null Mon 24 Dec 08:08:37 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 2ogi-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-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/2ogi-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-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 08:08:42 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/2ogi-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-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 271 and 0 Target number of residues in the AU: 271 Target solvent content: 0.6680 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 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: 63.833 3.800 Wilson plot Bfac: 90.13 4427 reflections ( 99.77 % complete ) and 0 restraints for refining 3458 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3648 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2983 (Rfree = 0.000) for 3458 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 3525 seeds are put forward NCS extension: 0 residues added, 3525 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 10 peptides. Score 0.291 Round 2: 188 peptides, 31 chains. Longest chain 15 peptides. Score 0.425 Round 3: 192 peptides, 31 chains. Longest chain 13 peptides. Score 0.439 Round 4: 197 peptides, 30 chains. Longest chain 13 peptides. Score 0.471 Round 5: 207 peptides, 32 chains. Longest chain 14 peptides. Score 0.475 Taking the results from Round 5 Chains 32, Residues 175, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6636 restraints for refining 2835 atoms. 5931 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2379 (Rfree = 0.000) for 2835 atoms. Found 12 (15 requested) and removed 24 (7 requested) atoms. Cycle 2: After refmac, R = 0.2199 (Rfree = 0.000) for 2788 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2145 (Rfree = 0.000) for 2765 atoms. Found 5 (15 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2087 (Rfree = 0.000) for 2754 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2048 (Rfree = 0.000) for 2737 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 2852 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2867 seeds are put forward Round 1: 169 peptides, 30 chains. Longest chain 11 peptides. Score 0.371 Round 2: 198 peptides, 29 chains. Longest chain 14 peptides. Score 0.488 Round 3: 201 peptides, 30 chains. Longest chain 17 peptides. Score 0.484 Round 4: 195 peptides, 28 chains. Longest chain 17 peptides. Score 0.493 Round 5: 199 peptides, 31 chains. Longest chain 12 peptides. Score 0.463 Taking the results from Round 4 Chains 30, Residues 167, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6400 restraints for refining 2792 atoms. 5689 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2260 (Rfree = 0.000) for 2792 atoms. Found 5 (15 requested) and removed 28 (7 requested) atoms. Cycle 7: After refmac, R = 0.2189 (Rfree = 0.000) for 2759 atoms. Found 7 (15 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2184 (Rfree = 0.000) for 2748 atoms. Found 6 (15 requested) and removed 23 (7 requested) atoms. Cycle 9: After refmac, R = 0.2034 (Rfree = 0.000) for 2726 atoms. Found 7 (15 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.1838 (Rfree = 0.000) for 2713 atoms. Found 2 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2857 seeds are put forward Round 1: 165 peptides, 29 chains. Longest chain 13 peptides. Score 0.372 Round 2: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.426 Round 3: 194 peptides, 28 chains. Longest chain 15 peptides. Score 0.490 Round 4: 180 peptides, 25 chains. Longest chain 15 peptides. Score 0.488 Round 5: 188 peptides, 24 chains. Longest chain 16 peptides. Score 0.528 Taking the results from Round 5 Chains 24, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6544 restraints for refining 2836 atoms. 5912 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2165 (Rfree = 0.000) for 2836 atoms. Found 9 (15 requested) and removed 20 (7 requested) atoms. Cycle 12: After refmac, R = 0.1985 (Rfree = 0.000) for 2813 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Cycle 13: After refmac, R = 0.1918 (Rfree = 0.000) for 2798 atoms. Found 2 (15 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.1912 (Rfree = 0.000) for 2785 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.1911 (Rfree = 0.000) for 2774 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 2906 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2926 seeds are put forward Round 1: 149 peptides, 25 chains. Longest chain 11 peptides. Score 0.377 Round 2: 178 peptides, 29 chains. Longest chain 14 peptides. Score 0.420 Round 3: 191 peptides, 30 chains. Longest chain 12 peptides. Score 0.450 Round 4: 187 peptides, 27 chains. Longest chain 13 peptides. Score 0.481 Round 5: 187 peptides, 26 chains. Longest chain 19 peptides. Score 0.496 Taking the results from Round 5 Chains 27, Residues 161, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6493 restraints for refining 2836 atoms. 5849 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2156 (Rfree = 0.000) for 2836 atoms. Found 14 (15 requested) and removed 17 (7 requested) atoms. Cycle 17: After refmac, R = 0.1982 (Rfree = 0.000) for 2816 atoms. Found 8 (15 requested) and removed 15 (7 requested) atoms. Cycle 18: After refmac, R = 0.2044 (Rfree = 0.000) for 2803 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.1994 (Rfree = 0.000) for 2796 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.2083 (Rfree = 0.000) for 2787 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 2909 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2929 seeds are put forward Round 1: 150 peptides, 28 chains. Longest chain 9 peptides. Score 0.331 Round 2: 177 peptides, 25 chains. Longest chain 16 peptides. Score 0.478 Round 3: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.408 Round 4: 183 peptides, 26 chains. Longest chain 13 peptides. Score 0.483 Round 5: 182 peptides, 24 chains. Longest chain 13 peptides. Score 0.509 Taking the results from Round 5 Chains 24, Residues 158, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6555 restraints for refining 2836 atoms. 