null Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vk8-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:06 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/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-3.8-parrot-hancs/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-hancs.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-hancs.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 3745 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3002 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3123 (Rfree = 0.000) for 3745 atoms. Found 20 (20 requested) and removed 83 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 3765 seeds are put forward NCS extension: 0 residues added, 3765 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 8 peptides. Score 0.239 Round 2: 161 peptides, 27 chains. Longest chain 11 peptides. Score 0.416 Round 3: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.413 Round 4: 177 peptides, 29 chains. Longest chain 12 peptides. Score 0.446 Round 5: 190 peptides, 27 chains. Longest chain 13 peptides. Score 0.529 Taking the results from Round 5 Chains 27, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 7331 restraints for refining 3068 atoms. 6706 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2264 (Rfree = 0.000) for 3068 atoms. Found 14 (16 requested) and removed 36 (8 requested) atoms. Cycle 2: After refmac, R = 0.2035 (Rfree = 0.000) for 2999 atoms. Found 12 (16 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.1885 (Rfree = 0.000) for 2968 atoms. Found 15 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.1993 (Rfree = 0.000) for 2952 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 5: After refmac, R = 0.1874 (Rfree = 0.000) for 2914 atoms. Found 14 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 4.05 Search for helices and strands: 0 residues in 0 chains, 3040 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3053 seeds are put forward Round 1: 139 peptides, 30 chains. Longest chain 14 peptides. Score 0.261 Round 2: 155 peptides, 30 chains. Longest chain 9 peptides. Score 0.335 Round 3: 152 peptides, 28 chains. Longest chain 10 peptides. Score 0.359 Round 4: 160 peptides, 29 chains. Longest chain 10 peptides. Score 0.376 Round 5: 162 peptides, 28 chains. Longest chain 10 peptides. Score 0.403 Taking the results from Round 5 Chains 28, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6907 restraints for refining 2875 atoms. 6399 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1949 (Rfree = 0.000) for 2875 atoms. Found 15 (15 requested) and removed 34 (7 requested) atoms. Cycle 7: After refmac, R = 0.1802 (Rfree = 0.000) for 2834 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 8: After refmac, R = 0.1876 (Rfree = 0.000) for 2819 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 9: After refmac, R = 0.1595 (Rfree = 0.000) for 2806 atoms. Found 14 (15 requested) and removed 18 (7 requested) atoms. Cycle 10: After refmac, R = 0.1668 (Rfree = 0.000) for 2798 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2937 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2948 seeds are put forward Round 1: 142 peptides, 31 chains. Longest chain 7 peptides. Score 0.256 Round 2: 149 peptides, 26 chains. Longest chain 9 peptides. Score 0.384 Round 3: 150 peptides, 24 chains. Longest chain 10 peptides. Score 0.425 Round 4: 147 peptides, 24 chains. Longest chain 10 peptides. Score 0.412 Round 5: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 24, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6964 restraints for refining 2893 atoms. 6484 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1783 (Rfree = 0.000) for 2893 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 12: After refmac, R = 0.2013 (Rfree = 0.000) for 2870 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. Cycle 13: After refmac, R = 0.1885 (Rfree = 0.000) for 2845 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 14: After refmac, R = 0.1730 (Rfree = 0.000) for 2829 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 15: After refmac, R = 0.1663 (Rfree = 0.000) for 2820 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 0 residues added, 2958 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 10 peptides. Score 0.239 Round 2: 142 peptides, 28 chains. Longest chain 9 peptides. Score 0.314 Round 3: 151 peptides, 28 chains. Longest chain 10 peptides. Score 0.355 Round 4: 147 peptides, 27 chains. Longest chain 10 peptides. Score 0.356 Round 5: 145 peptides, 25 chains. Longest chain 16 peptides. Score 0.385 Taking the results from Round 5 Chains 25, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6870 restraints for refining 2833 atoms. 6415 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2161 (Rfree = 0.000) for 2833 atoms. Found 15 (15 requested) and removed 29 (7 requested) atoms. Cycle 17: After refmac, R = 0.1852 (Rfree = 0.000) for 2805 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 18: After refmac, R = 0.1840 (Rfree = 0.000) for 2798 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 19: After refmac, R = 0.1987 (Rfree = 0.000) for 2787 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 20: After refmac, R = 0.1883 (Rfree = 0.000) for 2774 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2904 seeds are put forward Round 1: 109 peptides, 24 chains. Longest chain 7 peptides. Score 0.236 Round 2: 117 peptides, 22 chains. Longest chain 11 peptides. Score 0.317 Round 3: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.365 Round 4: 145 peptides, 24 chains. Longest chain 12 peptides. Score 0.404 Round 5: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 4 Chains 24, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6421 restraints for refining 2771 atoms. 