null Mon 24 Dec 07:27:24 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 1zko-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zko-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zko-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-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/1zko-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-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 07:27:28 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/1zko-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-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 173 and 0 Target number of residues in the AU: 173 Target solvent content: 0.6164 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.65 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: 47.500 3.600 Wilson plot Bfac: 59.59 2852 reflections ( 92.51 % complete ) and 0 restraints for refining 2404 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3705 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3557 (Rfree = 0.000) for 2404 atoms. Found 15 (15 requested) and removed 41 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 2407 seeds are put forward NCS extension: 0 residues added, 2407 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.197 Round 2: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.244 Round 3: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.284 Round 4: 64 peptides, 12 chains. Longest chain 11 peptides. Score 0.302 Round 5: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.307 Taking the results from Round 5 Chains 13, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4691 restraints for refining 1972 atoms. 4480 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3049 (Rfree = 0.000) for 1972 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 2: After refmac, R = 0.3080 (Rfree = 0.000) for 1945 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 3: After refmac, R = 0.2601 (Rfree = 0.000) for 1929 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 4: After refmac, R = 0.3014 (Rfree = 0.000) for 1908 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 5: After refmac, R = 0.2510 (Rfree = 0.000) for 1898 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 3.67 Search for helices and strands: 0 residues in 0 chains, 1920 seeds are put forward NCS extension: 0 residues added, 1920 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.251 Round 2: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.270 Round 3: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.320 Round 4: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.339 Round 5: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 5 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4188 restraints for refining 1785 atoms. 3972 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2370 (Rfree = 0.000) for 1785 atoms. Found 11 (11 requested) and removed 42 (5 requested) atoms. Cycle 7: After refmac, R = 0.2308 (Rfree = 0.000) for 1749 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 1737 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.1858 (Rfree = 0.000) for 1730 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2132 (Rfree = 0.000) for 1721 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward NCS extension: 0 residues added, 1762 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.284 Round 2: 87 peptides, 15 chains. Longest chain 9 peptides. Score 0.374 Round 3: 98 peptides, 17 chains. Longest chain 9 peptides. Score 0.390 Round 4: 93 peptides, 16 chains. Longest chain 8 peptides. Score 0.385 Round 5: 100 peptides, 17 chains. Longest chain 9 peptides. Score 0.403 Taking the results from Round 5 Chains 17, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3831 restraints for refining 1741 atoms. 3516 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2542 (Rfree = 0.000) for 1741 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 12: After refmac, R = 0.2155 (Rfree = 0.000) for 1708 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2050 (Rfree = 0.000) for 1699 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2171 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2031 (Rfree = 0.000) for 1694 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward NCS extension: 0 residues added, 1742 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.286 Round 2: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.282 Round 3: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.339 Round 4: 106 peptides, 20 chains. Longest chain 18 peptides. Score 0.358 Round 5: 111 peptides, 17 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 5 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3690 restraints for refining 1740 atoms. 3318 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2511 (Rfree = 0.000) for 1740 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 17: After refmac, R = 0.2194 (Rfree = 0.000) for 1728 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.2162 (Rfree = 0.000) for 1718 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2085 (Rfree = 0.000) for 1716 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2123 (Rfree = 0.000) for 1707 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 1740 seeds are put forward NCS extension: 0 residues added, 1740 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.272 Round 2: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.401 Round 3: 95 peptides, 15 chains. Longest chain 16 peptides. Score 0.427 Round 4: 104 peptides, 17 chains. Longest chain 20 peptides. Score 0.429 Round 5: 104 peptides, 18 chains. Longest chain 13 peptides. Score 0.401 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 3952 restraints for refining 1784 atoms. 3621 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2428 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 22: After refmac, R = 0.2268 (Rfree = 0.000) for 1768 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2120 (Rfree = 0.000) for 1766 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2162 (Rfree = 0.000) for 1762 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2073 (Rfree = 0.000) for 1761 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 1791 seeds are put forward NCS extension: 0 residues added, 1791 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.283 Round 2: 93 peptides, 19 chains. Longest chain 10 peptides. Score 0.296 Round 3: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.412 Round 4: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.385 Round 5: 104 peptides, 18 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 3 Chains 16, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4093 restraints for refining 1792 atoms. 3785 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2222 (Rfree = 0.000) for 1792 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2072 (Rfree = 0.000) for 1784 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.1918 (Rfree = 0.000) for 1781 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1895 (Rfree = 0.000) for 1779 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.2041 (Rfree = 0.000) for 1774 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1813 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 7 peptides. Score 0.232 Round 2: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.337 Round 3: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.293 Round 4: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.303 Round 5: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 5 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4276 restraints for refining 1827 atoms. 4034 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2273 (Rfree = 0.000) for 1827 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 32: After refmac, R = 0.2077 (Rfree = 0.000) for 1816 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.1782 (Rfree = 0.000) for 1810 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1805 (Rfree = 0.000) for 1807 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1802 (Rfree = 0.000) for 1800 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 0 residues added, 1818 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 6 peptides. Score 0.247 Round 2: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.341 Round 3: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.315 Round 4: 75 peptides, 15 chains. Longest chain 7 peptides. Score 0.288 Round 5: 74 peptides, 14 chains. Longest chain 7 peptides. Score 0.312 Taking the results from Round 2 Chains 14, Residues 64, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4235 restraints for refining 1828 atoms. 3978 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2044 (Rfree = 0.000) for 1828 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 37: After refmac, R = 0.1925 (Rfree = 0.000) for 1811 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.1924 (Rfree = 0.000) for 1803 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1888 (Rfree = 0.000) for 1803 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.1898 (Rfree = 0.000) for 1793 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 0 residues added, 1823 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 5 peptides. Score 0.191 Round 2: 82 peptides, 17 chains. Longest chain 10 peptides. Score 0.277 Round 3: 85 peptides, 17 chains. Longest chain 10 peptides. Score 0.299 Round 4: 93 peptides, 18 chains. Longest chain 11 peptides. Score 0.326 Round 5: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4256 restraints for refining 1834 atoms. 3960 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2204 (Rfree = 0.000) for 1834 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 42: After refmac, R = 0.2004 (Rfree = 0.000) for 1819 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 1816 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.1943 (Rfree = 0.000) for 1809 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.2019 (Rfree = 0.000) for 1803 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 0 residues added, 1827 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.229 Round 2: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.300 Round 3: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.252 Round 4: 68 peptides, 12 chains. Longest chain 10 peptides. Score 0.332 Round 5: 68 peptides, 11 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 57, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2852 reflections ( 92.51 % complete ) and 4215 restraints for refining 1825 atoms. 3960 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2129 (Rfree = 0.000) for 1825 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2199 (Rfree = 0.000) for 1818 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2152 (Rfree = 0.000) for 1810 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2066 (Rfree = 0.000) for 1805 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:52:13 GMT 2018 Job finished. TimeTaking 24.83 Used memory is bytes: 11689072