null Mon 24 Dec 07:26:40 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 1vk8-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-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/1vk8-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-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 07:26:45 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/1vk8-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-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 258 and 0 Target number of residues in the AU: 258 Target solvent content: 0.6313 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-3.8-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.55 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: 41.711 3.800 Wilson plot Bfac: 66.82 3467 reflections ( 95.99 % complete ) and 0 restraints for refining 3760 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2975 (Rfree = 0.000) for 3760 atoms. Found 20 (20 requested) and removed 77 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 3758 seeds are put forward NCS extension: 0 residues added, 3758 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 7 peptides. Score 0.227 Round 2: 125 peptides, 24 chains. Longest chain 10 peptides. Score 0.314 Round 3: 139 peptides, 24 chains. Longest chain 14 peptides. Score 0.378 Round 4: 152 peptides, 28 chains. Longest chain 14 peptides. Score 0.359 Round 5: 136 peptides, 25 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 3 Chains 24, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 7481 restraints for refining 3068 atoms. 7045 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2399 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 33 (8 requested) atoms. Cycle 2: After refmac, R = 0.1994 (Rfree = 0.000) for 3004 atoms. Found 8 (16 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.1906 (Rfree = 0.000) for 2958 atoms. Found 9 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2007 (Rfree = 0.000) for 2929 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 5: After refmac, R = 0.2220 (Rfree = 0.000) for 2909 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 3004 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3026 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.280 Round 2: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.322 Round 3: 126 peptides, 25 chains. Longest chain 10 peptides. Score 0.299 Round 4: 147 peptides, 28 chains. Longest chain 10 peptides. Score 0.337 Round 5: 139 peptides, 27 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 4 Chains 28, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6365 restraints for refining 2710 atoms. 5917 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1751 (Rfree = 0.000) for 2710 atoms. Found 10 (14 requested) and removed 26 (7 requested) atoms. Cycle 7: After refmac, R = 0.1960 (Rfree = 0.000) for 2678 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.1717 (Rfree = 0.000) for 2665 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 9: After refmac, R = 0.1795 (Rfree = 0.000) for 2651 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.1250 (Rfree = 0.000) for 2649 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2732 seeds are put forward NCS extension: 0 residues added, 2732 seeds are put forward Round 1: 132 peptides, 27 chains. Longest chain 8 peptides. Score 0.287 Round 2: 169 peptides, 33 chains. Longest chain 9 peptides. Score 0.341 Round 3: 166 peptides, 28 chains. Longest chain 15 peptides. Score 0.419 Round 4: 149 peptides, 25 chains. Longest chain 12 peptides. Score 0.402 Round 5: 163 peptides, 28 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 3 Chains 28, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6394 restraints for refining 2767 atoms. 5870 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1694 (Rfree = 0.000) for 2767 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 12: After refmac, R = 0.1948 (Rfree = 0.000) for 2748 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 13: After refmac, R = 0.1644 (Rfree = 0.000) for 2734 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 14: After refmac, R = 0.1645 (Rfree = 0.000) for 2724 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.1612 (Rfree = 0.000) for 2720 atoms. Found 13 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 2805 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2823 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.269 Round 2: 153 peptides, 31 chains. Longest chain 9 peptides. Score 0.307 Round 3: 146 peptides, 28 chains. Longest chain 10 peptides. Score 0.333 Round 4: 158 peptides, 25 chains. Longest chain 15 peptides. Score 0.440 Round 5: 149 peptides, 26 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 4 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6674 restraints for refining 2858 atoms. 6148 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1755 (Rfree = 0.000) for 2858 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.1882 (Rfree = 0.000) for 2844 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 18: After refmac, R = 0.1765 (Rfree = 0.000) for 2832 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 19: After refmac, R = 0.1692 (Rfree = 0.000) for 2822 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.1718 (Rfree = 0.000) for 2816 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2881 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2894 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 7 peptides. Score 0.239 Round 2: 139 peptides, 26 chains. Longest chain 16 peptides. Score 0.339 Round 3: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.306 Round 4: 132 peptides, 22 chains. Longest chain 11 peptides. Score 0.385 Round 5: 130 peptides, 23 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 4 Chains 22, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6832 restraints for refining 2857 atoms. 