null Tue 25 Dec 20:46:20 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 1vk8-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-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/1vk8-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-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 ============================================================ Tue 25 Dec 20:46:36 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/1vk8-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-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 266 and 0 Target number of residues in the AU: 266 Target solvent content: 0.6199 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: 1vk8-3.6-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.6-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 3.600 Wilson plot Bfac: 61.01 4070 reflections ( 95.85 % complete ) and 0 restraints for refining 3756 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3275 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3084 (Rfree = 0.000) for 3756 atoms. Found 24 (24 requested) and removed 60 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 3791 seeds are put forward NCS extension: 0 residues added, 3791 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.210 Round 2: 103 peptides, 21 chains. Longest chain 7 peptides. Score 0.269 Round 3: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.312 Round 4: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.359 Round 5: 104 peptides, 19 chains. Longest chain 8 peptides. Score 0.317 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7711 restraints for refining 3075 atoms. 7380 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2526 (Rfree = 0.000) for 3075 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2199 (Rfree = 0.000) for 3031 atoms. Found 12 (19 requested) and removed 22 (9 requested) atoms. Cycle 3: After refmac, R = 0.2056 (Rfree = 0.000) for 3003 atoms. Found 15 (19 requested) and removed 23 (9 requested) atoms. Cycle 4: After refmac, R = 0.2059 (Rfree = 0.000) for 2981 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2164 (Rfree = 0.000) for 2972 atoms. Found 16 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 3041 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3044 seeds are put forward Round 1: 106 peptides, 24 chains. Longest chain 6 peptides. Score 0.220 Round 2: 133 peptides, 27 chains. Longest chain 11 peptides. Score 0.292 Round 3: 140 peptides, 25 chains. Longest chain 12 peptides. Score 0.363 Round 4: 133 peptides, 23 chains. Longest chain 12 peptides. Score 0.371 Round 5: 141 peptides, 25 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 4 Chains 23, Residues 110, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6357 restraints for refining 2740 atoms. 5928 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1805 (Rfree = 0.000) for 2740 atoms. Found 13 (17 requested) and removed 25 (8 requested) atoms. Cycle 7: After refmac, R = 0.1744 (Rfree = 0.000) for 2710 atoms. Found 8 (17 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.1761 (Rfree = 0.000) for 2688 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.1915 (Rfree = 0.000) for 2677 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 10: After refmac, R = 0.1713 (Rfree = 0.000) for 2668 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.86 Search for helices and strands: 0 residues in 0 chains, 2767 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 2779 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 8 peptides. Score 0.275 Round 2: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.362 Round 3: 159 peptides, 28 chains. Longest chain 12 peptides. Score 0.390 Round 4: 166 peptides, 30 chains. Longest chain 12 peptides. Score 0.383 Round 5: 160 peptides, 30 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 3 Chains 29, Residues 131, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 5879 restraints for refining 2658 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1720 (Rfree = 0.000) for 2658 atoms. Found 11 (17 requested) and removed 20 (8 requested) atoms. Cycle 12: After refmac, R = 0.1559 (Rfree = 0.000) for 2634 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.1608 (Rfree = 0.000) for 2625 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.1595 (Rfree = 0.000) for 2608 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.1664 (Rfree = 0.000) for 2600 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2685 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2688 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 8 peptides. Score 0.265 Round 2: 138 peptides, 24 chains. Longest chain 11 peptides. Score 0.374 Round 3: 145 peptides, 26 chains. Longest chain 12 peptides. Score 0.366 Round 4: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.411 Round 5: 146 peptides, 26 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 4 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6158 restraints for refining 2727 atoms. 5659 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1655 (Rfree = 0.000) for 2727 atoms. Found 10 (17 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.1566 (Rfree = 0.000) for 2696 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.1630 (Rfree = 0.000) for 2687 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.1439 (Rfree = 0.000) for 2679 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.1494 (Rfree = 0.000) for 2670 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 2757 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2773 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 8 peptides. Score 0.288 Round 2: 143 peptides, 27 chains. Longest chain 10 peptides. Score 0.338 Round 3: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.394 Round 4: 160 peptides, 26 chains. Longest chain 11 peptides. Score 0.430 Round 5: 158 peptides, 25 chains. Longest chain 12 peptides. Score 0.440 Taking the results from Round 5 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6085 restraints for refining 2717 atoms. 