Sun 23 Dec 23:45:39 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 2ifx-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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/2ifx-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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 ============================================================ Sun 23 Dec 23:45:43 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/2ifx-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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 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-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-2.0-parrot-mrncs.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 2016 atoms. Observations/parameters ratio is 2.15 ------------------------------------------------------ Starting model: R = 0.3084 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2628 (Rfree = 0.000) for 2016 atoms. Found 23 (68 requested) and removed 44 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.31 2.19 NCS extension: 0 residues added, 1995 seeds are put forward Round 1: 158 peptides, 15 chains. Longest chain 20 peptides. Score 0.710 Round 2: 173 peptides, 11 chains. Longest chain 36 peptides. Score 0.811 Round 3: 182 peptides, 7 chains. Longest chain 48 peptides. Score 0.873 Round 4: 186 peptides, 5 chains. Longest chain 48 peptides. Score 0.897 Round 5: 185 peptides, 6 chains. Longest chain 48 peptides. Score 0.887 Taking the results from Round 4 Chains 5, Residues 181, Estimated correctness of the model 98.9 % 5 chains (181 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A 4 chains (183 residues) following loop building 4 chains (183 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1806 restraints for refining 1769 atoms. 269 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2827 (Rfree = 0.000) for 1769 atoms. Found 35 (60 requested) and removed 32 (30 requested) atoms. Cycle 2: After refmac, R = 0.2527 (Rfree = 0.000) for 1770 atoms. Found 25 (59 requested) and removed 25 (30 requested) atoms. Cycle 3: After refmac, R = 0.2403 (Rfree = 0.000) for 1754 atoms. Found 22 (58 requested) and removed 22 (30 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 1746 atoms. Found 32 (56 requested) and removed 16 (30 requested) atoms. Cycle 5: After refmac, R = 0.2282 (Rfree = 0.000) for 1754 atoms. Found 19 (56 requested) and removed 16 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.25 2.13 NCS extension: 0 residues added, 1758 seeds are put forward Round 1: 183 peptides, 4 chains. Longest chain 48 peptides. Score 0.902 Round 2: 183 peptides, 6 chains. Longest chain 48 peptides. Score 0.884 Round 3: 185 peptides, 4 chains. Longest chain 48 peptides. Score 0.904 Round 4: 183 peptides, 7 chains. Longest chain 48 peptides. Score 0.874 Round 5: 184 peptides, 6 chains. Longest chain 48 peptides. Score 0.885 Taking the results from Round 3 Chains 4, Residues 181, Estimated correctness of the model 99.0 % 4 chains (181 residues) have been docked in sequence Building loops using Loopy2018 4 chains (181 residues) following loop building 4 chains (181 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1829 restraints for refining 1760 atoms. 307 conditional restraints added. Observations/parameters ratio is 2.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2442 (Rfree = 0.000) for 1760 atoms. Found 25 (55 requested) and removed 30 (30 requested) atoms. Cycle 7: After refmac, R = 0.2291 (Rfree = 0.000) for 1750 atoms. Found 23 (54 requested) and removed 15 (30 requested) atoms. Cycle 8: After refmac, R = 0.2223 (Rfree = 0.000) for 1755 atoms. Found 19 (53 requested) and removed 13 (30 requested) atoms. Cycle 9: After refmac, R = 0.2166 (Rfree = 0.000) for 1759 atoms. Found 19 (52 requested) and removed 7 (30 requested) atoms. Cycle 10: After refmac, R = 0.2154 (Rfree = 0.000) for 1770 atoms. Found 15 (52 requested) and removed 14 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1771 seeds are put forward Round 1: 185 peptides, 4 chains. Longest chain 48 peptides. Score 0.904 Round 2: 184 peptides, 5 chains. Longest chain 48 peptides. Score 0.894 Round 3: 185 peptides, 6 chains. Longest chain 48 peptides. Score 0.887 Round 4: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 5: 185 peptides, 6 chains. Longest chain 49 peptides. Score 0.887 Taking the results from Round 4 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 1791 restraints for refining 1769 atoms. 257 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2323 (Rfree = 0.000) for 1769 atoms. Found 32 (50 requested) and removed 24 (30 requested) atoms. Cycle 12: After refmac, R = 0.2232 (Rfree = 0.000) for 1775 atoms. Found 25 (49 requested) and removed 23 (30 requested) atoms. Cycle 13: After refmac, R = 0.2162 (Rfree = 0.000) for 1777 atoms. Found 25 (48 requested) and removed 10 (30 requested) atoms. Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 1792 atoms. Found 14 (49 requested) and removed 17 (30 requested) atoms. Cycle 15: After refmac, R = 0.2076 (Rfree = 0.000) for 1788 atoms. Found 26 (48 requested) and removed 11 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1803 seeds are put forward Round 1: 189 peptides, 4 chains. Longest chain 49 peptides. Score 0.910 Round 2: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 3: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 4: 188 peptides, 6 chains. Longest chain 49 peptides. Score 0.891 Round 5: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Taking the results from Round 1 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 1776 restraints for refining 1769 atoms. 227 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2286 (Rfree = 0.000) for 1769 atoms. Found 47 (47 requested) and removed 23 (30 requested) atoms. Cycle 17: After refmac, R = 0.2195 (Rfree = 0.000) for 1792 atoms. Found 16 (48 requested) and removed 12 (30 requested) atoms. Cycle 18: After refmac, R = 0.2111 (Rfree = 0.000) for 1795 atoms. Found 18 (46 requested) and removed 8 (30 requested) atoms. Cycle 19: After refmac, R = 0.2074 (Rfree = 0.000) for 1804 atoms. Found 22 (46 requested) and removed 14 (30 requested) atoms. Cycle 20: After refmac, R = 0.2052 (Rfree = 0.000) for 1812 atoms. Found 22 (45 requested) and removed 13 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.24 2.12 NCS extension: 4 residues added (13 deleted due to clashes), 1826 seeds are put forward Round 1: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 2: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 3: 187 peptides, 6 chains. Longest chain 49 peptides. Score 0.890 Round 4: 188 peptides, 5 chains. Longest chain 50 peptides. Score 0.900 Round 5: 187 peptides, 7 chains. Longest chain 48 peptides. Score 0.881 Taking the results from Round 1 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 1849 restraints for refining 1777 atoms. 315 conditional restraints added. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2264 (Rfree = 0.000) for 1777 atoms. Found 32 (43 requested) and removed 18 (30 requested) atoms. Cycle 22: After refmac, R = 0.2194 (Rfree = 0.000) for 1790 atoms. Found 24 (43 requested) and removed 4 (30 requested) atoms. Cycle 23: After refmac, R = 0.2117 (Rfree = 0.000) for 1810 atoms. Found 14 (43 requested) and removed 8 (30 requested) atoms. Cycle 24: After refmac, R = 0.2064 (Rfree = 0.000) for 1812 atoms. Found 19 (42 requested) and removed 15 (31 requested) atoms. Cycle 25: After refmac, R = 0.2057 (Rfree = 0.000) for 1815 atoms. Found 28 (41 requested) and removed 9 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.23 2.11 NCS extension: 4 residues added (13 deleted due to clashes), 1840 seeds are put forward Round 1: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 2: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 3: 186 peptides, 6 chains. Longest chain 49 peptides. Score 0.888 Round 4: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 5: 183 peptides, 8 chains. Longest chain 30 peptides. Score 0.864 Taking the results from Round 1 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 1782 restraints for refining 1769 atoms. 248 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2240 (Rfree = 0.000) for 1769 atoms. Found 40 (40 requested) and removed 13 (30 requested) atoms. Cycle 27: After refmac, R = 0.2142 (Rfree = 0.000) for 1796 atoms. Found 20 (40 requested) and removed 9 (30 requested) atoms. Cycle 28: After refmac, R = 0.2058 (Rfree = 0.000) for 1807 atoms. Found 16 (40 requested) and removed 4 (30 requested) atoms. Cycle 29: After refmac, R = 0.2013 (Rfree = 0.000) for 1818 atoms. Found 11 (41 requested) and removed 9 (31 requested) atoms. Cycle 30: After refmac, R = 0.1990 (Rfree = 0.000) for 1819 atoms. Found 16 (40 requested) and removed 5 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.24 2.12 NCS extension: 5 residues added (12 deleted due to clashes), 1838 seeds are put forward Round 1: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 2: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 3: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 4: 188 peptides, 5 chains. Longest chain 49 peptides. Score 0.900 Round 5: 186 peptides, 7 chains. Longest chain 48 peptides. Score 0.879 Taking the results from Round 3 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 1778 restraints for refining 1780 atoms. 236 conditional restraints added. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2229 (Rfree = 0.000) for 1780 atoms. Found 38 (38 requested) and removed 15 (30 requested) atoms. Cycle 32: After refmac, R = 0.2137 (Rfree = 0.000) for 1802 atoms. Found 20 (39 requested) and removed 9 (30 requested) atoms. Cycle 33: After refmac, R = 0.2065 (Rfree = 0.000) for 1813 atoms. Found 16 (40 requested) and removed 7 (31 requested) atoms. Cycle 34: After refmac, R = 0.2011 (Rfree = 0.000) for 1822 atoms. Found 15 (40 requested) and removed 3 (31 requested) atoms. Cycle 35: After refmac, R = 0.1993 (Rfree = 0.000) for 1833 atoms. Found 12 (40 requested) and removed 12 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.25 2.13 NCS extension: 5 residues added (12 deleted due to clashes), 1841 seeds are put forward Round 1: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 2: 188 peptides, 5 chains. Longest chain 49 peptides. Score 0.900 Round 3: 190 peptides, 5 chains. Longest chain 49 peptides. Score 0.903 Round 4: 188 peptides, 5 chains. Longest chain 49 peptides. Score 0.900 Round 5: 187 peptides, 7 chains. Longest chain 48 peptides. Score 0.881 Taking the results from Round 3 Chains 5, Residues 185, Estimated correctness of the model 99.0 % 5 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 B and 90 B 4 chains (186 residues) following loop building 4 chains (186 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1772 restraints for refining 1781 atoms. 217 conditional restraints added. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2266 (Rfree = 0.000) for 1781 atoms. Found 37 (37 requested) and removed 22 (30 requested) atoms. Cycle 37: After refmac, R = 0.2164 (Rfree = 0.000) for 1794 atoms. Found 21 (37 requested) and removed 10 (30 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2073 (Rfree = 0.000) for 1805 atoms. Found 20 (37 requested) and removed 6 (30 requested) atoms. Cycle 39: After refmac, R = 0.2021 (Rfree = 0.000) for 1818 atoms. Found 15 (37 requested) and removed 11 (31 requested) atoms. Cycle 40: After refmac, R = 0.2010 (Rfree = 0.000) for 1822 atoms. Found 22 (36 requested) and removed 12 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.24 2.12 NCS extension: 2 residues added (11 deleted due to clashes), 1838 seeds are put forward Round 1: 189 peptides, 4 chains. Longest chain 48 peptides. Score 0.910 Round 2: 189 peptides, 5 chains. Longest chain 48 peptides. Score 0.901 Round 3: 189 peptides, 5 chains. Longest chain 48 peptides. Score 0.901 Round 4: 191 peptides, 4 chains. Longest chain 49 peptides. Score 0.912 Round 5: 187 peptides, 7 chains. Longest chain 48 peptides. Score 0.881 Taking the results from Round 4 Chains 4, Residues 187, Estimated correctness of the model 99.2 % 4 chains (187 residues) have been docked in sequence Building loops using Loopy2018 4 chains (187 residues) following loop building 4 chains (187 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1762 restraints for refining 1793 atoms. 199 conditional restraints added. Observations/parameters ratio is 2.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2262 (Rfree = 0.000) for 1793 atoms. Found 34 (34 requested) and removed 21 (30 requested) atoms. Cycle 42: After refmac, R = 0.2172 (Rfree = 0.000) for 1805 atoms. Found 30 (33 requested) and removed 9 (30 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2082 (Rfree = 0.000) for 1824 atoms. Found 27 (33 requested) and removed 11 (31 requested) atoms. Cycle 44: After refmac, R = 0.2050 (Rfree = 0.000) for 1840 atoms. Found 23 (33 requested) and removed 13 (31 requested) atoms. Cycle 45: After refmac, R = 0.2010 (Rfree = 0.000) for 1849 atoms. Found 22 (33 requested) and removed 12 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.23 2.11 NCS extension: 2 residues added (11 deleted due to clashes), 1863 seeds are put forward Round 1: 187 peptides, 6 chains. Longest chain 48 peptides. Score 0.890 Round 2: 189 peptides, 5 chains. Longest chain 48 peptides. Score 0.901 Round 3: 188 peptides, 5 chains. Longest chain 48 peptides. Score 0.900 Round 4: 187 peptides, 6 chains. Longest chain 48 peptides. Score 0.890 Round 5: 189 peptides, 4 chains. Longest chain 48 peptides. Score 0.910 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 185, Estimated correctness of the model 99.1 % 4 chains (185 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 48 A and 61 A 3 chains (197 residues) following loop building 3 chains (197 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 17355 reflections ( 98.91 % complete ) and 1651 restraints for refining 1604 atoms. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2881 (Rfree = 0.000) for 1604 atoms. Found 3 (27 requested) and removed 0 (27 requested) atoms. Cycle 47: After refmac, R = 0.2709 (Rfree = 0.000) for 1604 atoms. Found 2 (27 requested) and removed 0 (27 requested) atoms. Cycle 48: After refmac, R = 0.2591 (Rfree = 0.000) for 1604 atoms. Found 3 (27 requested) and removed 0 (27 requested) atoms. Cycle 49: After refmac, R = 0.2518 (Rfree = 0.000) for 1604 atoms. Found 1 (27 requested) and removed 0 (27 requested) atoms. Writing output files ... TimeTaking 28.58