null Sun 23 Dec 22:23:08 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 2ifx-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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/2ifx-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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 22:23:18 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/2ifx-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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 228 and 0 Target number of residues in the AU: 228 Target solvent content: 0.5352 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.54 Input MTZ file: 2ifx-2.0-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.50 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 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: 28.919 2.001 Wilson plot Bfac: 31.39 17355 reflections ( 98.91 % complete ) and 0 restraints for refining 2033 atoms. Observations/parameters ratio is 2.13 ------------------------------------------------------ Starting model: R = 0.3092 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2667 (Rfree = 0.000) for 2033 atoms. Found 31 (69 requested) and removed 50 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.31 2.19 NCS extension: 0 residues added, 2014 seeds are put forward Round 1: 147 peptides, 16 chains. Longest chain 20 peptides. Score 0.652 Round 2: 170 peptides, 13 chains. Longest chain 35 peptides. Score 0.777 Round 3: 181 peptides, 7 chains. Longest chain 49 peptides. Score 0.871 Round 4: 182 peptides, 9 chains. Longest chain 26 peptides. Score 0.852 Round 5: 188 peptides, 6 chains. Longest chain 49 peptides. Score 0.891 Taking the results from Round 5 Chains 8, Residues 182, Estimated correctness of the model 98.8 % 5 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 78 A 6 chains (184 residues) following loop building 4 chains (167 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1947 restraints for refining 1769 atoms. 472 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2681 (Rfree = 0.000) for 1769 atoms. Found 33 (60 requested) and removed 32 (30 requested) atoms. Cycle 2: After refmac, R = 0.2470 (Rfree = 0.000) for 1763 atoms. Found 22 (59 requested) and removed 18 (30 requested) atoms. Cycle 3: After refmac, R = 0.2352 (Rfree = 0.000) for 1761 atoms. Found 18 (58 requested) and removed 20 (30 requested) atoms. Cycle 4: After refmac, R = 0.2283 (Rfree = 0.000) for 1753 atoms. Found 28 (56 requested) and removed 13 (30 requested) atoms. Cycle 5: After refmac, R = 0.2207 (Rfree = 0.000) for 1761 atoms. Found 17 (56 requested) and removed 10 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.24 2.12 NCS extension: 5 residues added (4 deleted due to clashes), 1774 seeds are put forward Round 1: 185 peptides, 5 chains. Longest chain 49 peptides. Score 0.896 Round 2: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 3: 185 peptides, 6 chains. Longest chain 49 peptides. Score 0.887 Round 4: 185 peptides, 6 chains. Longest chain 49 peptides. Score 0.887 Round 5: 186 peptides, 5 chains. Longest chain 47 peptides. Score 0.897 Taking the results from Round 2 Chains 4, Residues 183, Estimated correctness of the model 99.1 % 4 chains (183 residues) have been docked in sequence Building loops using Loopy2018 4 chains (183 residues) following loop building 4 chains (183 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1804 restraints for refining 1769 atoms. 