Mon 24 Dec 00:18:43 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 1vk8-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-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/1vk8-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-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 00:18:47 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/1vk8-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.6-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 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-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: 1vk8-3.6-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 3.600 Wilson plot Bfac: 61.01 4070 reflections ( 95.85 % complete ) and 0 restraints for refining 3740 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.2978 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2908 (Rfree = 0.000) for 3740 atoms. Found 23 (23 requested) and removed 47 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.91 Search for helices and strands: 0 residues in 0 chains, 3796 seeds are put forward NCS extension: 0 residues added, 3796 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 7 peptides. Score 0.254 Round 2: 160 peptides, 30 chains. Longest chain 12 peptides. Score 0.357 Round 3: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.410 Round 4: 201 peptides, 32 chains. Longest chain 14 peptides. Score 0.489 Round 5: 212 peptides, 34 chains. Longest chain 11 peptides. Score 0.498 Taking the results from Round 5 Chains 35, Residues 178, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7000 restraints for refining 3074 atoms. 6293 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2048 (Rfree = 0.000) for 3074 atoms. Found 7 (19 requested) and removed 33 (9 requested) atoms. Cycle 2: After refmac, R = 0.1959 (Rfree = 0.000) for 3002 atoms. Found 6 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.1773 (Rfree = 0.000) for 2976 atoms. Found 3 (19 requested) and removed 16 (9 requested) atoms. Cycle 4: After refmac, R = 0.1495 (Rfree = 0.000) for 2945 atoms. Found 3 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.1697 (Rfree = 0.000) for 2929 atoms. Found 8 (18 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 3063 seeds are put forward NCS extension: 0 residues added, 3063 seeds are put forward Round 1: 144 peptides, 30 chains. Longest chain 8 peptides. Score 0.285 Round 2: 179 peptides, 32 chains. Longest chain 10 peptides. Score 0.402 Round 3: 189 peptides, 34 chains. Longest chain 12 peptides. Score 0.408 Round 4: 196 peptides, 35 chains. Longest chain 12 peptides. Score 0.420 Round 5: 196 peptides, 35 chains. Longest chain 10 peptides. Score 0.420 Taking the results from Round 5 Chains 35, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 7180 restraints for refining 2976 atoms. 6571 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1899 (Rfree = 0.000) for 2976 atoms. Found 15 (19 requested) and removed 23 (9 requested) atoms. Cycle 7: After refmac, R = 0.2073 (Rfree = 0.000) for 2942 atoms. Found 13 (19 requested) and removed 20 (9 requested) atoms. Cycle 8: After refmac, R = 0.1986 (Rfree = 0.000) for 2915 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.2052 (Rfree = 0.000) for 2900 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.1921 (Rfree = 0.000) for 2894 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 3019 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 3024 seeds are put forward Round 1: 135 peptides, 26 chains. Longest chain 12 peptides. Score 0.321 Round 2: 189 peptides, 36 chains. Longest chain 9 peptides. Score 0.373 Round 3: 192 peptides, 36 chains. Longest chain 10 peptides. Score 0.386 Round 4: 199 peptides, 34 chains. Longest chain 10 peptides. Score 0.448 Round 5: 188 peptides, 30 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 5 Chains 30, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6767 restraints for refining 2885 atoms. 6165 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2031 (Rfree = 0.000) for 2885 atoms. Found 16 (18 requested) and removed 26 (9 requested) atoms. Cycle 12: After refmac, R = 0.1730 (Rfree = 0.000) for 2860 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 13: After refmac, R = 0.1614 (Rfree = 0.000) for 2848 atoms. Found 14 (18 requested) and removed 19 (9 requested) atoms. Cycle 14: After refmac, R = 0.1697 (Rfree = 0.000) for 2837 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.1585 (Rfree = 0.000) for 2836 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 2931 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2952 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 11 peptides. Score 0.328 Round 2: 192 peptides, 32 chains. Longest chain 13 peptides. Score 0.454 Round 3: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.416 Round 4: 194 peptides, 31 chains. Longest chain 16 peptides. Score 0.479 Round 5: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.447 Taking the results from Round 4 Chains 31, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6743 restraints for refining 2904 atoms. 6122 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2143 (Rfree = 0.000) for 2904 atoms. Found 16 (18 requested) and removed 28 (9 requested) atoms. Cycle 17: After refmac, R = 0.1942 (Rfree = 0.000) for 2867 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 18: After refmac, R = 0.1862 (Rfree = 0.000) for 2860 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 19: After refmac, R = 0.1934 (Rfree = 0.000) for 2849 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1827 (Rfree = 0.000) for 2845 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 0 residues added, 2948 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 11 peptides. Score 0.271 Round 2: 165 peptides, 27 chains. Longest chain 10 peptides. Score 0.433 Round 3: 157 peptides, 26 chains. Longest chain 15 peptides. Score 0.418 Round 4: 156 peptides, 25 chains. Longest chain 14 peptides. Score 0.432 Round 5: 163 peptides, 26 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 5 Chains 26, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6504 restraints for refining 2820 atoms. 