5578 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1743 (Rfree = 0.000) for 2717 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.1597 (Rfree = 0.000) for 2701 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.1511 (Rfree = 0.000) for 2696 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.1480 (Rfree = 0.000) for 2689 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.1504 (Rfree = 0.000) for 2685 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2767 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.270 Round 2: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.359 Round 3: 136 peptides, 23 chains. Longest chain 13 peptides. Score 0.384 Round 4: 134 peptides, 23 chains. Longest chain 12 peptides. Score 0.375 Round 5: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 5 Chains 25, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6512 restraints for refining 2811 atoms. 6049 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1556 (Rfree = 0.000) for 2811 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 27: After refmac, R = 0.1430 (Rfree = 0.000) for 2787 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.1554 (Rfree = 0.000) for 2779 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 29: After refmac, R = 0.1368 (Rfree = 0.000) for 2777 atoms. Found 14 (17 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1450 (Rfree = 0.000) for 2777 atoms. Found 10 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward NCS extension: 0 residues added, 2844 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 8 peptides. Score 0.271 Round 2: 151 peptides, 30 chains. Longest chain 8 peptides. Score 0.317 Round 3: 153 peptides, 28 chains. Longest chain 10 peptides. Score 0.364 Round 4: 151 peptides, 26 chains. Longest chain 11 peptides. Score 0.392 Round 5: 159 peptides, 27 chains. Longest chain 15 peptides. Score 0.408 Taking the results from Round 5 Chains 27, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6735 restraints for refining 2899 atoms. 6234 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1717 (Rfree = 0.000) for 2899 atoms. Found 13 (18 requested) and removed 23 (9 requested) atoms. Cycle 32: After refmac, R = 0.1600 (Rfree = 0.000) for 2874 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.1084 (Rfree = 0.000) for 2864 atoms. Found 2 (18 requested) and removed 13 (9 requested) atoms. Cycle 34: After refmac, R = 0.1201 (Rfree = 0.000) for 2853 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.0943 (Rfree = 0.000) for 2848 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2952 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 8 peptides. Score 0.220 Round 2: 109 peptides, 22 chains. Longest chain 8 peptides. Score 0.278 Round 3: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.314 Round 4: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.323 Round 5: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.329 Taking the results from Round 5 Chains 20, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6952 restraints for refining 2903 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1511 (Rfree = 0.000) for 2903 atoms. Found 8 (18 requested) and removed 18 (9 requested) atoms. Cycle 37: After refmac, R = 0.1511 (Rfree = 0.000) for 2885 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 38: After refmac, R = 0.1536 (Rfree = 0.000) for 2880 atoms. Found 17 (18 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.1485 (Rfree = 0.000) for 2880 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 40: After refmac, R = 0.0965 (Rfree = 0.000) for 2884 atoms. Found 2 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.82 Search for helices and strands: 0 residues in 0 chains, 2960 seeds are put forward NCS extension: 0 residues added, 2960 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.259 Round 2: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.262 Round 3: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.350 Round 4: 115 peptides, 19 chains. Longest chain 16 peptides. Score 0.369 Round 5: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.348 Taking the results from Round 4 Chains 19, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6835 restraints for refining 2901 atoms. 6470 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1411 (Rfree = 0.000) for 2901 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. Cycle 42: After refmac, R = 0.1567 (Rfree = 0.000) for 2893 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 43: After refmac, R = 0.1443 (Rfree = 0.000) for 2888 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.1410 (Rfree = 0.000) for 2884 atoms. Found 11 (18 requested) and removed 18 (9 requested) atoms. Cycle 45: After refmac, R = 0.1458 (Rfree = 0.000) for 2876 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.82 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 2994 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.217 Round 2: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.250 Round 3: 108 peptides, 21 chains. Longest chain 9 peptides. Score 0.294 Round 4: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.336 Round 5: 113 peptides, 23 chains. Longest chain 9 peptides. Score 0.277 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 89, 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. 4070 reflections ( 95.85 % complete ) and 6760 restraints for refining 2900 atoms. 6423 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1415 (Rfree = 0.000) for 2900 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1532 (Rfree = 0.000) for 2884 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1484 (Rfree = 0.000) for 2872 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.0933 (Rfree = 0.000) for 2860 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:43:49 GMT 2018 Job finished. TimeTaking 57.48 Used memory is bytes: 10822704