null Sun 23 Dec 22:22:41 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 2pn2-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn2-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-4.0-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/2pn2-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-4.0-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 22:22:50 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/2pn2-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn2-4.0-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 82 and 0 Target number of residues in the AU: 82 Target solvent content: 0.6847 Checking the provided sequence file Detected sequence length: 155 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 155 Adjusted target solvent content: 0.40 Input MTZ file: 2pn2-4.0-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: 20 Cell parameters: 47.282 57.586 103.372 90.000 90.000 90.000 Input sequence file: 2pn2-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1240 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 Loops will be built when appropriate and at the last cycle Resolution range: 51.686 4.001 Wilson plot Bfac: 102.49 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1300 reflections ( 98.71 % complete ) and 0 restraints for refining 1366 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3553 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2482 (Rfree = 0.000) for 1366 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 4.34 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 12 peptides. Score 0.362 Round 2: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.474 Round 3: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.504 Round 4: 62 peptides, 10 chains. Longest chain 12 peptides. Score 0.442 Round 5: 65 peptides, 9 chains. Longest chain 11 peptides. Score 0.518 Taking the results from Round 5 Chains 9, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 2908 restraints for refining 1118 atoms. 2693 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2459 (Rfree = 0.000) for 1118 atoms. Found 3 (5 requested) and removed 32 (2 requested) atoms. Cycle 2: After refmac, R = 0.2778 (Rfree = 0.000) for 1057 atoms. Found 3 (5 requested) and removed 8 (2 requested) atoms. Cycle 3: After refmac, R = 0.2710 (Rfree = 0.000) for 1037 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 4: After refmac, R = 0.2850 (Rfree = 0.000) for 1016 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. Cycle 5: After refmac, R = 0.2462 (Rfree = 0.000) for 994 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.92 4.49 Search for helices and strands: 0 residues in 0 chains, 1038 seeds are put forward Round 1: 38 peptides, 7 chains. Longest chain 10 peptides. Score 0.312 Round 2: 51 peptides, 10 chains. Longest chain 10 peptides. Score 0.314 Round 3: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.314 Round 4: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.416 Round 5: 56 peptides, 9 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 5 Chains 9, Residues 47, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 2006 restraints for refining 857 atoms. 1816 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2179 (Rfree = 0.000) for 857 atoms. Found 2 (4 requested) and removed 9 (2 requested) atoms. Cycle 7: After refmac, R = 0.2215 (Rfree = 0.000) for 846 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2613 (Rfree = 0.000) for 839 atoms. Found 1 (3 requested) and removed 4 (1 requested) atoms. Cycle 9: After refmac, R = 0.2527 (Rfree = 0.000) for 829 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 10: After refmac, R = 0.2549 (Rfree = 0.000) for 823 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 4.44 Search for helices and strands: 0 residues in 0 chains, 841 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.301 Round 2: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.356 Round 3: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.438 Round 4: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.438 Round 5: 69 peptides, 11 chains. Longest chain 14 peptides. Score 0.470 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 1841 restraints for refining 842 atoms. 1620 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2276 (Rfree = 0.000) for 842 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 12: After refmac, R = 0.2160 (Rfree = 0.000) for 834 atoms. Found 0 (3 requested) and removed 7 (1 requested) atoms. Cycle 13: After refmac, R = 0.1736 (Rfree = 0.000) for 826 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 14: After refmac, R = 0.2007 (Rfree = 0.000) for 824 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 15: After refmac, R = 0.1766 (Rfree = 0.000) for 820 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 4.44 Search for helices and strands: 0 residues in 0 chains, 841 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.296 Round 2: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.413 Round 3: 63 peptides, 10 chains. Longest chain 11 peptides. Score 0.452 Round 4: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.394 Round 5: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.504 Taking the results from Round 5 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 1976 restraints for refining 910 atoms. 1754 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2648 (Rfree = 0.000) for 910 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 17: After refmac, R = 0.2151 (Rfree = 0.000) for 898 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 18: After refmac, R = 0.1967 (Rfree = 0.000) for 887 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.1868 (Rfree = 0.000) for 878 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.1942 (Rfree = 0.000) for 873 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 4.36 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.263 Round 2: 60 peptides, 9 chains. Longest chain 14 peptides. Score 0.467 Round 3: 52 peptides, 9 chains. Longest chain 14 peptides. Score 0.378 Round 4: 57 peptides, 9 chains. Longest chain 14 peptides. Score 0.435 Round 5: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.394 Taking the results from Round 2 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 1903 restraints for refining 842 atoms. 