272 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2378 (Rfree = 0.000) for 1769 atoms. Found 33 (55 requested) and removed 25 (30 requested) atoms. Cycle 7: After refmac, R = 0.2256 (Rfree = 0.000) for 1774 atoms. Found 16 (54 requested) and removed 14 (30 requested) atoms. Cycle 8: After refmac, R = 0.2197 (Rfree = 0.000) for 1774 atoms. Found 19 (53 requested) and removed 12 (30 requested) atoms. Cycle 9: After refmac, R = 0.2150 (Rfree = 0.000) for 1780 atoms. Found 18 (52 requested) and removed 7 (30 requested) atoms. Cycle 10: After refmac, R = 0.2129 (Rfree = 0.000) for 1788 atoms. Found 22 (52 requested) and removed 15 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1795 seeds are put forward Round 1: 188 peptides, 4 chains. Longest chain 50 peptides. Score 0.908 Round 2: 186 peptides, 4 chains. Longest chain 51 peptides. Score 0.906 Round 3: 187 peptides, 6 chains. Longest chain 50 peptides. Score 0.890 Round 4: 187 peptides, 4 chains. Longest chain 50 peptides. Score 0.907 Round 5: 182 peptides, 6 chains. Longest chain 47 peptides. Score 0.882 Taking the results from Round 1 Chains 4, Residues 184, Estimated correctness of the model 99.1 % 4 chains (184 residues) have been docked in sequence Building loops using Loopy2018 4 chains (184 residues) following loop building 4 chains (184 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1784 restraints for refining 1769 atoms. 244 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2325 (Rfree = 0.000) for 1769 atoms. Found 39 (50 requested) and removed 23 (30 requested) atoms. Cycle 12: After refmac, R = 0.2226 (Rfree = 0.000) for 1785 atoms. Found 22 (50 requested) and removed 21 (30 requested) atoms. Cycle 13: After refmac, R = 0.2137 (Rfree = 0.000) for 1783 atoms. Found 29 (49 requested) and removed 12 (30 requested) atoms. Cycle 14: After refmac, R = 0.2120 (Rfree = 0.000) for 1796 atoms. Found 24 (49 requested) and removed 20 (30 requested) atoms. Cycle 15: After refmac, R = 0.2092 (Rfree = 0.000) for 1800 atoms. Found 21 (48 requested) and removed 23 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.25 2.13 NCS extension: 0 residues added, 1800 seeds are put forward Round 1: 188 peptides, 4 chains. Longest chain 50 peptides. Score 0.908 Round 2: 189 peptides, 4 chains. Longest chain 50 peptides. Score 0.910 Round 3: 188 peptides, 5 chains. Longest chain 50 peptides. Score 0.900 Round 4: 189 peptides, 4 chains. Longest chain 50 peptides. Score 0.910 Round 5: 187 peptides, 6 chains. Longest chain 48 peptides. Score 0.890 Taking the results from Round 4 Chains 4, Residues 185, Estimated correctness of the model 99.1 % 4 chains (185 residues) have been docked in sequence Building loops using Loopy2018 4 chains (185 residues) following loop building 4 chains (185 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1765 restraints for refining 1769 atoms. 216 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2307 (Rfree = 0.000) for 1769 atoms. Found 41 (46 requested) and removed 26 (30 requested) atoms. Cycle 17: After refmac, R = 0.2204 (Rfree = 0.000) for 1784 atoms. Found 27 (45 requested) and removed 15 (30 requested) atoms. Cycle 18: After refmac, R = 0.2112 (Rfree = 0.000) for 1795 atoms. Found 19 (44 requested) and removed 11 (30 requested) atoms. Cycle 19: After refmac, R = 0.2087 (Rfree = 0.000) for 1798 atoms. Found 17 (43 requested) and removed 14 (30 requested) atoms. Cycle 20: After refmac, R = 0.2062 (Rfree = 0.000) for 1800 atoms. Found 12 (41 requested) and removed 12 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.24 2.12 NCS extension: 7 residues added (13 deleted due to clashes), 1808 seeds are put forward Round 1: 189 peptides, 4 chains. Longest chain 50 peptides. Score 0.910 Round 2: 188 peptides, 5 chains. Longest chain 50 peptides. Score 0.900 Round 3: 189 peptides, 4 chains. Longest chain 50 peptides. Score 0.910 Round 4: 188 peptides, 5 chains. Longest chain 50 peptides. Score 0.900 Round 5: 186 peptides, 6 chains. Longest chain 48 peptides. Score 0.888 Taking the results from Round 3 Chains 4, Residues 185, Estimated correctness of the model 99.1 % 4 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 59 A 3 chains (195 residues) following loop building 3 chains (195 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1798 restraints for refining 1821 atoms. 160 conditional restraints added. Observations/parameters ratio is 2.