6414 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2268 (Rfree = 0.000) for 2857 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 22: After refmac, R = 0.1459 (Rfree = 0.000) for 2835 atoms. Found 8 (15 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.1610 (Rfree = 0.000) for 2817 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 24: After refmac, R = 0.2074 (Rfree = 0.000) for 2806 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 25: After refmac, R = 0.1680 (Rfree = 0.000) for 2802 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 2882 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2894 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 8 peptides. Score 0.226 Round 2: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.317 Round 3: 121 peptides, 21 chains. Longest chain 9 peptides. Score 0.356 Round 4: 125 peptides, 20 chains. Longest chain 13 peptides. Score 0.394 Round 5: 127 peptides, 21 chains. Longest chain 11 peptides. Score 0.383 Taking the results from Round 4 Chains 20, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6304 restraints for refining 2718 atoms. 5904 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2072 (Rfree = 0.000) for 2718 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 27: After refmac, R = 0.1887 (Rfree = 0.000) for 2705 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 28: After refmac, R = 0.1802 (Rfree = 0.000) for 2703 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.1703 (Rfree = 0.000) for 2695 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.1926 (Rfree = 0.000) for 2694 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 2766 seeds are put forward NCS extension: 0 residues added, 2766 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 8 peptides. Score 0.234 Round 2: 124 peptides, 25 chains. Longest chain 9 peptides. Score 0.289 Round 3: 126 peptides, 24 chains. Longest chain 11 peptides. Score 0.319 Round 4: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.299 Round 5: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 5 Chains 23, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6592 restraints for refining 2792 atoms. 6183 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2047 (Rfree = 0.000) for 2792 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 32: After refmac, R = 0.1697 (Rfree = 0.000) for 2772 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.1761 (Rfree = 0.000) for 2764 atoms. Found 10 (15 requested) and removed 15 (7 requested) atoms. Cycle 34: After refmac, R = 0.1715 (Rfree = 0.000) for 2757 atoms. Found 10 (15 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.1746 (Rfree = 0.000) for 2750 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2833 seeds are put forward Round 1: 89 peptides, 21 chains. Longest chain 7 peptides. Score 0.195 Round 2: 102 peptides, 22 chains. Longest chain 8 peptides. Score 0.242 Round 3: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.262 Round 4: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.275 Round 5: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 5 Chains 19, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6253 restraints for refining 2693 atoms. 5924 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1613 (Rfree = 0.000) for 2693 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 37: After refmac, R = 0.1725 (Rfree = 0.000) for 2683 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.1726 (Rfree = 0.000) for 2682 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 39: After refmac, R = 0.1655 (Rfree = 0.000) for 2675 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.1706 (Rfree = 0.000) for 2671 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2755 seeds are put forward Round 1: 75 peptides, 18 chains. Longest chain 6 peptides. Score 0.185 Round 2: 89 peptides, 19 chains. Longest chain 10 peptides. Score 0.240 Round 3: 96 peptides, 18 chains. Longest chain 13 peptides. Score 0.299 Round 4: 101 peptides, 20 chains. Longest chain 12 peptides. Score 0.281 Round 5: 103 peptides, 19 chains. Longest chain 16 peptides. Score 0.312 Taking the results from Round 5 Chains 19, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6139 restraints for refining 2658 atoms. 5822 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1709 (Rfree = 0.000) for 2658 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 42: After refmac, R = 0.1868 (Rfree = 0.000) for 2647 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 43: After refmac, R = 0.1905 (Rfree = 0.000) for 2634 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 44: After refmac, R = 0.1617 (Rfree = 0.000) for 2631 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1190 (Rfree = 0.000) for 2625 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2735 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 8 peptides. Score 0.224 Round 2: 91 peptides, 19 chains. Longest chain 9 peptides. Score 0.251 Round 3: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.250 Round 4: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.279 Round 5: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.279 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 84, 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 1vk8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3467 reflections ( 95.99 % complete ) and 6127 restraints for refining 2679 atoms. 5812 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1720 (Rfree = 0.000) for 2679 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1873 (Rfree = 0.000) for 2666 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1641 (Rfree = 0.000) for 2653 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1160 (Rfree = 0.000) for 2642 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:00:03 GMT 2018 Job finished. TimeTaking 33.39 Used memory is bytes: 14349248