1708 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2156 (Rfree = 0.000) for 842 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 22: After refmac, R = 0.2308 (Rfree = 0.000) for 833 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 23: After refmac, R = 0.2922 (Rfree = 0.000) for 832 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 24: After refmac, R = 0.2295 (Rfree = 0.000) for 826 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 25: After refmac, R = 0.2169 (Rfree = 0.000) for 823 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 4.41 Search for helices and strands: 0 residues in 0 chains, 864 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 13 peptides. Score 0.338 Round 2: 55 peptides, 9 chains. Longest chain 13 peptides. Score 0.412 Round 3: 52 peptides, 8 chains. Longest chain 10 peptides. Score 0.428 Round 4: 51 peptides, 8 chains. Longest chain 14 peptides. Score 0.417 Round 5: 42 peptides, 8 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 3 Chains 8, Residues 44, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 1924 restraints for refining 875 atoms. 1720 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2236 (Rfree = 0.000) for 875 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 27: After refmac, R = 0.1933 (Rfree = 0.000) for 871 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.1770 (Rfree = 0.000) for 870 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.1699 (Rfree = 0.000) for 866 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.1645 (Rfree = 0.000) for 860 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.90 4.46 Search for helices and strands: 0 residues in 0 chains, 906 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.265 Round 2: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.314 Round 3: 42 peptides, 8 chains. Longest chain 9 peptides. Score 0.307 Round 4: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.275 Round 5: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.317 Taking the results from Round 5 Chains 9, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 2088 restraints for refining 897 atoms. 1945 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2900 (Rfree = 0.000) for 897 atoms. Found 4 (4 requested) and removed 16 (2 requested) atoms. Cycle 32: After refmac, R = 0.2099 (Rfree = 0.000) for 882 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.1976 (Rfree = 0.000) for 880 atoms. Found 0 (4 requested) and removed 8 (2 requested) atoms. Cycle 34: After refmac, R = 0.1987 (Rfree = 0.000) for 872 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1896 (Rfree = 0.000) for 868 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.98 4.56 Search for helices and strands: 0 residues in 0 chains, 904 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.224 Round 2: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.329 Round 3: 48 peptides, 8 chains. Longest chain 14 peptides. Score 0.382 Round 4: 52 peptides, 9 chains. Longest chain 8 peptides. Score 0.378 Round 5: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 3 Chains 8, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 2093 restraints for refining 898 atoms. 1941 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2642 (Rfree = 0.000) for 898 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 37: After refmac, R = 0.2199 (Rfree = 0.000) for 890 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.2263 (Rfree = 0.000) for 886 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.1741 (Rfree = 0.000) for 887 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2191 (Rfree = 0.000) for 882 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.96 4.53 Search for helices and strands: 0 residues in 0 chains, 926 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.183 Round 2: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.275 Round 3: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.265 Round 4: 31 peptides, 5 chains. Longest chain 12 peptides. Score 0.337 Round 5: 42 peptides, 7 chains. Longest chain 12 peptides. Score 0.363 Taking the results from Round 5 Chains 7, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1300 reflections ( 98.71 % complete ) and 2235 restraints for refining 942 atoms. 2102 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2523 (Rfree = 0.000) for 942 atoms. Found 2 (4 requested) and removed 13 (2 requested) atoms. Cycle 42: After refmac, R = 0.1904 (Rfree = 0.000) for 927 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.1745 (Rfree = 0.000) for 923 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1733 (Rfree = 0.000) for 921 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2004 (Rfree = 0.000) for 918 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 4.49 Search for helices and strands: 0 residues in 0 chains, 944 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.228 Round 2: 29 peptides, 6 chains. Longest chain 6 peptides. Score 0.246 Round 3: 30 peptides, 6 chains. Longest chain 7 peptides. Score 0.261 Round 4: 32 peptides, 6 chains. Longest chain 8 peptides. Score 0.289 Round 5: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.285 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 26, 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 2pn2-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1300 reflections ( 98.71 % complete ) and 2278 restraints for refining 931 atoms. 2180 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2117 (Rfree = 0.000) for 931 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 47: After refmac, R = 0.2064 (Rfree = 0.000) for 930 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Cycle 48: After refmac, R = 0.2192 (Rfree = 0.000) for 930 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1905 (Rfree = 0.000) for 927 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:56 GMT 2018 Job finished. TimeTaking 23.26 Used memory is bytes: 2535016