5982 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1979 (Rfree = 0.000) for 2820 atoms. Found 16 (18 requested) and removed 28 (9 requested) atoms. Cycle 22: After refmac, R = 0.1769 (Rfree = 0.000) for 2792 atoms. Found 12 (18 requested) and removed 20 (9 requested) atoms. Cycle 23: After refmac, R = 0.1469 (Rfree = 0.000) for 2774 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.1382 (Rfree = 0.000) for 2768 atoms. Found 7 (17 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1403 (Rfree = 0.000) for 2756 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2861 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2875 seeds are put forward Round 1: 150 peptides, 31 chains. Longest chain 12 peptides. Score 0.293 Round 2: 169 peptides, 32 chains. Longest chain 10 peptides. Score 0.360 Round 3: 165 peptides, 26 chains. Longest chain 13 peptides. Score 0.450 Round 4: 177 peptides, 27 chains. Longest chain 19 peptides. Score 0.480 Round 5: 178 peptides, 29 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 4 Chains 27, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6287 restraints for refining 2820 atoms. 5714 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1730 (Rfree = 0.000) for 2820 atoms. Found 15 (18 requested) and removed 19 (9 requested) atoms. Cycle 27: After refmac, R = 0.1621 (Rfree = 0.000) for 2798 atoms. Found 17 (18 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.1460 (Rfree = 0.000) for 2793 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.1468 (Rfree = 0.000) for 2789 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 30: After refmac, R = 0.1399 (Rfree = 0.000) for 2786 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.84 Search for helices and strands: 0 residues in 0 chains, 2882 seeds are put forward NCS extension: 43 residues added (1 deleted due to clashes), 2925 seeds are put forward Round 1: 128 peptides, 27 chains. Longest chain 8 peptides. Score 0.268 Round 2: 140 peptides, 26 chains. Longest chain 12 peptides. Score 0.344 Round 3: 148 peptides, 27 chains. Longest chain 10 peptides. Score 0.361 Round 4: 144 peptides, 24 chains. Longest chain 11 peptides. Score 0.400 Round 5: 149 peptides, 24 chains. Longest chain 10 peptides. Score 0.421 Taking the results from Round 5 Chains 24, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6423 restraints for refining 2809 atoms. 5947 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1440 (Rfree = 0.000) for 2809 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 32: After refmac, R = 0.1515 (Rfree = 0.000) for 2803 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.1450 (Rfree = 0.000) for 2799 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.0998 (Rfree = 0.000) for 2802 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.1129 (Rfree = 0.000) for 2791 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2895 seeds are put forward Round 1: 134 peptides, 28 chains. Longest chain 8 peptides. Score 0.277 Round 2: 165 peptides, 28 chains. Longest chain 16 peptides. Score 0.415 Round 3: 161 peptides, 31 chains. Longest chain 10 peptides. Score 0.343 Round 4: 172 peptides, 28 chains. Longest chain 14 peptides. Score 0.444 Round 5: 152 peptides, 27 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 28, Residues 144, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6255 restraints for refining 2834 atoms. 5686 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1532 (Rfree = 0.000) for 2834 atoms. Found 11 (18 requested) and removed 19 (9 requested) atoms. Cycle 37: After refmac, R = 0.1431 (Rfree = 0.000) for 2821 atoms. Found 16 (18 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.1360 (Rfree = 0.000) for 2816 atoms. Found 12 (18 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.1307 (Rfree = 0.000) for 2809 atoms. Found 13 (18 requested) and removed 15 (9 requested) atoms. Cycle 40: After refmac, R = 0.1280 (Rfree = 0.000) for 2807 atoms. Found 6 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2890 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2914 seeds are put forward Round 1: 125 peptides, 25 chains. Longest chain 9 peptides. Score 0.294 Round 2: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.345 Round 3: 139 peptides, 24 chains. Longest chain 10 peptides. Score 0.378 Round 4: 132 peptides, 24 chains. Longest chain 8 peptides. Score 0.347 Round 5: 134 peptides, 22 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4070 reflections ( 95.85 % complete ) and 6705 restraints for refining 2867 atoms. 6279 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1437 (Rfree = 0.000) for 2867 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. Cycle 42: After refmac, R = 0.1307 (Rfree = 0.000) for 2857 atoms. Found 14 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1256 (Rfree = 0.000) for 2856 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.1238 (Rfree = 0.000) for 2851 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.1344 (Rfree = 0.000) for 2847 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.83 Search for helices and strands: 0 residues in 0 chains, 2934 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2937 seeds are put forward Round 1: 125 peptides, 29 chains. Longest chain 7 peptides. Score 0.213 Round 2: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.378 Round 3: 143 peptides, 25 chains. Longest chain 10 peptides. Score 0.377 Round 4: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.390 Round 5: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 121, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % 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 6787 restraints for refining 2919 atoms. 6316 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1321 (Rfree = 0.000) for 2919 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1085 (Rfree = 0.000) for 2905 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1015 (Rfree = 0.000) for 2891 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1100 (Rfree = 0.000) for 2880 atoms. TimeTaking 39.28