null Mon 24 Dec 07:37:36 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 2anu-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2anu-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-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/2anu-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-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 ============================================================ Mon 24 Dec 07:37:40 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/2anu-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2anu-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 1275 and 0 Target number of residues in the AU: 1275 Target solvent content: 0.6221 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.80 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: 127.729 3.600 Wilson plot Bfac: 62.51 20479 reflections ( 99.79 % complete ) and 0 restraints for refining 13575 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.2922 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2716 (Rfree = 0.000) for 13575 atoms. Found 87 (87 requested) and removed 62 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 13831 seeds are put forward NCS extension: 0 residues added, 13831 seeds are put forward Round 1: 626 peptides, 112 chains. Longest chain 13 peptides. Score 0.352 Round 2: 839 peptides, 129 chains. Longest chain 21 peptides. Score 0.473 Round 3: 900 peptides, 120 chains. Longest chain 21 peptides. Score 0.550 Round 4: 911 peptides, 120 chains. Longest chain 27 peptides. Score 0.558 Round 5: 926 peptides, 115 chains. Longest chain 38 peptides. Score 0.584 Taking the results from Round 5 Chains 121, Residues 811, Estimated correctness of the model 8.3 % 5 chains (104 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 24326 restraints for refining 11092 atoms. 20749 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2287 (Rfree = 0.000) for 11092 atoms. Found 66 (71 requested) and removed 58 (35 requested) atoms. Cycle 2: After refmac, R = 0.2141 (Rfree = 0.000) for 10927 atoms. Found 61 (71 requested) and removed 79 (35 requested) atoms. Cycle 3: After refmac, R = 0.2052 (Rfree = 0.000) for 10835 atoms. Found 54 (69 requested) and removed 63 (34 requested) atoms. Cycle 4: After refmac, R = 0.2040 (Rfree = 0.000) for 10792 atoms. Found 37 (69 requested) and removed 45 (34 requested) atoms. Cycle 5: After refmac, R = 0.2008 (Rfree = 0.000) for 10747 atoms. Found 62 (69 requested) and removed 53 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 11113 seeds are put forward NCS extension: 26 residues added (10 deleted due to clashes), 11139 seeds are put forward Round 1: 807 peptides, 125 chains. Longest chain 32 peptides. Score 0.461 Round 2: 880 peptides, 119 chains. Longest chain 34 peptides. Score 0.538 Round 3: 891 peptides, 112 chains. Longest chain 35 peptides. Score 0.569 Round 4: 895 peptides, 108 chains. Longest chain 41 peptides. Score 0.584 Round 5: 932 peptides, 108 chains. Longest chain 28 peptides. Score 0.609 Taking the results from Round 5 Chains 110, Residues 824, Estimated correctness of the model 18.1 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25562 restraints for refining 11095 atoms. 22260 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2218 (Rfree = 0.000) for 11095 atoms. Found 61 (71 requested) and removed 70 (35 requested) atoms. Cycle 7: After refmac, R = 0.2047 (Rfree = 0.000) for 11029 atoms. Found 40 (71 requested) and removed 65 (35 requested) atoms. Cycle 8: After refmac, R = 0.1972 (Rfree = 0.000) for 10962 atoms. Found 36 (70 requested) and removed 73 (35 requested) atoms. Cycle 9: After refmac, R = 0.1922 (Rfree = 0.000) for 10887 atoms. Found 24 (70 requested) and removed 111 (35 requested) atoms. Cycle 10: After refmac, R = 0.1922 (Rfree = 0.000) for 10775 atoms. Found 22 (69 requested) and removed 53 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11101 seeds are put forward NCS extension: 9 residues added (10 deleted due to clashes), 11110 seeds are put forward Round 1: 786 peptides, 123 chains. Longest chain 19 peptides. Score 0.451 Round 2: 886 peptides, 119 chains. Longest chain 25 peptides. Score 0.543 Round 3: 908 peptides, 123 chains. Longest chain 21 peptides. Score 0.546 Round 4: 893 peptides, 115 chains. Longest chain 26 peptides. Score 0.561 Round 5: 918 peptides, 110 chains. Longest chain 36 peptides. Score 0.594 Taking the results from Round 5 Chains 115, Residues 808, Estimated correctness of the model 12.3 % 4 chains (87 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 24354 restraints for refining 11095 atoms. 