Mon 24 Dec 00:46:53 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 2anu-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-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/2anu-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-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 00:46:58 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/2anu-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-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 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-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.6-parrot-mrncs.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 Failed to save intermediate PDB 20479 reflections ( 99.79 % complete ) and 0 restraints for refining 13494 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.2824 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2724 (Rfree = 0.000) for 13494 atoms. Found 86 (86 requested) and removed 53 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 13750 seeds are put forward NCS extension: 0 residues added, 13750 seeds are put forward Round 1: 655 peptides, 113 chains. Longest chain 13 peptides. Score 0.375 Round 2: 857 peptides, 131 chains. Longest chain 18 peptides. Score 0.480 Round 3: 898 peptides, 124 chains. Longest chain 35 peptides. Score 0.535 Round 4: 921 peptides, 113 chains. Longest chain 24 peptides. Score 0.586 Round 5: 926 peptides, 111 chains. Longest chain 23 peptides. Score 0.596 Taking the results from Round 5 Chains 115, Residues 815, Estimated correctness of the model 13.1 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 24981 restraints for refining 11092 atoms. 21674 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2340 (Rfree = 0.000) for 11092 atoms. Found 71 (71 requested) and removed 57 (35 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2232 (Rfree = 0.000) for 10956 atoms. Found 69 (71 requested) and removed 50 (35 requested) atoms. Cycle 3: After refmac, R = 0.2165 (Rfree = 0.000) for 10905 atoms. Found 70 (70 requested) and removed 52 (35 requested) atoms. Cycle 4: After refmac, R = 0.2125 (Rfree = 0.000) for 10861 atoms. Found 67 (70 requested) and removed 45 (35 requested) atoms. Cycle 5: After refmac, R = 0.2100 (Rfree = 0.000) for 10831 atoms. Found 69 (69 requested) and removed 48 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 11241 seeds are put forward NCS extension: 7 residues added (8 deleted due to clashes), 11248 seeds are put forward Round 1: 843 peptides, 127 chains. Longest chain 18 peptides. Score 0.483 Round 2: 906 peptides, 117 chains. Longest chain 30 peptides. Score 0.564 Round 3: 930 peptides, 108 chains. Longest chain 33 peptides. Score 0.608 Round 4: 934 peptides, 114 chains. Longest chain 21 peptides. Score 0.592 Round 5: 922 peptides, 114 chains. Longest chain 39 peptides. Score 0.584 Taking the results from Round 3 Chains 110, Residues 822, Estimated correctness of the model 17.8 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20479 reflections ( 99.79 % complete ) and 25044 restraints for refining 11094 atoms. 21623 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2269 (Rfree = 0.000) for 11094 atoms. Found 60 (71 requested) and removed 66 (35 requested) atoms. Cycle 7: After refmac, R = 0.2175 (Rfree = 0.000) for 11003 atoms. Found 53 (71 requested) and removed 55 (35 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2123 (Rfree = 0.000) for 10964 atoms. Found 70 (70 requested) and removed 59 (35 requested) atoms. Cycle 9: After refmac, R = 0.2065 (Rfree = 0.000) for 10949 atoms. Found 66 (70 requested) and removed 44 (35 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2012 (Rfree = 0.000) for 10948 atoms. Found 59 (70 requested) and removed 58 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 11291 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11307 seeds are put forward Round 1: 821 peptides, 130 chains. Longest chain 20 peptides. Score 0.455 Round 2: 895 peptides, 112 chains. Longest chain 23 peptides. Score 0.572 Round 3: 888 peptides, 115 chains. Longest chain 22 peptides. Score 0.557 Round 4: 889 peptides, 108 chains. Longest chain 23 peptides. Score 0.580 Round 5: 890 peptides, 114 chains. Longest chain 42 peptides. Score 0.562 Taking the results from Round 4 Chains 111, Residues 781, Estimated correctness of the model 6.7 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25292 restraints for refining 11093 atoms. 