null Tue 25 Dec 19:27:57 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 1vp8-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-1.5-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/1vp8-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-1.5-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 ============================================================ Tue 25 Dec 19:28:06 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/1vp8-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-1.5-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 278 and 0 Target number of residues in the AU: 278 Target solvent content: 0.4346 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.59 Input MTZ file: 1vp8-1.5-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: 182 Cell parameters: 109.749 109.749 76.534 90.000 90.000 120.000 Input sequence file: 1vp8-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.30 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 1 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: 18.945 1.531 Wilson plot Bfac: 12.19 41043 reflections ( 99.33 % complete ) and 0 restraints for refining 1773 atoms. Observations/parameters ratio is 5.79 ------------------------------------------------------ Starting model: R = 0.3144 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2693 (Rfree = 0.000) for 1773 atoms. Found 130 (130 requested) and removed 43 (65 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.54 1.36 Round 1: 175 peptides, 10 chains. Longest chain 57 peptides. Score 0.826 Round 2: 189 peptides, 2 chains. Longest chain 99 peptides. Score 0.925 Round 3: 186 peptides, 5 chains. Longest chain 77 peptides. Score 0.896 Round 4: 188 peptides, 3 chains. Longest chain 99 peptides. Score 0.916 Round 5: 189 peptides, 2 chains. Longest chain 160 peptides. Score 0.925 Taking the results from Round 5 Chains 3, Residues 187, Estimated correctness of the model 99.7 % 2 chains (186 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 171 A and 174 A 2 chains (189 residues) following loop building 1 chains (188 residues) in sequence following loop building ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1769 restraints for refining 1739 atoms. 302 conditional restraints added. Observations/parameters ratio is 5.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2587 (Rfree = 0.000) for 1739 atoms. Found 98 (127 requested) and removed 30 (63 requested) atoms. Cycle 2: After refmac, R = 0.2371 (Rfree = 0.000) for 1807 atoms. Found 67 (132 requested) and removed 27 (66 requested) atoms. Cycle 3: After refmac, R = 0.2047 (Rfree = 0.000) for 1840 atoms. Found 100 (135 requested) and removed 24 (67 requested) atoms. Cycle 4: After refmac, R = 0.1974 (Rfree = 0.000) for 1912 atoms. Found 76 (140 requested) and removed 42 (70 requested) atoms. Cycle 5: After refmac, R = 0.1926 (Rfree = 0.000) for 1936 atoms. Found 78 (139 requested) and removed 37 (71 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.51 1.34 Round 1: 187 peptides, 3 chains. Longest chain 130 peptides. Score 0.914 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 3: 186 peptides, 3 chains. Longest chain 130 peptides. Score 0.913 Round 4: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.932 Round 5: 187 peptides, 3 chains. Longest chain 130 peptides. Score 0.914 Taking the results from Round 2 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1831 restraints for refining 1828 atoms. 356 conditional restraints added. Observations/parameters ratio is 5.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2234 (Rfree = 0.000) for 1828 atoms. Found 95 (131 requested) and removed 26 (67 requested) atoms. Cycle 7: After refmac, R = 0.1990 (Rfree = 0.000) for 1895 atoms. Found 78 (136 requested) and removed 26 (69 requested) atoms. Cycle 8: After refmac, R = 0.1923 (Rfree = 0.000) for 1941 atoms. Found 65 (139 requested) and removed 36 (71 requested) atoms. Cycle 9: After refmac, R = 0.1890 (Rfree = 0.000) for 1960 atoms. Found 77 (138 requested) and removed 33 (72 requested) atoms. Cycle 10: After refmac, R = 0.1874 (Rfree = 0.000) for 1997 atoms. Found 75 (141 requested) and removed 47 (73 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.50 1.33 Round 1: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.932 Round 2: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.932 Round 3: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 4: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.932 Round 5: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Taking the results from Round 5 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1832 restraints for refining 1842 atoms. 357 conditional restraints added. Observations/parameters ratio is 5.