Mon 24 Dec 01:12:40 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 1vk8-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-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/1vk8-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-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 01:12:45 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-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 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-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.8-parrot-mrncs.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 3772 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3055 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3241 (Rfree = 0.000) for 3772 atoms. Found 20 (20 requested) and removed 81 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 3785 seeds are put forward NCS extension: 0 residues added, 3785 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 7 peptides. Score 0.242 Round 2: 156 peptides, 28 chains. Longest chain 11 peptides. Score 0.377 Round 3: 171 peptides, 29 chains. Longest chain 13 peptides. Score 0.422 Round 4: 158 peptides, 24 chains. Longest chain 12 peptides. Score 0.458 Round 5: 166 peptides, 27 chains. Longest chain 17 peptides. Score 0.437 Taking the results from Round 4 Chains 24, Residues 134, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 7465 restraints for refining 3065 atoms. 6934 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2289 (Rfree = 0.000) for 3065 atoms. Found 13 (16 requested) and removed 30 (8 requested) atoms. Cycle 2: After refmac, R = 0.2092 (Rfree = 0.000) for 3009 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 3: After refmac, R = 0.2043 (Rfree = 0.000) for 2965 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 4: After refmac, R = 0.1476 (Rfree = 0.000) for 2930 atoms. Found 5 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.1928 (Rfree = 0.000) for 2907 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 3024 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 3034 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 8 peptides. Score 0.271 Round 2: 154 peptides, 28 chains. Longest chain 12 peptides. Score 0.368 Round 3: 168 peptides, 30 chains. Longest chain 10 peptides. Score 0.392 Round 4: 170 peptides, 28 chains. Longest chain 13 peptides. Score 0.436 Round 5: 176 peptides, 30 chains. Longest chain 11 peptides. Score 0.425 Taking the results from Round 4 Chains 28, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6609 restraints for refining 2808 atoms. 6069 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2199 (Rfree = 0.000) for 2808 atoms. Found 15 (15 requested) and removed 38 (7 requested) atoms. Cycle 7: After refmac, R = 0.1894 (Rfree = 0.000) for 2756 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.1767 (Rfree = 0.000) for 2735 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.1850 (Rfree = 0.000) for 2717 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.1790 (Rfree = 0.000) for 2711 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 2802 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2820 seeds are put forward Round 1: 140 peptides, 32 chains. Longest chain 6 peptides. Score 0.226 Round 2: 156 peptides, 29 chains. Longest chain 11 peptides. Score 0.358 Round 3: 175 peptides, 29 chains. Longest chain 12 peptides. Score 0.438 Round 4: 162 peptides, 29 chains. Longest chain 11 peptides. Score 0.384 Round 5: 158 peptides, 27 chains. Longest chain 14 peptides. Score 0.404 Taking the results from Round 3 Chains 29, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6236 restraints for refining 2713 atoms. 5681 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1784 (Rfree = 0.000) for 2713 atoms. Found 11 (14 requested) and removed 32 (7 requested) atoms. Cycle 12: After refmac, R = 0.1728 (Rfree = 0.000) for 2683 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 13: After refmac, R = 0.1775 (Rfree = 0.000) for 2668 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 14: After refmac, R = 0.1432 (Rfree = 0.000) for 2658 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.1490 (Rfree = 0.000) for 2650 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward NCS extension: 0 residues added, 2804 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 7 peptides. Score 0.261 Round 2: 157 peptides, 27 chains. Longest chain 12 peptides. Score 0.400 Round 3: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.390 Round 4: 158 peptides, 28 chains. Longest chain 11 peptides. Score 0.386 Round 5: 159 peptides, 29 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 2 Chains 27, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6336 restraints for refining 2740 atoms. 5843 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1535 (Rfree = 0.000) for 2740 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.1668 (Rfree = 0.000) for 2727 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 18: After refmac, R = 0.1735 (Rfree = 0.000) for 2713 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1747 (Rfree = 0.000) for 2696 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 20: After refmac, R = 0.1481 (Rfree = 0.000) for 2677 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 2796 seeds are put forward NCS extension: 0 residues added, 2796 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 8 peptides. Score 0.249 Round 2: 145 peptides, 28 chains. Longest chain 12 peptides. Score 0.328 Round 3: 157 peptides, 25 chains. Longest chain 12 peptides. Score 0.436 Round 4: 159 peptides, 27 chains. Longest chain 11 peptides. Score 0.408 Round 5: 167 peptides, 27 chains. Longest chain 11 peptides. Score 0.441 Taking the results from Round 5 Chains 27, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6599 restraints for refining 2821 atoms. 