null Mon 24 Dec 00:24:38 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 2i51-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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/2i51-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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 00:24:43 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/2i51-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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 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-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.6-parrot-mrncs.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 3473 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3334 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3040 (Rfree = 0.000) for 3473 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 3504 seeds are put forward NCS extension: 0 residues added, 3504 seeds are put forward Round 1: 185 peptides, 37 chains. Longest chain 9 peptides. Score 0.308 Round 2: 217 peptides, 35 chains. Longest chain 11 peptides. Score 0.445 Round 3: 230 peptides, 32 chains. Longest chain 21 peptides. Score 0.523 Round 4: 229 peptides, 32 chains. Longest chain 16 peptides. Score 0.520 Round 5: 241 peptides, 33 chains. Longest chain 18 peptides. Score 0.541 Taking the results from Round 5 Chains 34, Residues 208, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 5900 restraints for refining 2828 atoms. 5014 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2453 (Rfree = 0.000) for 2828 atoms. Found 9 (18 requested) and removed 21 (9 requested) atoms. Cycle 2: After refmac, R = 0.2261 (Rfree = 0.000) for 2789 atoms. Found 10 (18 requested) and removed 18 (9 requested) atoms. Cycle 3: After refmac, R = 0.2111 (Rfree = 0.000) for 2771 atoms. Found 9 (17 requested) and removed 18 (8 requested) atoms. Cycle 4: After refmac, R = 0.2134 (Rfree = 0.000) for 2758 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.1954 (Rfree = 0.000) for 2753 atoms. Found 4 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 2814 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2834 seeds are put forward Round 1: 217 peptides, 33 chains. Longest chain 13 peptides. Score 0.471 Round 2: 235 peptides, 33 chains. Longest chain 23 peptides. Score 0.524 Round 3: 220 peptides, 32 chains. Longest chain 32 peptides. Score 0.494 Round 4: 228 peptides, 29 chains. Longest chain 16 peptides. Score 0.554 Round 5: 225 peptides, 30 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 4 Chains 30, Residues 199, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6053 restraints for refining 2826 atoms. 5244 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2415 (Rfree = 0.000) for 2826 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 7: After refmac, R = 0.2187 (Rfree = 0.000) for 2796 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2108 (Rfree = 0.000) for 2789 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2050 (Rfree = 0.000) for 2782 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.1879 (Rfree = 0.000) for 2774 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.14 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2839 seeds are put forward Round 1: 214 peptides, 37 chains. Longest chain 13 peptides. Score 0.407 Round 2: 235 peptides, 36 chains. Longest chain 14 peptides. Score 0.486 Round 3: 219 peptides, 29 chains. Longest chain 18 peptides. Score 0.529 Round 4: 215 peptides, 34 chains. Longest chain 22 peptides. Score 0.452 Round 5: 230 peptides, 29 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 5 Chains 30, Residues 201, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 5989 restraints for refining 2828 atoms. 5175 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2314 (Rfree = 0.000) for 2828 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 12: After refmac, R = 0.2058 (Rfree = 0.000) for 2818 atoms. Found 10 (18 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.1958 (Rfree = 0.000) for 2805 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.1934 (Rfree = 0.000) for 2799 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.1849 (Rfree = 0.000) for 2791 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2875 seeds are put forward Round 1: 201 peptides, 36 chains. Longest chain 10 peptides. Score 0.379 Round 2: 234 peptides, 33 chains. Longest chain 17 peptides. Score 0.521 Round 3: 215 peptides, 30 chains. Longest chain 13 peptides. Score 0.505 Round 4: 222 peptides, 29 chains. Longest chain 16 peptides. Score 0.538 Round 5: 230 peptides, 32 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 4 Chains 29, Residues 193, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6202 restraints for refining 2828 atoms. 5405 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2175 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 17: After refmac, R = 0.2108 (Rfree = 0.000) for 2825 atoms. Found 15 (18 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.1933 (Rfree = 0.000) for 2820 atoms. Found 8 (18 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.1874 (Rfree = 0.000) for 2805 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.1842 (Rfree = 0.000) for 2796 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2869 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2885 seeds are put forward Round 1: 189 peptides, 32 chains. Longest chain 11 peptides. Score 0.396 Round 2: 206 peptides, 32 chains. Longest chain 14 peptides. Score 0.451 Round 3: 208 peptides, 31 chains. Longest chain 16 peptides. Score 0.471 Round 4: 207 peptides, 26 chains. Longest chain 23 peptides. Score 0.534 Round 5: 224 peptides, 29 chains. Longest chain 19 peptides. Score 0.543 Taking the results from Round 5 Chains 30, Residues 195, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6139 restraints for refining 2827 atoms. 