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2544 (Rfree = 0.000) for 1821 atoms. Found 41 (41 requested) and removed 31 (31 requested) atoms. Cycle 22: After refmac, R = 0.2310 (Rfree = 0.000) for 1830 atoms. Found 34 (40 requested) and removed 6 (31 requested) atoms. Cycle 23: After refmac, R = 0.2210 (Rfree = 0.000) for 1856 atoms. Found 18 (40 requested) and removed 16 (31 requested) atoms. Cycle 24: After refmac, R = 0.2161 (Rfree = 0.000) for 1857 atoms. Found 21 (39 requested) and removed 16 (31 requested) atoms. Cycle 25: After refmac, R = 0.2124 (Rfree = 0.000) for 1859 atoms. Found 29 (38 requested) and removed 17 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.23 2.11 NCS extension: 0 residues added, 1872 seeds are put forward Round 1: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 2: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 3: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 4: 189 peptides, 4 chains. Longest chain 49 peptides. Score 0.910 Round 5: 187 peptides, 6 chains. Longest chain 49 peptides. Score 0.890 Taking the results from Round 4 Chains 4, Residues 185, Estimated correctness of the model 99.1 % 4 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 60 A 3 chains (195 residues) following loop building 3 chains (195 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1845 restraints for refining 1856 atoms. 207 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2534 (Rfree = 0.000) for 1856 atoms. Found 32 (37 requested) and removed 36 (31 requested) atoms. Cycle 27: After refmac, R = 0.2326 (Rfree = 0.000) for 1849 atoms. Found 27 (35 requested) and removed 28 (31 requested) atoms. Cycle 28: After refmac, R = 0.2205 (Rfree = 0.000) for 1846 atoms. Found 26 (34 requested) and removed 17 (31 requested) atoms. Cycle 29: After refmac, R = 0.2135 (Rfree = 0.000) for 1853 atoms. Found 26 (33 requested) and removed 12 (31 requested) atoms. Cycle 30: After refmac, R = 0.2091 (Rfree = 0.000) for 1865 atoms. Found 28 (33 requested) and removed 20 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.23 2.11 NCS extension: 13 residues added (15 deleted due to clashes), 1891 seeds are put forward Round 1: 190 peptides, 6 chains. Longest chain 49 peptides. Score 0.894 Round 2: 191 peptides, 5 chains. Longest chain 51 peptides. Score 0.904 Round 3: 188 peptides, 6 chains. Longest chain 50 peptides. Score 0.891 Round 4: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 5: 188 peptides, 6 chains. Longest chain 49 peptides. Score 0.891 Taking the results from Round 2 Chains 5, Residues 186, Estimated correctness of the model 99.0 % 4 chains (177 residues) have been docked in sequence Building loops using Loopy2018 5 chains (186 residues) following loop building 4 chains (177 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1926 restraints for refining 1809 atoms. 416 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2371 (Rfree = 0.000) for 1809 atoms. Found 30 (30 requested) and removed 30 (30 requested) atoms. Cycle 32: After refmac, R = 0.2252 (Rfree = 0.000) for 1808 atoms. Found 25 (30 requested) and removed 8 (30 requested) atoms. Cycle 33: After refmac, R = 0.2168 (Rfree = 0.000) for 1825 atoms. Found 20 (31 requested) and removed 11 (31 requested) atoms. Cycle 34: After refmac, R = 0.2118 (Rfree = 0.000) for 1833 atoms. Found 18 (31 requested) and removed 14 (31 requested) atoms. Cycle 35: After refmac, R = 0.2103 (Rfree = 0.000) for 1836 atoms. Found 23 (31 requested) and removed 17 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.23 2.11 NCS extension: 4 residues added (2 deleted due to clashes), 1848 seeds are put forward Round 1: 190 peptides, 4 chains. Longest chain 50 peptides. Score 0.911 Round 2: 193 peptides, 3 chains. Longest chain 100 peptides. Score 0.922 Round 3: 193 peptides, 4 chains. Longest chain 77 peptides. Score 0.914 Round 4: 190 peptides, 6 chains. Longest chain 69 peptides. Score 0.894 Round 5: 183 peptides, 7 chains. Longest chain 49 peptides. Score 0.874 Taking the results from Round 2 Chains 5, Residues 190, Estimated correctness of the model 99.3 % 4 chains (186 residues) have been docked in sequence Building loops using Loopy2018 5 chains (190 residues) following loop building 4 chains (186 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1779 restraints for refining 1800 atoms. 