Mon 24 Dec 07:52:46 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 2i51-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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/2i51-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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 07:52:51 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/2i51-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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 330 and 0 Target number of residues in the AU: 330 Target solvent content: 0.6326 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-3.6-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3120 target number of atoms Had to go as low as 0.85 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: 56.880 3.600 Wilson plot Bfac: 67.45 5129 reflections ( 85.23 % complete ) and 0 restraints for refining 3457 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3468 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3125 (Rfree = 0.000) for 3457 atoms. Found 19 (22 requested) and removed 46 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 3473 seeds are put forward NCS extension: 0 residues added, 3473 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 7 peptides. Score 0.256 Round 2: 183 peptides, 37 chains. Longest chain 11 peptides. Score 0.301 Round 3: 196 peptides, 33 chains. Longest chain 16 peptides. Score 0.405 Round 4: 205 peptides, 35 chains. Longest chain 14 peptides. Score 0.406 Round 5: 210 peptides, 37 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 4 Chains 35, Residues 170, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6376 restraints for refining 2827 atoms. 5706 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2880 (Rfree = 0.000) for 2827 atoms. Found 14 (18 requested) and removed 19 (9 requested) atoms. Cycle 2: After refmac, R = 0.2604 (Rfree = 0.000) for 2783 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 3: After refmac, R = 0.2199 (Rfree = 0.000) for 2770 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2534 (Rfree = 0.000) for 2760 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.2382 (Rfree = 0.000) for 2753 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 2803 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2821 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 10 peptides. Score 0.313 Round 2: 191 peptides, 32 chains. Longest chain 10 peptides. Score 0.403 Round 3: 210 peptides, 38 chains. Longest chain 11 peptides. Score 0.380 Round 4: 199 peptides, 32 chains. Longest chain 16 peptides. Score 0.429 Round 5: 197 peptides, 32 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 4 Chains 32, Residues 167, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6488 restraints for refining 2828 atoms. 5838 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2616 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 7: After refmac, R = 0.2340 (Rfree = 0.000) for 2793 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2388 (Rfree = 0.000) for 2785 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 2773 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2197 (Rfree = 0.000) for 2768 atoms. Found 10 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2834 seeds are put forward Round 1: 187 peptides, 35 chains. Longest chain 11 peptides. Score 0.345 Round 2: 192 peptides, 31 chains. Longest chain 14 peptides. Score 0.420 Round 3: 194 peptides, 30 chains. Longest chain 18 peptides. Score 0.441 Round 4: 200 peptides, 32 chains. Longest chain 15 peptides. Score 0.432 Round 5: 194 peptides, 32 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 3 Chains 31, Residues 164, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6368 restraints for refining 2828 atoms. 5696 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2404 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 12: After refmac, R = 0.2229 (Rfree = 0.000) for 2820 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. Cycle 13: After refmac, R = 0.2095 (Rfree = 0.000) for 2813 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2003 (Rfree = 0.000) for 2806 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.1947 (Rfree = 0.000) for 2803 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2865 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2878 seeds are put forward Round 1: 177 peptides, 33 chains. Longest chain 12 peptides. Score 0.340 Round 2: 185 peptides, 31 chains. Longest chain 15 peptides. Score 0.397 Round 3: 200 peptides, 30 chains. Longest chain 19 peptides. Score 0.460 Round 4: 189 peptides, 30 chains. Longest chain 14 peptides. Score 0.425 Round 5: 190 peptides, 29 chains. Longest chain 15 peptides. Score 0.442 Taking the results from Round 3 Chains 31, Residues 170, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6306 restraints for refining 2828 atoms. 5570 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2206 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 17: After refmac, R = 0.2176 (Rfree = 0.000) for 2827 atoms. Found 16 (18 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2203 (Rfree = 0.000) for 2831 atoms. Found 17 (18 requested) and removed 13 (9 requested) atoms. Cycle 19: After refmac, R = 0.1959 (Rfree = 0.000) for 2830 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2044 (Rfree = 0.000) for 2821 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 2882 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2909 seeds are put forward Round 1: 169 peptides, 30 chains. Longest chain 16 peptides. Score 0.357 Round 2: 186 peptides, 32 chains. Longest chain 15 peptides. Score 0.386 Round 3: 183 peptides, 28 chains. Longest chain 21 peptides. Score 0.434 Round 4: 204 peptides, 30 chains. Longest chain 18 peptides. Score 0.472 Round 5: 198 peptides, 30 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 4 Chains 30, Residues 174, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6307 restraints for refining 2827 atoms. 