null Mon 24 Dec 00:22:10 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 2i51-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-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/2i51-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-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 00:22:15 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/2i51-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-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 322 and 0 Target number of residues in the AU: 322 Target solvent content: 0.6415 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: 2i51-3.8-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: 2i51-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3120 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: 56.880 3.800 Wilson plot Bfac: 72.52 4372 reflections ( 84.88 % complete ) and 0 restraints for refining 3458 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3185 (Rfree = 0.000) for 3458 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 3486 seeds are put forward NCS extension: 0 residues added, 3486 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 13 peptides. Score 0.303 Round 2: 198 peptides, 35 chains. Longest chain 10 peptides. Score 0.383 Round 3: 213 peptides, 35 chains. Longest chain 12 peptides. Score 0.432 Round 4: 216 peptides, 36 chains. Longest chain 13 peptides. Score 0.428 Round 5: 219 peptides, 32 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 5 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6243 restraints for refining 2821 atoms. 5527 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2508 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 2: After refmac, R = 0.2350 (Rfree = 0.000) for 2789 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2246 (Rfree = 0.000) for 2777 atoms. Found 7 (15 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2093 (Rfree = 0.000) for 2759 atoms. Found 13 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.1864 (Rfree = 0.000) for 2752 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 2806 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2821 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 13 peptides. Score 0.384 Round 2: 191 peptides, 29 chains. Longest chain 15 peptides. Score 0.446 Round 3: 210 peptides, 32 chains. Longest chain 17 peptides. Score 0.464 Round 4: 205 peptides, 28 chains. Longest chain 18 peptides. Score 0.502 Round 5: 204 peptides, 30 chains. Longest chain 22 peptides. Score 0.472 Taking the results from Round 4 Chains 28, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6393 restraints for refining 2822 atoms. 5713 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2466 (Rfree = 0.000) for 2822 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. Cycle 7: After refmac, R = 0.2155 (Rfree = 0.000) for 2796 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2053 (Rfree = 0.000) for 2780 atoms. Found 11 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2003 (Rfree = 0.000) for 2769 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.1874 (Rfree = 0.000) for 2770 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 2875 seeds are put forward Round 1: 180 peptides, 31 chains. Longest chain 17 peptides. Score 0.380 Round 2: 194 peptides, 30 chains. Longest chain 21 peptides. Score 0.441 Round 3: 200 peptides, 30 chains. Longest chain 22 peptides. Score 0.460 Round 4: 202 peptides, 30 chains. Longest chain 18 peptides. Score 0.466 Round 5: 207 peptides, 30 chains. Longest chain 22 peptides. Score 0.481 Taking the results from Round 5 Chains 30, Residues 177, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6157 restraints for refining 2822 atoms. 5390 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2173 (Rfree = 0.000) for 2822 atoms. Found 14 (15 requested) and removed 10 (7 requested) atoms. Cycle 12: After refmac, R = 0.1970 (Rfree = 0.000) for 2800 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 13: After refmac, R = 0.1740 (Rfree = 0.000) for 2783 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.1700 (Rfree = 0.000) for 2769 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.1771 (Rfree = 0.000) for 2761 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 2817 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2836 seeds are put forward Round 1: 180 peptides, 30 chains. Longest chain 20 peptides. Score 0.395 Round 2: 196 peptides, 32 chains. Longest chain 18 peptides. Score 0.419 Round 3: 200 peptides, 29 chains. Longest chain 22 peptides. Score 0.474 Round 4: 201 peptides, 28 chains. Longest chain 21 peptides. Score 0.490 Round 5: 208 peptides, 30 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 28, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6517 restraints for refining 2822 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2177 (Rfree = 0.000) for 2822 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 17: After refmac, R = 0.2041 (Rfree = 0.000) for 2811 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.1951 (Rfree = 0.000) for 2807 atoms. Found 0 (15 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.1921 (Rfree = 0.000) for 2792 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.1832 (Rfree = 0.000) for 2786 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 2825 seeds are put forward NCS extension: 0 residues added, 2825 seeds are put forward Round 1: 176 peptides, 33 chains. Longest chain 12 peptides. Score 0.337 Round 2: 194 peptides, 31 chains. Longest chain 16 peptides. Score 0.427 Round 3: 196 peptides, 31 chains. Longest chain 22 peptides. Score 0.433 Round 4: 187 peptides, 28 chains. Longest chain 19 peptides. Score 0.447 Round 5: 199 peptides, 29 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 5 Chains 29, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6564 restraints for refining 2822 atoms. 