22049 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2131 (Rfree = 0.000) for 11093 atoms. Found 69 (71 requested) and removed 53 (35 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1948 (Rfree = 0.000) for 11049 atoms. Found 46 (71 requested) and removed 44 (35 requested) atoms. Cycle 13: After refmac, R = 0.1927 (Rfree = 0.000) for 11013 atoms. Found 60 (70 requested) and removed 51 (35 requested) atoms. Cycle 14: After refmac, R = 0.1875 (Rfree = 0.000) for 10995 atoms. Found 41 (70 requested) and removed 39 (35 requested) atoms. Cycle 15: After refmac, R = 0.1878 (Rfree = 0.000) for 10969 atoms. Found 58 (70 requested) and removed 45 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 11308 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 11324 seeds are put forward Round 1: 794 peptides, 132 chains. Longest chain 17 peptides. Score 0.425 Round 2: 840 peptides, 113 chains. Longest chain 19 peptides. Score 0.529 Round 3: 877 peptides, 114 chains. Longest chain 19 peptides. Score 0.553 Round 4: 867 peptides, 109 chains. Longest chain 28 peptides. Score 0.562 Round 5: 889 peptides, 108 chains. Longest chain 22 peptides. Score 0.580 Taking the results from Round 5 Chains 110, Residues 781, Estimated correctness of the model 6.7 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25322 restraints for refining 11095 atoms. 22064 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2205 (Rfree = 0.000) for 11095 atoms. Found 71 (71 requested) and removed 55 (35 requested) atoms. Cycle 17: After refmac, R = 0.1978 (Rfree = 0.000) for 11026 atoms. Found 55 (71 requested) and removed 49 (35 requested) atoms. Cycle 18: After refmac, R = 0.1909 (Rfree = 0.000) for 10980 atoms. Found 52 (70 requested) and removed 42 (35 requested) atoms. Cycle 19: After refmac, R = 0.1879 (Rfree = 0.000) for 10962 atoms. Found 49 (70 requested) and removed 46 (35 requested) atoms. Cycle 20: After refmac, R = 0.1904 (Rfree = 0.000) for 10937 atoms. Found 58 (70 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 11283 seeds are put forward NCS extension: 12 residues added (8 deleted due to clashes), 11295 seeds are put forward Round 1: 790 peptides, 128 chains. Longest chain 17 peptides. Score 0.436 Round 2: 853 peptides, 117 chains. Longest chain 16 peptides. Score 0.525 Round 3: 848 peptides, 119 chains. Longest chain 17 peptides. Score 0.515 Round 4: 833 peptides, 111 chains. Longest chain 18 peptides. Score 0.530 Round 5: 829 peptides, 110 chains. Longest chain 23 peptides. Score 0.531 Taking the results from Round 5 Chains 112, Residues 719, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26111 restraints for refining 11096 atoms. 23276 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2072 (Rfree = 0.000) for 11096 atoms. Found 58 (71 requested) and removed 40 (35 requested) atoms. Cycle 22: After refmac, R = 0.1937 (Rfree = 0.000) for 11059 atoms. Found 40 (71 requested) and removed 37 (35 requested) atoms. Cycle 23: After refmac, R = 0.1961 (Rfree = 0.000) for 11030 atoms. Found 49 (70 requested) and removed 42 (35 requested) atoms. Cycle 24: After refmac, R = 0.1900 (Rfree = 0.000) for 11010 atoms. Found 55 (70 requested) and removed 41 (35 requested) atoms. Cycle 25: After refmac, R = 0.2006 (Rfree = 0.000) for 10990 atoms. Found 69 (70 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 11342 seeds are put forward NCS extension: 45 residues added (1 deleted due to clashes), 11387 seeds are put forward Round 1: 743 peptides, 132 chains. Longest chain 16 peptides. Score 0.380 Round 2: 802 peptides, 122 chains. Longest chain 18 peptides. Score 0.468 Round 3: 810 peptides, 112 chains. Longest chain 20 peptides. Score 0.509 Round 4: 796 peptides, 113 chains. Longest chain 20 peptides. Score 0.495 Round 5: 785 peptides, 108 chains. Longest chain 26 peptides. Score 0.504 Taking the results from Round 3 Chains 112, Residues 698, Estimated correctness of the model 0.0 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 25751 restraints for refining 11093 atoms. 22827 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2121 (Rfree = 0.000) for 11093 atoms. Found 59 (71 requested) and removed 52 (35 requested) atoms. Cycle 27: After refmac, R = 0.1956 (Rfree = 0.000) for 11052 atoms. Found 40 (71 requested) and removed 41 (35 requested) atoms. Cycle 28: After refmac, R = 0.1954 (Rfree = 0.000) for 11015 atoms. Found 48 (70 requested) and removed 41 (35 requested) atoms. Cycle 29: After refmac, R = 0.1973 (Rfree = 0.000) for 10997 atoms. Found 69 (70 requested) and removed 41 (35 requested) atoms. Cycle 30: After refmac, R = 0.1893 (Rfree = 0.000) for 10998 atoms. Found 45 (70 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 11290 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 11314 seeds are put forward Round 1: 692 peptides, 127 chains. Longest chain 14 peptides. Score 0.353 Round 2: 738 peptides, 120 chains. Longest chain 16 peptides. Score 0.422 Round 3: 762 peptides, 111 chains. Longest chain 21 peptides. Score 0.475 Round 4: 781 peptides, 117 chains. Longest chain 20 peptides. Score 0.469 Round 5: 756 peptides, 111 chains. Longest chain 21 peptides. Score 0.470 Taking the results from Round 3 Chains 113, Residues 651, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26562 restraints for refining 11094 atoms. 