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2174 (Rfree = 0.000) for 1842 atoms. Found 93 (127 requested) and removed 24 (67 requested) atoms. Cycle 12: After refmac, R = 0.1963 (Rfree = 0.000) for 1904 atoms. Found 90 (132 requested) and removed 35 (70 requested) atoms. Cycle 13: After refmac, R = 0.1912 (Rfree = 0.000) for 1952 atoms. Found 80 (134 requested) and removed 49 (71 requested) atoms. Cycle 14: After refmac, R = 0.1884 (Rfree = 0.000) for 1972 atoms. Found 73 (133 requested) and removed 42 (72 requested) atoms. Cycle 15: After refmac, R = 0.1849 (Rfree = 0.000) for 1989 atoms. Found 87 (131 requested) and removed 39 (73 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.51 1.34 Round 1: 187 peptides, 2 chains. Longest chain 130 peptides. Score 0.922 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 3: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.924 Round 4: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 5: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Taking the results from Round 5 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1830 restraints for refining 1853 atoms. 355 conditional restraints added. Observations/parameters ratio is 5.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2186 (Rfree = 0.000) for 1853 atoms. Found 96 (121 requested) and removed 26 (67 requested) atoms. Cycle 17: After refmac, R = 0.1971 (Rfree = 0.000) for 1916 atoms. Found 78 (127 requested) and removed 28 (70 requested) atoms. Cycle 18: After refmac, R = 0.1911 (Rfree = 0.000) for 1962 atoms. Found 67 (130 requested) and removed 35 (72 requested) atoms. Cycle 19: After refmac, R = 0.1869 (Rfree = 0.000) for 1989 atoms. Found 71 (128 requested) and removed 34 (73 requested) atoms. Cycle 20: After refmac, R = 0.1844 (Rfree = 0.000) for 2015 atoms. Found 77 (130 requested) and removed 42 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.51 1.34 Round 1: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.924 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 3: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.924 Round 4: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 5: 189 peptides, 2 chains. Longest chain 172 peptides. Score 0.925 Taking the results from Round 4 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1823 restraints for refining 1869 atoms. 348 conditional restraints added. Observations/parameters ratio is 5.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2194 (Rfree = 0.000) for 1869 atoms. Found 89 (118 requested) and removed 29 (68 requested) atoms. Cycle 22: After refmac, R = 0.1954 (Rfree = 0.000) for 1924 atoms. Found 86 (121 requested) and removed 30 (70 requested) atoms. Cycle 23: After refmac, R = 0.1896 (Rfree = 0.000) for 1972 atoms. Found 69 (125 requested) and removed 47 (72 requested) atoms. Cycle 24: After refmac, R = 0.1860 (Rfree = 0.000) for 1987 atoms. Found 71 (123 requested) and removed 38 (73 requested) atoms. Cycle 25: After refmac, R = 0.1843 (Rfree = 0.000) for 2009 atoms. Found 71 (121 requested) and removed 37 (74 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.50 1.33 Round 1: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 2: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.932 Round 3: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 4: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 5: 189 peptides, 1 chains. Longest chain 189 peptides. Score 0.932 Taking the results from Round 4 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1826 restraints for refining 1841 atoms. 351 conditional restraints added. Observations/parameters ratio is 5.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2170 (Rfree = 0.000) for 1841 atoms. Found 108 (108 requested) and removed 33 (67 requested) atoms. Cycle 27: After refmac, R = 0.1974 (Rfree = 0.000) for 1913 atoms. Found 77 (112 requested) and removed 39 (70 requested) atoms. Cycle 28: After refmac, R = 0.1911 (Rfree = 0.000) for 1939 atoms. Found 96 (112 requested) and removed 33 (71 requested) atoms. Cycle 29: After refmac, R = 0.1898 (Rfree = 0.000) for 1995 atoms. Found 60 (114 requested) and removed 45 (73 requested) atoms. Cycle 30: After refmac, R = 0.1852 (Rfree = 0.000) for 2001 atoms. Found 76 (112 requested) and removed 36 (73 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.52 1.35 Round 1: 187 peptides, 3 chains. Longest chain 130 peptides. Score 0.914 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 3: 189 peptides, 2 chains. Longest chain 156 peptides. Score 0.925 Round 4: 187 peptides, 3 chains. Longest chain 130 peptides. Score 0.914 Round 5: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Taking the results from Round 5 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1853 restraints for refining 1857 atoms. 378 conditional restraints added. Observations/parameters ratio is 5.