5913 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2201 (Rfree = 0.000) for 2822 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.2149 (Rfree = 0.000) for 2813 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 23: After refmac, R = 0.1957 (Rfree = 0.000) for 2808 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.1721 (Rfree = 0.000) for 2794 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.1695 (Rfree = 0.000) for 2787 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2845 seeds are put forward Round 1: 171 peptides, 36 chains. Longest chain 8 peptides. Score 0.272 Round 2: 191 peptides, 33 chains. Longest chain 19 peptides. Score 0.388 Round 3: 191 peptides, 34 chains. Longest chain 11 peptides. Score 0.374 Round 4: 201 peptides, 34 chains. Longest chain 22 peptides. Score 0.407 Round 5: 193 peptides, 30 chains. Longest chain 17 peptides. Score 0.438 Taking the results from Round 5 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6593 restraints for refining 2822 atoms. 5971 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2450 (Rfree = 0.000) for 2822 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2237 (Rfree = 0.000) for 2815 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.2105 (Rfree = 0.000) for 2809 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1669 (Rfree = 0.000) for 2805 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1603 (Rfree = 0.000) for 2796 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2848 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2865 seeds are put forward Round 1: 140 peptides, 30 chains. Longest chain 9 peptides. Score 0.249 Round 2: 166 peptides, 30 chains. Longest chain 15 peptides. Score 0.347 Round 3: 173 peptides, 31 chains. Longest chain 14 peptides. Score 0.356 Round 4: 174 peptides, 31 chains. Longest chain 10 peptides. Score 0.360 Round 5: 190 peptides, 31 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 5 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6608 restraints for refining 2822 atoms. 6003 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1929 (Rfree = 0.000) for 2822 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 2806 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1830 (Rfree = 0.000) for 2806 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1921 (Rfree = 0.000) for 2800 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1632 (Rfree = 0.000) for 2800 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2876 seeds are put forward Round 1: 141 peptides, 30 chains. Longest chain 8 peptides. Score 0.253 Round 2: 162 peptides, 30 chains. Longest chain 10 peptides. Score 0.332 Round 3: 171 peptides, 30 chains. Longest chain 13 peptides. Score 0.364 Round 4: 176 peptides, 30 chains. Longest chain 13 peptides. Score 0.382 Round 5: 183 peptides, 28 chains. Longest chain 18 peptides. Score 0.434 Taking the results from Round 5 Chains 28, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6511 restraints for refining 2819 atoms. 5919 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1965 (Rfree = 0.000) for 2819 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.1772 (Rfree = 0.000) for 2809 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.1860 (Rfree = 0.000) for 2800 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1843 (Rfree = 0.000) for 2800 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1862 (Rfree = 0.000) for 2799 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 2869 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 2902 seeds are put forward Round 1: 153 peptides, 32 chains. Longest chain 10 peptides. Score 0.267 Round 2: 172 peptides, 31 chains. Longest chain 15 peptides. Score 0.353 Round 3: 171 peptides, 31 chains. Longest chain 10 peptides. Score 0.349 Round 4: 174 peptides, 32 chains. Longest chain 12 peptides. Score 0.345 Round 5: 162 peptides, 29 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 2 Chains 31, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6614 restraints for refining 2821 atoms. 6081 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1913 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.1963 (Rfree = 0.000) for 2814 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 43: After refmac, R = 0.1653 (Rfree = 0.000) for 2808 atoms. Found 14 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1718 (Rfree = 0.000) for 2808 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1597 (Rfree = 0.000) for 2803 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2880 seeds are put forward Round 1: 145 peptides, 32 chains. Longest chain 6 peptides. Score 0.236 Round 2: 147 peptides, 27 chains. Longest chain 12 peptides. Score 0.325 Round 3: 148 peptides, 26 chains. Longest chain 11 peptides. Score 0.344 Round 4: 145 peptides, 24 chains. Longest chain 14 peptides. Score 0.365 Round 5: 151 peptides, 26 chains. Longest chain 10 peptides. Score 0.355 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 121, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4372 reflections ( 84.88 % complete ) and 6548 restraints for refining 2821 atoms. 6031 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1930 (Rfree = 0.000) for 2821 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2009 (Rfree = 0.000) for 2800 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1914 (Rfree = 0.000) for 2784 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1817 (Rfree = 0.000) for 2774 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:54:05 GMT 2018 Job finished. TimeTaking 31.91 Used memory is bytes: 16116216