5609 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2299 (Rfree = 0.000) for 2827 atoms. Found 11 (18 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.2170 (Rfree = 0.000) for 2794 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. Cycle 23: After refmac, R = 0.2082 (Rfree = 0.000) for 2783 atoms. Found 9 (17 requested) and removed 21 (8 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 2768 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1954 (Rfree = 0.000) for 2764 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2830 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 16 peptides. Score 0.356 Round 2: 189 peptides, 30 chains. Longest chain 15 peptides. Score 0.425 Round 3: 181 peptides, 31 chains. Longest chain 13 peptides. Score 0.384 Round 4: 182 peptides, 28 chains. Longest chain 16 peptides. Score 0.431 Round 5: 179 peptides, 27 chains. Longest chain 20 peptides. Score 0.436 Taking the results from Round 5 Chains 28, Residues 152, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6379 restraints for refining 2828 atoms. 5740 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2380 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 27: After refmac, R = 0.2139 (Rfree = 0.000) for 2820 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.2206 (Rfree = 0.000) for 2810 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 2807 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1997 (Rfree = 0.000) for 2801 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2883 seeds are put forward Round 1: 149 peptides, 28 chains. Longest chain 11 peptides. Score 0.316 Round 2: 177 peptides, 31 chains. Longest chain 16 peptides. Score 0.370 Round 3: 185 peptides, 29 chains. Longest chain 18 peptides. Score 0.426 Round 4: 185 peptides, 29 chains. Longest chain 19 peptides. Score 0.426 Round 5: 176 peptides, 27 chains. Longest chain 19 peptides. Score 0.426 Taking the results from Round 5 Chains 29, Residues 149, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6154 restraints for refining 2828 atoms. 5494 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2383 (Rfree = 0.000) for 2828 atoms. Found 17 (18 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.2209 (Rfree = 0.000) for 2819 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.2106 (Rfree = 0.000) for 2817 atoms. Found 15 (18 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.2075 (Rfree = 0.000) for 2814 atoms. Found 15 (18 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.2019 (Rfree = 0.000) for 2809 atoms. Found 12 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 0 residues added, 2862 seeds are put forward Round 1: 163 peptides, 31 chains. Longest chain 10 peptides. Score 0.320 Round 2: 167 peptides, 27 chains. Longest chain 19 peptides. Score 0.396 Round 3: 164 peptides, 29 chains. Longest chain 12 peptides. Score 0.355 Round 4: 182 peptides, 29 chains. Longest chain 17 peptides. Score 0.416 Round 5: 176 peptides, 29 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 4 Chains 29, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6549 restraints for refining 2828 atoms. 5966 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2300 (Rfree = 0.000) for 2828 atoms. Found 13 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2254 (Rfree = 0.000) for 2815 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.1784 (Rfree = 0.000) for 2812 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1803 (Rfree = 0.000) for 2811 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.1893 (Rfree = 0.000) for 2808 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 2867 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2882 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 10 peptides. Score 0.288 Round 2: 180 peptides, 29 chains. Longest chain 14 peptides. Score 0.410 Round 3: 170 peptides, 29 chains. Longest chain 11 peptides. Score 0.376 Round 4: 176 peptides, 28 chains. Longest chain 11 peptides. Score 0.411 Round 5: 168 peptides, 27 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 4 Chains 28, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6447 restraints for refining 2828 atoms. 5883 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2061 (Rfree = 0.000) for 2828 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. Cycle 42: After refmac, R = 0.1863 (Rfree = 0.000) for 2820 atoms. Found 10 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1896 (Rfree = 0.000) for 2817 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.1819 (Rfree = 0.000) for 2810 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 2807 atoms. Found 6 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 2853 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2867 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 9 peptides. Score 0.277 Round 2: 179 peptides, 30 chains. Longest chain 14 peptides. Score 0.392 Round 3: 162 peptides, 24 chains. Longest chain 15 peptides. Score 0.424 Round 4: 171 peptides, 29 chains. Longest chain 12 peptides. Score 0.379 Round 5: 178 peptides, 28 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 138, 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 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5129 reflections ( 85.23 % complete ) and 6499 restraints for refining 2828 atoms. 5971 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2013 (Rfree = 0.000) for 2828 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1978 (Rfree = 0.000) for 2814 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1921 (Rfree = 0.000) for 2802 atoms. Found 0 (17 requested) and removed 3 (8 requested) atoms. Cycle 49: After refmac, R = 0.1986 (Rfree = 0.000) for 2796 atoms. Found 0 (17 requested) and removed 1 (8 requested) atoms. Writing output files ... TimeTaking 32.88