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2165 (Rfree = 0.000) for 1857 atoms. Found 103 (103 requested) and removed 27 (68 requested) atoms. Cycle 32: After refmac, R = 0.1970 (Rfree = 0.000) for 1928 atoms. Found 86 (107 requested) and removed 39 (70 requested) atoms. Cycle 33: After refmac, R = 0.1903 (Rfree = 0.000) for 1970 atoms. Found 80 (109 requested) and removed 45 (72 requested) atoms. Cycle 34: After refmac, R = 0.1904 (Rfree = 0.000) for 1992 atoms. Found 75 (109 requested) and removed 44 (73 requested) atoms. Cycle 35: After refmac, R = 0.1875 (Rfree = 0.000) for 2009 atoms. Found 71 (107 requested) and removed 44 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.51 1.34 Round 1: 187 peptides, 3 chains. Longest chain 127 peptides. Score 0.914 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 3: 187 peptides, 3 chains. Longest chain 127 peptides. Score 0.914 Round 4: 189 peptides, 2 chains. Longest chain 172 peptides. Score 0.925 Round 5: 184 peptides, 2 chains. Longest chain 127 peptides. Score 0.919 Taking the results from Round 2 Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1811 restraints for refining 1851 atoms. 336 conditional restraints added. Observations/parameters ratio is 5.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2188 (Rfree = 0.000) for 1851 atoms. Found 94 (94 requested) and removed 27 (67 requested) atoms. Cycle 37: After refmac, R = 0.1959 (Rfree = 0.000) for 1912 atoms. Found 82 (98 requested) and removed 30 (70 requested) atoms. Cycle 38: After refmac, R = 0.1904 (Rfree = 0.000) for 1954 atoms. Found 77 (101 requested) and removed 35 (72 requested) atoms. Cycle 39: After refmac, R = 0.1873 (Rfree = 0.000) for 1990 atoms. Found 77 (102 requested) and removed 33 (73 requested) atoms. Cycle 40: After refmac, R = 0.1869 (Rfree = 0.000) for 2023 atoms. Found 73 (104 requested) and removed 32 (74 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.51 1.34 Round 1: 188 peptides, 2 chains. Longest chain 127 peptides. Score 0.924 Round 2: 189 peptides, 2 chains. Longest chain 156 peptides. Score 0.925 Round 3: 188 peptides, 2 chains. Longest chain 127 peptides. Score 0.924 Round 4: 189 peptides, 2 chains. Longest chain 156 peptides. Score 0.925 Round 5: 188 peptides, 2 chains. Longest chain 127 peptides. Score 0.924 Taking the results from Round 4 Chains 3, Residues 187, Estimated correctness of the model 99.7 % 2 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 170 A 2 chains (189 residues) following loop building 1 chains (187 residues) in sequence following loop building ------------------------------------------------------ 41043 reflections ( 99.33 % complete ) and 1864 restraints for refining 1856 atoms. 402 conditional restraints added. Observations/parameters ratio is 5.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2190 (Rfree = 0.000) for 1856 atoms. Found 95 (95 requested) and removed 26 (68 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 1924 atoms. Found 83 (99 requested) and removed 31 (70 requested) atoms. Cycle 43: After refmac, R = 0.1884 (Rfree = 0.000) for 1970 atoms. Found 85 (101 requested) and removed 34 (72 requested) atoms. Cycle 44: After refmac, R = 0.1878 (Rfree = 0.000) for 2014 atoms. Found 72 (104 requested) and removed 44 (74 requested) atoms. Cycle 45: After refmac, R = 0.1861 (Rfree = 0.000) for 2033 atoms. Found 71 (101 requested) and removed 42 (74 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.50 1.33 Round 1: 189 peptides, 2 chains. Longest chain 129 peptides. Score 0.925 Round 2: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 3: 188 peptides, 2 chains. Longest chain 130 peptides. Score 0.924 Round 4: 190 peptides, 1 chains. Longest chain 190 peptides. Score 0.933 Round 5: 188 peptides, 3 chains. Longest chain 129 peptides. Score 0.916 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 189, Estimated correctness of the model 99.8 % 1 chains (189 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 41043 reflections ( 99.33 % complete ) and 1475 restraints for refining 1457 atoms. Observations/parameters ratio is 7.04 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2833 (Rfree = 0.000) for 1457 atoms. Found 70 (70 requested) and removed 0 (70 requested) atoms. Cycle 47: After refmac, R = 0.2328 (Rfree = 0.000) for 1457 atoms. Found 63 (74 requested) and removed 1 (56 requested) atoms. Cycle 48: After refmac, R = 0.2135 (Rfree = 0.000) for 1457 atoms. Found 28 (77 requested) and removed 2 (58 requested) atoms. Cycle 49: After refmac, R = 0.2016 (Rfree = 0.000) for 1457 atoms. Found 15 (78 requested) and removed 3 (59 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:46:33 GMT 2018 Job finished. TimeTaking 78.61 Used memory is bytes: 18650024