5912 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2252 (Rfree = 0.000) for 2836 atoms. Found 13 (15 requested) and removed 23 (7 requested) atoms. Cycle 22: After refmac, R = 0.2203 (Rfree = 0.000) for 2805 atoms. Found 9 (15 requested) and removed 23 (7 requested) atoms. Cycle 23: After refmac, R = 0.2135 (Rfree = 0.000) for 2783 atoms. Found 9 (15 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.2054 (Rfree = 0.000) for 2774 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.1682 (Rfree = 0.000) for 2764 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2896 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2912 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 11 peptides. Score 0.305 Round 2: 176 peptides, 28 chains. Longest chain 13 peptides. Score 0.428 Round 3: 184 peptides, 28 chains. Longest chain 14 peptides. Score 0.456 Round 4: 195 peptides, 27 chains. Longest chain 14 peptides. Score 0.508 Round 5: 206 peptides, 30 chains. Longest chain 18 peptides. Score 0.500 Taking the results from Round 4 Chains 27, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6503 restraints for refining 2834 atoms. 5858 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2096 (Rfree = 0.000) for 2834 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.2014 (Rfree = 0.000) for 2822 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2175 (Rfree = 0.000) for 2814 atoms. Found 14 (15 requested) and removed 18 (7 requested) atoms. Cycle 29: After refmac, R = 0.1891 (Rfree = 0.000) for 2806 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.1616 (Rfree = 0.000) for 2797 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 2896 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2911 seeds are put forward Round 1: 138 peptides, 27 chains. Longest chain 10 peptides. Score 0.300 Round 2: 158 peptides, 27 chains. Longest chain 17 peptides. Score 0.378 Round 3: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.365 Round 4: 144 peptides, 26 chains. Longest chain 11 peptides. Score 0.341 Round 5: 162 peptides, 28 chains. Longest chain 15 peptides. Score 0.377 Taking the results from Round 2 Chains 27, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6654 restraints for refining 2812 atoms. 6157 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1878 (Rfree = 0.000) for 2812 atoms. Found 11 (15 requested) and removed 15 (7 requested) atoms. Cycle 32: After refmac, R = 0.1982 (Rfree = 0.000) for 2802 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.1637 (Rfree = 0.000) for 2796 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.1567 (Rfree = 0.000) for 2787 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1565 (Rfree = 0.000) for 2779 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 2887 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2909 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 9 peptides. Score 0.242 Round 2: 156 peptides, 29 chains. Longest chain 10 peptides. Score 0.338 Round 3: 158 peptides, 29 chains. Longest chain 9 peptides. Score 0.345 Round 4: 170 peptides, 30 chains. Longest chain 10 peptides. Score 0.375 Round 5: 168 peptides, 30 chains. Longest chain 9 peptides. Score 0.367 Taking the results from Round 4 Chains 30, Residues 140, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6489 restraints for refining 2836 atoms. 5934 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2085 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 37: After refmac, R = 0.2084 (Rfree = 0.000) for 2825 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 38: After refmac, R = 0.1836 (Rfree = 0.000) for 2814 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 39: After refmac, R = 0.2032 (Rfree = 0.000) for 2806 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.2046 (Rfree = 0.000) for 2806 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 0 residues added, 2940 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 12 peptides. Score 0.269 Round 2: 144 peptides, 27 chains. Longest chain 14 peptides. Score 0.324 Round 3: 128 peptides, 25 chains. Longest chain 8 peptides. Score 0.293 Round 4: 137 peptides, 25 chains. Longest chain 9 peptides. Score 0.330 Round 5: 140 peptides, 25 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 5 Chains 25, Residues 115, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6784 restraints for refining 2836 atoms. 6330 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1899 (Rfree = 0.000) for 2836 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 42: After refmac, R = 0.1775 (Rfree = 0.000) for 2820 atoms. Found 10 (15 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.1759 (Rfree = 0.000) for 2816 atoms. Found 8 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1826 (Rfree = 0.000) for 2814 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.1910 (Rfree = 0.000) for 2813 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 0 residues added, 2940 seeds are put forward Round 1: 128 peptides, 28 chains. Longest chain 7 peptides. Score 0.239 Round 2: 122 peptides, 23 chains. Longest chain 11 peptides. Score 0.304 Round 3: 139 peptides, 26 chains. Longest chain 12 peptides. Score 0.321 Round 4: 128 peptides, 24 chains. Longest chain 12 peptides. Score 0.311 Round 5: 133 peptides, 25 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 113, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2ogi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4427 reflections ( 99.77 % complete ) and 6549 restraints for refining 2835 atoms. 6083 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1889 (Rfree = 0.000) for 2835 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2131 (Rfree = 0.000) for 2813 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1822 (Rfree = 0.000) for 2798 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1850 (Rfree = 0.000) for 2783 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:40:09 GMT 2018 Job finished. TimeTaking 31.54 Used memory is bytes: 2369920