5355 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2331 (Rfree = 0.000) for 2827 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.2061 (Rfree = 0.000) for 2807 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.1948 (Rfree = 0.000) for 2802 atoms. Found 15 (18 requested) and removed 11 (9 requested) atoms. Cycle 24: After refmac, R = 0.1853 (Rfree = 0.000) for 2796 atoms. Found 10 (18 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1767 (Rfree = 0.000) for 2787 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 2864 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2880 seeds are put forward Round 1: 187 peptides, 34 chains. Longest chain 11 peptides. Score 0.360 Round 2: 214 peptides, 35 chains. Longest chain 13 peptides. Score 0.435 Round 3: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.467 Round 4: 222 peptides, 36 chains. Longest chain 12 peptides. Score 0.447 Round 5: 213 peptides, 30 chains. Longest chain 26 peptides. Score 0.499 Taking the results from Round 5 Chains 32, Residues 183, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6023 restraints for refining 2828 atoms. 5227 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2367 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2151 (Rfree = 0.000) for 2806 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.2006 (Rfree = 0.000) for 2804 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.1992 (Rfree = 0.000) for 2796 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.1918 (Rfree = 0.000) for 2788 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2861 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 11 peptides. Score 0.346 Round 2: 203 peptides, 33 chains. Longest chain 18 peptides. Score 0.428 Round 3: 213 peptides, 33 chains. Longest chain 18 peptides. Score 0.459 Round 4: 208 peptides, 27 chains. Longest chain 22 peptides. Score 0.524 Round 5: 203 peptides, 31 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 4 Chains 28, Residues 181, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6102 restraints for refining 2828 atoms. 5352 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2248 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 32: After refmac, R = 0.2121 (Rfree = 0.000) for 2814 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.2032 (Rfree = 0.000) for 2804 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.1995 (Rfree = 0.000) for 2813 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.1635 (Rfree = 0.000) for 2813 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2863 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 2894 seeds are put forward Round 1: 158 peptides, 32 chains. Longest chain 11 peptides. Score 0.286 Round 2: 180 peptides, 32 chains. Longest chain 12 peptides. Score 0.366 Round 3: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.400 Round 4: 184 peptides, 30 chains. Longest chain 13 peptides. Score 0.409 Round 5: 190 peptides, 32 chains. Longest chain 15 peptides. Score 0.400 Taking the results from Round 4 Chains 30, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6398 restraints for refining 2828 atoms. 5812 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2124 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.1965 (Rfree = 0.000) for 2833 atoms. Found 16 (18 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.1772 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1815 (Rfree = 0.000) for 2834 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1686 (Rfree = 0.000) for 2832 atoms. Found 12 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2900 seeds are put forward Round 1: 140 peptides, 30 chains. Longest chain 7 peptides. Score 0.249 Round 2: 169 peptides, 32 chains. Longest chain 8 peptides. Score 0.327 Round 3: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.372 Round 4: 160 peptides, 27 chains. Longest chain 10 peptides. Score 0.372 Round 5: 178 peptides, 30 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 5 Chains 30, Residues 148, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6432 restraints for refining 2828 atoms. 5832 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1950 (Rfree = 0.000) for 2828 atoms. Found 11 (18 requested) and removed 13 (9 requested) atoms. Cycle 42: After refmac, R = 0.2069 (Rfree = 0.000) for 2814 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.1952 (Rfree = 0.000) for 2812 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.1871 (Rfree = 0.000) for 2815 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1793 (Rfree = 0.000) for 2816 atoms. Found 14 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2863 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2874 seeds are put forward Round 1: 161 peptides, 36 chains. Longest chain 6 peptides. Score 0.234 Round 2: 169 peptides, 33 chains. Longest chain 9 peptides. Score 0.311 Round 3: 168 peptides, 31 chains. Longest chain 8 peptides. Score 0.339 Round 4: 159 peptides, 30 chains. Longest chain 8 peptides. Score 0.321 Round 5: 162 peptides, 28 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 134, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (134 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5129 reflections ( 85.23 % complete ) and 6409 restraints for refining 2828 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2089 (Rfree = 0.000) for 2828 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1934 (Rfree = 0.000) for 2805 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1914 (Rfree = 0.000) for 2790 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1799 (Rfree = 0.000) for 2778 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:03:53 GMT 2018 Job finished. TimeTaking 39.25 Used memory is bytes: 11151416