20826 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2223 (Rfree = 0.000) for 11095 atoms. Found 68 (71 requested) and removed 66 (35 requested) atoms. Cycle 12: After refmac, R = 0.2015 (Rfree = 0.000) for 11028 atoms. Found 45 (71 requested) and removed 45 (35 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 10993 atoms. Found 30 (70 requested) and removed 41 (35 requested) atoms. Cycle 14: After refmac, R = 0.1869 (Rfree = 0.000) for 10956 atoms. Found 20 (70 requested) and removed 38 (35 requested) atoms. Cycle 15: After refmac, R = 0.1827 (Rfree = 0.000) for 10923 atoms. Found 7 (70 requested) and removed 38 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11201 seeds are put forward NCS extension: 42 residues added (9 deleted due to clashes), 11243 seeds are put forward Round 1: 814 peptides, 133 chains. Longest chain 17 peptides. Score 0.438 Round 2: 830 peptides, 112 chains. Longest chain 22 peptides. Score 0.525 Round 3: 863 peptides, 112 chains. Longest chain 34 peptides. Score 0.549 Round 4: 881 peptides, 113 chains. Longest chain 25 peptides. Score 0.559 Round 5: 879 peptides, 112 chains. Longest chain 31 peptides. Score 0.560 Taking the results from Round 5 Chains 113, Residues 767, Estimated correctness of the model 0.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25495 restraints for refining 11096 atoms. 22385 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2122 (Rfree = 0.000) for 11096 atoms. Found 61 (71 requested) and removed 51 (35 requested) atoms. Cycle 17: After refmac, R = 0.1950 (Rfree = 0.000) for 11028 atoms. Found 62 (71 requested) and removed 51 (35 requested) atoms. Cycle 18: After refmac, R = 0.1809 (Rfree = 0.000) for 10997 atoms. Found 32 (70 requested) and removed 40 (35 requested) atoms. Cycle 19: After refmac, R = 0.1794 (Rfree = 0.000) for 10955 atoms. Found 45 (70 requested) and removed 40 (35 requested) atoms. Cycle 20: After refmac, R = 0.1835 (Rfree = 0.000) for 10938 atoms. Found 67 (70 requested) and removed 44 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11316 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 11337 seeds are put forward Round 1: 732 peptides, 126 chains. Longest chain 16 peptides. Score 0.393 Round 2: 824 peptides, 123 chains. Longest chain 21 peptides. Score 0.482 Round 3: 832 peptides, 112 chains. Longest chain 20 peptides. Score 0.526 Round 4: 829 peptides, 110 chains. Longest chain 26 peptides. Score 0.531 Round 5: 818 peptides, 110 chains. Longest chain 23 peptides. Score 0.522 Taking the results from Round 4 Chains 110, Residues 719, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26176 restraints for refining 11095 atoms. 23410 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2177 (Rfree = 0.000) for 11095 atoms. Found 71 (71 requested) and removed 47 (35 requested) atoms. Cycle 22: After refmac, R = 0.2007 (Rfree = 0.000) for 11058 atoms. Found 71 (71 requested) and removed 38 (35 requested) atoms. Cycle 23: After refmac, R = 0.1960 (Rfree = 0.000) for 11047 atoms. Found 71 (71 requested) and removed 42 (35 requested) atoms. Cycle 24: After refmac, R = 0.1923 (Rfree = 0.000) for 11042 atoms. Found 57 (71 requested) and removed 44 (35 requested) atoms. Cycle 25: After refmac, R = 0.1991 (Rfree = 0.000) for 11027 atoms. Found 70 (70 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 11408 seeds are put forward NCS extension: 51 residues added (3 deleted due to clashes), 11459 seeds are put forward Round 1: 697 peptides, 124 chains. Longest chain 16 peptides. Score 0.370 Round 2: 809 peptides, 121 chains. Longest chain 21 peptides. Score 0.477 Round 3: 829 peptides, 112 chains. Longest chain 25 peptides. Score 0.524 Round 4: 830 peptides, 114 chains. Longest chain 18 peptides. Score 0.518 Round 5: 836 peptides, 110 chains. Longest chain 26 peptides. Score 0.536 Taking the results from Round 5 Chains 112, Residues 726, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25964 restraints for refining 11095 atoms. 23113 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2075 (Rfree = 0.000) for 11095 atoms. Found 53 (71 requested) and removed 47 (35 requested) atoms. Cycle 27: After refmac, R = 0.1854 (Rfree = 0.000) for 11057 atoms. Found 59 (71 requested) and removed 45 (35 requested) atoms. Cycle 28: After refmac, R = 0.1811 (Rfree = 0.000) for 11040 atoms. Found 44 (71 requested) and removed 43 (35 requested) atoms. Cycle 29: After refmac, R = 0.1822 (Rfree = 0.000) for 11018 atoms. Found 70 (70 requested) and removed 40 (35 requested) atoms. Cycle 30: After refmac, R = 0.1799 (Rfree = 0.000) for 11035 atoms. Found 46 (70 requested) and removed 45 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11397 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 11415 seeds are put forward Round 1: 701 peptides, 129 chains. Longest chain 16 peptides. Score 0.354 Round 2: 755 peptides, 117 chains. Longest chain 17 peptides. Score 0.447 Round 3: 780 peptides, 115 chains. Longest chain 21 peptides. Score 0.475 Round 4: 779 peptides, 115 chains. Longest chain 22 peptides. Score 0.474 Round 5: 796 peptides, 115 chains. Longest chain 22 peptides. Score 0.488 Taking the results from Round 5 Chains 118, Residues 681, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25851 restraints for refining 11095 atoms. 