5961 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1801 (Rfree = 0.000) for 2771 atoms. Found 15 (15 requested) and removed 26 (7 requested) atoms. Cycle 22: After refmac, R = 0.1642 (Rfree = 0.000) for 2754 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 23: After refmac, R = 0.1781 (Rfree = 0.000) for 2737 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 24: After refmac, R = 0.1589 (Rfree = 0.000) for 2730 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.1661 (Rfree = 0.000) for 2727 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 4.10 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward NCS extension: 0 residues added, 2820 seeds are put forward Round 1: 115 peptides, 26 chains. Longest chain 8 peptides. Score 0.224 Round 2: 149 peptides, 28 chains. Longest chain 10 peptides. Score 0.346 Round 3: 143 peptides, 25 chains. Longest chain 13 peptides. Score 0.377 Round 4: 147 peptides, 24 chains. Longest chain 13 peptides. Score 0.412 Round 5: 148 peptides, 27 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 4 Chains 24, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6667 restraints for refining 2807 atoms. 6199 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1664 (Rfree = 0.000) for 2807 atoms. Found 6 (15 requested) and removed 19 (7 requested) atoms. Cycle 27: After refmac, R = 0.1716 (Rfree = 0.000) for 2783 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 28: After refmac, R = 0.1557 (Rfree = 0.000) for 2768 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.1673 (Rfree = 0.000) for 2753 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 30: After refmac, R = 0.1069 (Rfree = 0.000) for 2749 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 2830 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2847 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 6 peptides. Score 0.220 Round 2: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.342 Round 3: 113 peptides, 23 chains. Longest chain 7 peptides. Score 0.277 Round 4: 111 peptides, 21 chains. Longest chain 9 peptides. Score 0.309 Round 5: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.354 Taking the results from Round 5 Chains 22, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6679 restraints for refining 2775 atoms. 6289 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1654 (Rfree = 0.000) for 2775 atoms. Found 8 (15 requested) and removed 25 (7 requested) atoms. Cycle 32: After refmac, R = 0.1766 (Rfree = 0.000) for 2750 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 33: After refmac, R = 0.1672 (Rfree = 0.000) for 2746 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 34: After refmac, R = 0.1042 (Rfree = 0.000) for 2742 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. Cycle 35: After refmac, R = 0.0829 (Rfree = 0.000) for 2730 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 4.10 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward NCS extension: 0 residues added, 2822 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 7 peptides. Score 0.220 Round 2: 128 peptides, 24 chains. Longest chain 12 peptides. Score 0.328 Round 3: 135 peptides, 24 chains. Longest chain 12 peptides. Score 0.360 Round 4: 122 peptides, 23 chains. Longest chain 12 peptides. Score 0.320 Round 5: 133 peptides, 24 chains. Longest chain 9 peptides. Score 0.351 Taking the results from Round 3 Chains 24, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6587 restraints for refining 2804 atoms. 6167 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1684 (Rfree = 0.000) for 2804 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 37: After refmac, R = 0.1491 (Rfree = 0.000) for 2791 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.1458 (Rfree = 0.000) for 2784 atoms. Found 13 (15 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.1592 (Rfree = 0.000) for 2777 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1464 (Rfree = 0.000) for 2779 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 4.10 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 0 residues added, 2879 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 5 peptides. Score 0.218 Round 2: 120 peptides, 24 chains. Longest chain 8 peptides. Score 0.290 Round 3: 116 peptides, 21 chains. Longest chain 8 peptides. Score 0.333 Round 4: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.357 Round 5: 112 peptides, 19 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 4 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3467 reflections ( 95.99 % complete ) and 6820 restraints for refining 2803 atoms. 6452 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1719 (Rfree = 0.000) for 2803 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 42: After refmac, R = 0.1942 (Rfree = 0.000) for 2793 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 43: After refmac, R = 0.1509 (Rfree = 0.000) for 2783 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.1094 (Rfree = 0.000) for 2780 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.0879 (Rfree = 0.000) for 2773 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.11 Search for helices and strands: 0 residues in 0 chains, 2864 seeds are put forward NCS extension: 0 residues added, 2864 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 6 peptides. Score 0.206 Round 2: 125 peptides, 25 chains. Longest chain 8 peptides. Score 0.294 Round 3: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.331 Round 4: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.350 Round 5: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.355 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 93, 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 7013 restraints for refining 2852 atoms. 6660 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1702 (Rfree = 0.000) for 2852 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1613 (Rfree = 0.000) for 2838 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1500 (Rfree = 0.000) for 2824 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1660 (Rfree = 0.000) for 2816 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:15:53 GMT 2018 Job finished. TimeTaking 52.95 Used memory is bytes: 1743744