618 (Rfree = 0.000) for 1905 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.2437 (Rfree = 0.000) for 1883 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 39: After refmac, R = 0.2497 (Rfree = 0.000) for 1866 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.2186 (Rfree = 0.000) for 1854 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.04 Search for helices and strands: 0 residues in 0 chains, 1905 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1924 seeds are put forward Round 1: 130 peptides, 24 chains. Longest chain 12 peptides. Score 0.331 Round 2: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.384 Round 3: 131 peptides, 20 chains. Longest chain 14 peptides. Score 0.411 Round 4: 136 peptides, 19 chains. Longest chain 14 peptides. Score 0.449 Round 5: 142 peptides, 22 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 4 Chains 19, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4450 restraints for refining 1936 atoms. 4001 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2758 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 42: After refmac, R = 0.2665 (Rfree = 0.000) for 1918 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 43: After refmac, R = 0.2420 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2460 (Rfree = 0.000) for 1894 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 45: After refmac, R = 0.2298 (Rfree = 0.000) for 1885 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.05 Search for helices and strands: 0 residues in 0 chains, 1932 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1949 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 12 peptides. Score 0.280 Round 2: 142 peptides, 22 chains. Longest chain 13 peptides. Score 0.419 Round 3: 129 peptides, 21 chains. Longest chain 12 peptides. Score 0.384 Round 4: 136 peptides, 20 chains. Longest chain 19 peptides. Score 0.431 Round 5: 133 peptides, 19 chains. Longest chain 18 peptides. Score 0.437 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 114, 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 2o8q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3635 reflections ( 98.22 % complete ) and 4432 restraints for refining 1935 atoms. 3995 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2665 (Rfree = 0.000) for 1935 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2541 (Rfree = 0.000) for 1917 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2153 (Rfree = 0.000) for 1902 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2109 (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 01:05:38 GMT 2018 Job finished. TimeTaking 30.08 Used memory is bytes: 17994760