null Mon 24 Dec 07:34:13 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 2i5i-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-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/2i5i-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 07:34:18 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/2i5i-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6594 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 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: 29.446 3.800 Wilson plot Bfac: 83.92 5326 reflections ( 99.05 % complete ) and 0 restraints for refining 4645 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3516 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3311 (Rfree = 0.000) for 4645 atoms. Found 25 (25 requested) and removed 87 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.78 Search for helices and strands: 0 residues in 0 chains, 4622 seeds are put forward NCS extension: 0 residues added, 4622 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 6 peptides. Score 0.198 Round 2: 114 peptides, 23 chains. Longest chain 10 peptides. Score 0.255 Round 3: 125 peptides, 26 chains. Longest chain 10 peptides. Score 0.248 Round 4: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.272 Round 5: 150 peptides, 30 chains. Longest chain 16 peptides. Score 0.276 Taking the results from Round 5 Chains 30, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 9403 restraints for refining 3807 atoms. 8953 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2842 (Rfree = 0.000) for 3807 atoms. Found 20 (20 requested) and removed 37 (10 requested) atoms. Cycle 2: After refmac, R = 0.2755 (Rfree = 0.000) for 3750 atoms. Found 20 (20 requested) and removed 43 (10 requested) atoms. Cycle 3: After refmac, R = 0.2609 (Rfree = 0.000) for 3706 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 4: After refmac, R = 0.2538 (Rfree = 0.000) for 3666 atoms. Found 20 (20 requested) and removed 40 (10 requested) atoms. Cycle 5: After refmac, R = 0.2587 (Rfree = 0.000) for 3634 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 3681 seeds are put forward NCS extension: 0 residues added, 3681 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 16 peptides. Score 0.247 Round 2: 173 peptides, 31 chains. Longest chain 13 peptides. Score 0.337 Round 3: 162 peptides, 31 chains. Longest chain 12 peptides. Score 0.302 Round 4: 159 peptides, 29 chains. Longest chain 12 peptides. Score 0.320 Round 5: 159 peptides, 28 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 2 Chains 32, Residues 142, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6970 restraints for refining 3264 atoms. 6383 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2455 (Rfree = 0.000) for 3264 atoms. Found 17 (17 requested) and removed 55 (8 requested) atoms. Cycle 7: After refmac, R = 0.2489 (Rfree = 0.000) for 3185 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 8: After refmac, R = 0.2385 (Rfree = 0.000) for 3158 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 9: After refmac, R = 0.2414 (Rfree = 0.000) for 3125 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 10: After refmac, R = 0.2407 (Rfree = 0.000) for 3101 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 3182 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3201 seeds are put forward Round 1: 158 peptides, 34 chains. Longest chain 11 peptides. Score 0.246 Round 2: 203 peptides, 40 chains. Longest chain 12 peptides. Score 0.311 Round 3: 179 peptides, 35 chains. Longest chain 10 peptides. Score 0.302 Round 4: 190 peptides, 36 chains. Longest chain 11 peptides. Score 0.323 Round 5: 189 peptides, 34 chains. Longest chain 10 peptides. Score 0.347 Taking the results from Round 5 Chains 34, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7243 restraints for refining 3273 atoms. 6657 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2576 (Rfree = 0.000) for 3273 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.2540 (Rfree = 0.000) for 3232 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 13: After refmac, R = 0.2533 (Rfree = 0.000) for 3210 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.2533 (Rfree = 0.000) for 3195 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 15: After refmac, R = 0.2461 (Rfree = 0.000) for 3181 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 3244 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3250 seeds are put forward Round 1: 146 peptides, 34 chains. Longest chain 8 peptides. Score 0.204 Round 2: 180 peptides, 36 chains. Longest chain 9 peptides. Score 0.291 Round 3: 191 peptides, 35 chains. Longest chain 13 peptides. Score 0.340 Round 4: 192 peptides, 34 chains. Longest chain 14 peptides. Score 0.356 Round 5: 218 peptides, 39 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 5 Chains 39, Residues 179, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6712 restraints for refining 3172 atoms. 6022 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2578 (Rfree = 0.000) for 3172 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 17: After refmac, R = 0.2562 (Rfree = 0.000) for 3133 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 18: After refmac, R = 0.2394 (Rfree = 0.000) for 3109 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.2337 (Rfree = 0.000) for 3091 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 20: After refmac, R = 0.2304 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 3134 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3153 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 8 peptides. Score 0.245 Round 2: 188 peptides, 36 chains. Longest chain 12 peptides. Score 0.317 Round 3: 191 peptides, 34 chains. Longest chain 14 peptides. Score 0.353 Round 4: 192 peptides, 36 chains. Longest chain 10 peptides. Score 0.329 Round 5: 198 peptides, 36 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 3 Chains 34, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6631 restraints for refining 3090 atoms. 