6066 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1991 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 41 (7 requested) atoms. Cycle 22: After refmac, R = 0.1973 (Rfree = 0.000) for 2779 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 23: After refmac, R = 0.1693 (Rfree = 0.000) for 2762 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 24: After refmac, R = 0.1738 (Rfree = 0.000) for 2744 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.1724 (Rfree = 0.000) for 2742 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 2840 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2846 seeds are put forward Round 1: 121 peptides, 26 chains. Longest chain 6 peptides. Score 0.254 Round 2: 127 peptides, 23 chains. Longest chain 9 peptides. Score 0.343 Round 3: 131 peptides, 23 chains. Longest chain 9 peptides. Score 0.362 Round 4: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.339 Round 5: 139 peptides, 25 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 3 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 6600 restraints for refining 2755 atoms. 6191 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1677 (Rfree = 0.000) for 2755 atoms. Found 15 (15 requested) and removed 34 (7 requested) atoms. Cycle 27: After refmac, R = 0.1758 (Rfree = 0.000) for 2724 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 28: After refmac, R = 0.1178 (Rfree = 0.000) for 2708 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.1044 (Rfree = 0.000) for 2702 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1608 (Rfree = 0.000) for 2693 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward NCS extension: 0 residues added, 2804 seeds are put forward Round 1: 113 peptides, 25 chains. Longest chain 7 peptides. Score 0.235 Round 2: 136 peptides, 27 chains. Longest chain 8 peptides. Score 0.306 Round 3: 151 peptides, 29 chains. Longest chain 8 peptides. Score 0.336 Round 4: 135 peptides, 27 chains. Longest chain 8 peptides. Score 0.301 Round 5: 136 peptides, 25 chains. Longest chain 12 peptides. Score 0.345 Taking the results from Round 5 Chains 25, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6519 restraints for refining 2795 atoms. 6100 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1657 (Rfree = 0.000) for 2795 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 32: After refmac, R = 0.1929 (Rfree = 0.000) for 2776 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 33: After refmac, R = 0.1626 (Rfree = 0.000) for 2764 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.1619 (Rfree = 0.000) for 2760 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 35: After refmac, R = 0.1014 (Rfree = 0.000) for 2758 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 0 residues added, 2883 seeds are put forward Round 1: 101 peptides, 23 chains. Longest chain 7 peptides. Score 0.216 Round 2: 125 peptides, 22 chains. Longest chain 14 peptides. Score 0.354 Round 3: 128 peptides, 24 chains. Longest chain 10 peptides. Score 0.328 Round 4: 132 peptides, 21 chains. Longest chain 10 peptides. Score 0.405 Round 5: 135 peptides, 23 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 4 Chains 21, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6514 restraints for refining 2755 atoms. 6091 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1705 (Rfree = 0.000) for 2755 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 37: After refmac, R = 0.1838 (Rfree = 0.000) for 2748 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 38: After refmac, R = 0.1832 (Rfree = 0.000) for 2733 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.1607 (Rfree = 0.000) for 2733 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.1904 (Rfree = 0.000) for 2730 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 4.07 Search for helices and strands: 0 residues in 0 chains, 2853 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2865 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 8 peptides. Score 0.240 Round 2: 119 peptides, 22 chains. Longest chain 12 peptides. Score 0.326 Round 3: 117 peptides, 24 chains. Longest chain 7 peptides. Score 0.276 Round 4: 133 peptides, 23 chains. Longest chain 12 peptides. Score 0.371 Round 5: 127 peptides, 23 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 4 Chains 23, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6395 restraints for refining 2697 atoms. 5978 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1737 (Rfree = 0.000) for 2697 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 42: After refmac, R = 0.1642 (Rfree = 0.000) for 2684 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.1768 (Rfree = 0.000) for 2681 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 44: After refmac, R = 0.1633 (Rfree = 0.000) for 2676 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1711 (Rfree = 0.000) for 2671 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 2775 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2789 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 6 peptides. Score 0.220 Round 2: 112 peptides, 21 chains. Longest chain 11 peptides. Score 0.314 Round 3: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.310 Round 4: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.319 Round 5: 104 peptides, 21 chains. Longest chain 12 peptides. Score 0.274 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 82, 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 6557 restraints for refining 2717 atoms. 6247 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1630 (Rfree = 0.000) for 2717 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1625 (Rfree = 0.000) for 2706 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1745 (Rfree = 0.000) for 2692 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1576 (Rfree = 0.000) for 2681 atoms. TimeTaking 41.72