24030 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2058 (Rfree = 0.000) for 11094 atoms. Found 71 (71 requested) and removed 41 (35 requested) atoms. Cycle 32: After refmac, R = 0.2033 (Rfree = 0.000) for 11063 atoms. Found 71 (71 requested) and removed 40 (35 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2006 (Rfree = 0.000) for 11052 atoms. Found 71 (71 requested) and removed 47 (35 requested) atoms. Cycle 34: After refmac, R = 0.1960 (Rfree = 0.000) for 11044 atoms. Found 71 (71 requested) and removed 40 (35 requested) atoms. Cycle 35: After refmac, R = 0.1899 (Rfree = 0.000) for 11044 atoms. Found 66 (71 requested) and removed 39 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 11364 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 11395 seeds are put forward Round 1: 629 peptides, 119 chains. Longest chain 11 peptides. Score 0.326 Round 2: 714 peptides, 117 chains. Longest chain 18 peptides. Score 0.412 Round 3: 707 peptides, 105 chains. Longest chain 16 peptides. Score 0.451 Round 4: 741 peptides, 116 chains. Longest chain 20 peptides. Score 0.439 Round 5: 771 peptides, 111 chains. Longest chain 20 peptides. Score 0.482 Taking the results from Round 5 Chains 111, Residues 660, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26573 restraints for refining 11095 atoms. 24044 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1982 (Rfree = 0.000) for 11095 atoms. Found 58 (71 requested) and removed 38 (35 requested) atoms. Cycle 37: After refmac, R = 0.1898 (Rfree = 0.000) for 11054 atoms. Found 52 (71 requested) and removed 38 (35 requested) atoms. Cycle 38: After refmac, R = 0.1863 (Rfree = 0.000) for 11033 atoms. Found 61 (71 requested) and removed 39 (35 requested) atoms. Cycle 39: After refmac, R = 0.1830 (Rfree = 0.000) for 11023 atoms. Found 55 (70 requested) and removed 39 (35 requested) atoms. Cycle 40: After refmac, R = 0.1884 (Rfree = 0.000) for 11015 atoms. Found 70 (70 requested) and removed 38 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 11386 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 11410 seeds are put forward Round 1: 596 peptides, 118 chains. Longest chain 13 peptides. Score 0.298 Round 2: 675 peptides, 112 chains. Longest chain 18 peptides. Score 0.397 Round 3: 687 peptides, 108 chains. Longest chain 19 peptides. Score 0.423 Round 4: 700 peptides, 110 chains. Longest chain 20 peptides. Score 0.427 Round 5: 693 peptides, 100 chains. Longest chain 21 peptides. Score 0.458 Taking the results from Round 5 Chains 100, Residues 593, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20479 reflections ( 99.79 % complete ) and 26765 restraints for refining 11094 atoms. 24493 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2021 (Rfree = 0.000) for 11094 atoms. Found 71 (71 requested) and removed 42 (35 requested) atoms. Cycle 42: After refmac, R = 0.1838 (Rfree = 0.000) for 11076 atoms. Found 56 (71 requested) and removed 36 (35 requested) atoms. Cycle 43: After refmac, R = 0.1769 (Rfree = 0.000) for 11072 atoms. Found 54 (71 requested) and removed 41 (35 requested) atoms. Cycle 44: After refmac, R = 0.1715 (Rfree = 0.000) for 11059 atoms. Found 41 (71 requested) and removed 35 (35 requested) atoms. Cycle 45: After refmac, R = 0.1696 (Rfree = 0.000) for 11041 atoms. Found 52 (70 requested) and removed 39 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.07 Search for helices and strands: 0 residues in 0 chains, 11365 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 11400 seeds are put forward Round 1: 507 peptides, 104 chains. Longest chain 12 peptides. Score 0.268 Round 2: 646 peptides, 112 chains. Longest chain 22 peptides. Score 0.370 Round 3: 654 peptides, 108 chains. Longest chain 22 peptides. Score 0.394 Round 4: 672 peptides, 112 chains. Longest chain 16 peptides. Score 0.394 Round 5: 679 peptides, 110 chains. Longest chain 16 peptides. Score 0.408 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 110, Residues 569, 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 2anu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20479 reflections ( 99.79 % complete ) and 27036 restraints for refining 11096 atoms. 24870 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1924 (Rfree = 0.000) for 11096 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.1966 (Rfree = 0.000) for 11017 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1962 (Rfree = 0.000) for 10954 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1684 (Rfree = 0.000) for 10894 atoms. TimeTaking 157