6037 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2404 (Rfree = 0.000) for 3090 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 22: After refmac, R = 0.2468 (Rfree = 0.000) for 3059 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 23: After refmac, R = 0.2445 (Rfree = 0.000) for 3046 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 24: After refmac, R = 0.2381 (Rfree = 0.000) for 3026 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 25: After refmac, R = 0.2325 (Rfree = 0.000) for 3010 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 3082 seeds are put forward NCS extension: 0 residues added, 3082 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 8 peptides. Score 0.264 Round 2: 184 peptides, 37 chains. Longest chain 11 peptides. Score 0.290 Round 3: 169 peptides, 31 chains. Longest chain 11 peptides. Score 0.325 Round 4: 176 peptides, 33 chains. Longest chain 13 peptides. Score 0.319 Round 5: 180 peptides, 33 chains. Longest chain 9 peptides. Score 0.332 Taking the results from Round 5 Chains 33, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6579 restraints for refining 3105 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2511 (Rfree = 0.000) for 3105 atoms. Found 17 (17 requested) and removed 40 (8 requested) atoms. Cycle 27: After refmac, R = 0.2342 (Rfree = 0.000) for 3061 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 28: After refmac, R = 0.2460 (Rfree = 0.000) for 3037 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 3013 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 30: After refmac, R = 0.2326 (Rfree = 0.000) for 3005 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 3085 seeds are put forward NCS extension: 0 residues added, 3085 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 8 peptides. Score 0.264 Round 2: 184 peptides, 32 chains. Longest chain 14 peptides. Score 0.358 Round 3: 182 peptides, 30 chains. Longest chain 16 peptides. Score 0.379 Round 4: 177 peptides, 31 chains. Longest chain 12 peptides. Score 0.350 Round 5: 190 peptides, 33 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 3 Chains 30, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6139 restraints for refining 2942 atoms. 5561 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2428 (Rfree = 0.000) for 2942 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 32: After refmac, R = 0.2352 (Rfree = 0.000) for 2921 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.2339 (Rfree = 0.000) for 2912 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.2323 (Rfree = 0.000) for 2900 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 35: After refmac, R = 0.1965 (Rfree = 0.000) for 2890 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2983 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 6 peptides. Score 0.223 Round 2: 150 peptides, 29 chains. Longest chain 8 peptides. Score 0.291 Round 3: 158 peptides, 31 chains. Longest chain 9 peptides. Score 0.289 Round 4: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.364 Round 5: 152 peptides, 26 chains. Longest chain 12 peptides. Score 0.340 Taking the results from Round 4 Chains 27, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6165 restraints for refining 2920 atoms. 5644 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2538 (Rfree = 0.000) for 2920 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 37: After refmac, R = 0.2360 (Rfree = 0.000) for 2896 atoms. Found 15 (15 requested) and removed 28 (7 requested) atoms. Cycle 38: After refmac, R = 0.2534 (Rfree = 0.000) for 2871 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.2325 (Rfree = 0.000) for 2863 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 40: After refmac, R = 0.2264 (Rfree = 0.000) for 2854 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 2918 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2933 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 7 peptides. Score 0.215 Round 2: 146 peptides, 29 chains. Longest chain 10 peptides. Score 0.277 Round 3: 156 peptides, 28 chains. Longest chain 9 peptides. Score 0.325 Round 4: 162 peptides, 29 chains. Longest chain 8 peptides. Score 0.330 Round 5: 138 peptides, 26 chains. Longest chain 8 peptides. Score 0.294 Taking the results from Round 4 Chains 29, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 6280 restraints for refining 2916 atoms. 5777 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2448 (Rfree = 0.000) for 2916 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 42: After refmac, R = 0.2383 (Rfree = 0.000) for 2890 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 43: After refmac, R = 0.2237 (Rfree = 0.000) for 2874 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2335 (Rfree = 0.000) for 2866 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.2252 (Rfree = 0.000) for 2857 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2925 seeds are put forward NCS extension: 0 residues added, 2925 seeds are put forward Round 1: 114 peptides, 26 chains. Longest chain 6 peptides. Score 0.207 Round 2: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.258 Round 3: 129 peptides, 26 chains. Longest chain 7 peptides. Score 0.263 Round 4: 129 peptides, 26 chains. Longest chain 7 peptides. Score 0.263 Round 5: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.299 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 110, 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 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5326 reflections ( 99.05 % complete ) and 6325 restraints for refining 2901 atoms. 5910 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2312 (Rfree = 0.000) for 2901 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2341 (Rfree = 0.000) for 2881 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2279 (Rfree = 0.000) for 2865 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2288 (Rfree = 0.000) for 2852 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:11:17 GMT 2018 Job finished. TimeTaking 37.06 Used memory is bytes: 9782576