211 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2267 (Rfree = 0.000) for 1800 atoms. Found 30 (30 requested) and removed 30 (30 requested) atoms. Cycle 37: After refmac, R = 0.2167 (Rfree = 0.000) for 1798 atoms. Found 24 (30 requested) and removed 14 (30 requested) atoms. Cycle 38: After refmac, R = 0.2107 (Rfree = 0.000) for 1807 atoms. Found 20 (30 requested) and removed 13 (30 requested) atoms. Cycle 39: After refmac, R = 0.2068 (Rfree = 0.000) for 1813 atoms. Found 17 (31 requested) and removed 13 (31 requested) atoms. Cycle 40: After refmac, R = 0.2024 (Rfree = 0.000) for 1817 atoms. Found 23 (31 requested) and removed 10 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.23 2.11 NCS extension: 7 residues added (8 deleted due to clashes), 1840 seeds are put forward Round 1: 185 peptides, 4 chains. Longest chain 48 peptides. Score 0.904 Round 2: 186 peptides, 4 chains. Longest chain 48 peptides. Score 0.906 Round 3: 185 peptides, 6 chains. Longest chain 48 peptides. Score 0.887 Round 4: 185 peptides, 5 chains. Longest chain 48 peptides. Score 0.896 Round 5: 184 peptides, 6 chains. Longest chain 48 peptides. Score 0.885 Taking the results from Round 2 Chains 4, Residues 182, Estimated correctness of the model 99.1 % 4 chains (182 residues) have been docked in sequence Building loops using Loopy2018 4 chains (182 residues) following loop building 4 chains (182 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1810 restraints for refining 1782 atoms. 282 conditional restraints added. Observations/parameters ratio is 2.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2230 (Rfree = 0.000) for 1782 atoms. Found 30 (30 requested) and removed 19 (30 requested) atoms. Cycle 42: After refmac, R = 0.2150 (Rfree = 0.000) for 1792 atoms. Found 26 (30 requested) and removed 14 (30 requested) atoms. Cycle 43: After refmac, R = 0.2081 (Rfree = 0.000) for 1803 atoms. Found 29 (30 requested) and removed 9 (30 requested) atoms. Cycle 44: After refmac, R = 0.2063 (Rfree = 0.000) for 1823 atoms. Found 22 (31 requested) and removed 17 (31 requested) atoms. Cycle 45: After refmac, R = 0.2028 (Rfree = 0.000) for 1828 atoms. Found 27 (31 requested) and removed 18 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1838 seeds are put forward Round 1: 186 peptides, 4 chains. Longest chain 48 peptides. Score 0.906 Round 2: 186 peptides, 4 chains. Longest chain 48 peptides. Score 0.906 Round 3: 186 peptides, 4 chains. Longest chain 48 peptides. Score 0.906 Round 4: 183 peptides, 7 chains. Longest chain 48 peptides. Score 0.874 Round 5: 186 peptides, 4 chains. Longest chain 48 peptides. Score 0.906 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 182, Estimated correctness of the model 99.1 % 4 chains (182 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Loop building was unsuccessful. The job will continue without loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 17355 reflections ( 98.91 % complete ) and 1528 restraints for refining 1487 atoms. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2722 (Rfree = 0.000) for 1487 atoms. Found 9 (25 requested) and removed 0 (25 requested) atoms. Cycle 47: After refmac, R = 0.2599 (Rfree = 0.000) for 1487 atoms. Found 5 (25 requested) and removed 0 (25 requested) atoms. Cycle 48: After refmac, R = 0.2510 (Rfree = 0.000) for 1487 atoms. Found 2 (25 requested) and removed 0 (25 requested) atoms. Cycle 49: After refmac, R = 0.2450 (Rfree = 0.000) for 1487 atoms. Found 1 (25 requested) and removed 0 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:47 GMT 2018 Job finished. TimeTaking 43.65 Used memory is bytes: 6678816