23073 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1965 (Rfree = 0.000) for 11095 atoms. Found 59 (71 requested) and removed 42 (35 requested) atoms. Cycle 32: After refmac, R = 0.1879 (Rfree = 0.000) for 11055 atoms. Found 53 (71 requested) and removed 45 (35 requested) atoms. Cycle 33: After refmac, R = 0.1831 (Rfree = 0.000) for 11037 atoms. Found 38 (70 requested) and removed 39 (35 requested) atoms. Cycle 34: After refmac, R = 0.1803 (Rfree = 0.000) for 11026 atoms. Found 63 (70 requested) and removed 44 (35 requested) atoms. Cycle 35: After refmac, R = 0.1782 (Rfree = 0.000) for 11026 atoms. Found 37 (70 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 11340 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 11354 seeds are put forward Round 1: 676 peptides, 119 chains. Longest chain 17 peptides. Score 0.370 Round 2: 762 peptides, 112 chains. Longest chain 18 peptides. Score 0.471 Round 3: 745 peptides, 112 chains. Longest chain 17 peptides. Score 0.457 Round 4: 795 peptides, 109 chains. Longest chain 23 peptides. Score 0.508 Round 5: 810 peptides, 109 chains. Longest chain 24 peptides. Score 0.520 Taking the results from Round 5 Chains 112, Residues 701, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25832 restraints for refining 11095 atoms. 22987 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2084 (Rfree = 0.000) for 11095 atoms. Found 62 (71 requested) and removed 42 (35 requested) atoms. Cycle 37: After refmac, R = 0.1956 (Rfree = 0.000) for 11065 atoms. Found 71 (71 requested) and removed 41 (35 requested) atoms. Cycle 38: After refmac, R = 0.1936 (Rfree = 0.000) for 11058 atoms. Found 71 (71 requested) and removed 38 (35 requested) atoms. Cycle 39: After refmac, R = 0.1872 (Rfree = 0.000) for 11061 atoms. Found 67 (71 requested) and removed 41 (35 requested) atoms. Cycle 40: After refmac, R = 0.1858 (Rfree = 0.000) for 11073 atoms. Found 60 (71 requested) and removed 43 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 11406 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11422 seeds are put forward Round 1: 644 peptides, 121 chains. Longest chain 14 peptides. Score 0.332 Round 2: 689 peptides, 113 chains. Longest chain 18 peptides. Score 0.405 Round 3: 742 peptides, 119 chains. Longest chain 17 peptides. Score 0.429 Round 4: 738 peptides, 117 chains. Longest chain 23 peptides. Score 0.433 Round 5: 723 peptides, 110 chains. Longest chain 18 peptides. Score 0.446 Taking the results from Round 5 Chains 110, Residues 613, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26735 restraints for refining 11096 atoms. 24341 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2014 (Rfree = 0.000) for 11096 atoms. Found 66 (71 requested) and removed 44 (35 requested) atoms. Cycle 42: After refmac, R = 0.1814 (Rfree = 0.000) for 11067 atoms. Found 54 (71 requested) and removed 40 (35 requested) atoms. Cycle 43: After refmac, R = 0.1727 (Rfree = 0.000) for 11057 atoms. Found 31 (71 requested) and removed 37 (35 requested) atoms. Cycle 44: After refmac, R = 0.1638 (Rfree = 0.000) for 11029 atoms. Found 38 (70 requested) and removed 38 (35 requested) atoms. Cycle 45: After refmac, R = 0.1625 (Rfree = 0.000) for 11013 atoms. Found 35 (70 requested) and removed 38 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11318 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 11330 seeds are put forward Round 1: 615 peptides, 123 chains. Longest chain 10 peptides. Score 0.296 Round 2: 645 peptides, 112 chains. Longest chain 13 peptides. Score 0.370 Round 3: 677 peptides, 108 chains. Longest chain 15 peptides. Score 0.414 Round 4: 678 peptides, 104 chains. Longest chain 20 peptides. Score 0.431 Round 5: 683 peptides, 104 chains. Longest chain 17 peptides. Score 0.435 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 106, Residues 579, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20479 reflections ( 99.79 % complete ) and 26756 restraints for refining 11096 atoms. 24475 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1894 (Rfree = 0.000) for 11096 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 11018 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1840 (Rfree = 0.000) for 10961 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1787 (Rfree = 0.000) for 10900 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:49:56 GMT 2018 Job finished. TimeTaking 132.33 Used memory is bytes: 10686576