null Mon 24 Dec 07:32:36 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 2ifx-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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/2ifx-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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 07:32:40 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/2ifx-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-2.0-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 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-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-2.0-parrot-noncs.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 2023 atoms. Observations/parameters ratio is 2.14 ------------------------------------------------------ Starting model: R = 0.3122 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2708 (Rfree = 0.000) for 2023 atoms. Found 37 (69 requested) and removed 46 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.32 2.20 NCS extension: 0 residues added, 2014 seeds are put forward Round 1: 145 peptides, 16 chains. Longest chain 18 peptides. Score 0.643 Round 2: 153 peptides, 12 chains. Longest chain 26 peptides. Score 0.742 Round 3: 169 peptides, 8 chains. Longest chain 42 peptides. Score 0.838 Round 4: 172 peptides, 9 chains. Longest chain 30 peptides. Score 0.832 Round 5: 175 peptides, 12 chains. Longest chain 24 peptides. Score 0.803 Taking the results from Round 3 Chains 9, Residues 161, Estimated correctness of the model 97.5 % 8 chains (160 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 73 A and 82 A Built loop between residues 71 B and 74 B Built loop between residues 89 B and 96 B 4 chains (178 residues) following loop building 4 chains (178 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1841 restraints for refining 1768 atoms. 348 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2863 (Rfree = 0.000) for 1768 atoms. Found 42 (60 requested) and removed 31 (30 requested) atoms. Cycle 2: After refmac, R = 0.2592 (Rfree = 0.000) for 1771 atoms. Found 26 (59 requested) and removed 30 (30 requested) atoms. Cycle 3: After refmac, R = 0.2442 (Rfree = 0.000) for 1758 atoms. Found 22 (58 requested) and removed 18 (30 requested) atoms. Cycle 4: After refmac, R = 0.2353 (Rfree = 0.000) for 1758 atoms. Found 10 (56 requested) and removed 10 (30 requested) atoms. Cycle 5: After refmac, R = 0.2301 (Rfree = 0.000) for 1754 atoms. Found 10 (55 requested) and removed 9 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.27 2.15 NCS extension: 0 residues added, 1758 seeds are put forward Round 1: 181 peptides, 6 chains. Longest chain 47 peptides. Score 0.881 Round 2: 184 peptides, 5 chains. Longest chain 47 peptides. Score 0.894 Round 3: 184 peptides, 6 chains. Longest chain 47 peptides. Score 0.885 Round 4: 177 peptides, 8 chains. Longest chain 47 peptides. Score 0.854 Round 5: 180 peptides, 9 chains. Longest chain 44 peptides. Score 0.849 Taking the results from Round 2 Chains 5, Residues 179, Estimated correctness of the model 98.8 % 5 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 12 B and 15 B 4 chains (181 residues) following loop building 4 chains (181 residues) in sequence following loop building ------------------------------------------------------ 17355 reflections ( 98.91 % complete ) and 1793 restraints for refining 1758 atoms. 276 conditional restraints added. Observations/parameters ratio is 2.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 1758 atoms. Found 29 (54 requested) and removed 30 (30 requested) atoms. Cycle 7: After refmac, R = 0.2341 (Rfree = 0.000) for 1754 atoms. Found 21 (53 requested) and removed 22 (30 requested) atoms. Cycle 8: After refmac, R = 0.2269 (Rfree = 0.000) for 1751 atoms. Found 26 (51 requested) and removed 14 (29 requested) atoms. Cycle 9: After refmac, R = 0.2222 (Rfree = 0.000) for 1762 atoms. Found 17 (50 requested) and removed 20 (30 requested) atoms. Cycle 10: After refmac, R = 0.2192 (Rfree = 0.000) for 1757 atoms. Found 18 (49 requested) and removed 14 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1761 seeds are put forward Round 1: 185 peptides, 4 chains. Longest chain 47 peptides. Score 0.904 Round 2: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 3: 186 peptides, 5 chains. Longest chain 49 peptides. Score 0.897 Round 4: 185 peptides, 6 chains. Longest chain 49 peptides. Score 0.887 Round 5: 181 peptides, 6 chains. Longest chain 47 peptides. Score 0.881 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 1773 restraints for refining 1769 atoms. 240 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2378 (Rfree = 0.000) for 1769 atoms. Found 26 (48 requested) and removed 30 (30 requested) atoms. Cycle 12: After refmac, R = 0.2264 (Rfree = 0.000) for 1763 atoms. Found 24 (47 requested) and removed 23 (30 requested) atoms. Cycle 13: After refmac, R = 0.2187 (Rfree = 0.000) for 1763 atoms. Found 17 (46 requested) and removed 12 (30 requested) atoms. Cycle 14: After refmac, R = 0.2151 (Rfree = 0.000) for 1766 atoms. Found 22 (44 requested) and removed 8 (30 requested) atoms. Cycle 15: After refmac, R = 0.2142 (Rfree = 0.000) for 1778 atoms. Found 19 (44 requested) and removed 12 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1785 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: 186 peptides, 7 chains. Longest chain 48 peptides. Score 0.879 Round 5: 186 peptides, 6 chains. Longest chain 49 peptides. Score 0.888 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 1781 restraints for refining 1769 atoms. 239 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2350 (Rfree = 0.000) for 1769 atoms. Found 31 (43 requested) and removed 28 (30 requested) atoms. Cycle 17: After refmac, R = 0.2221 (Rfree = 0.000) for 1770 atoms. Found 16 (42 requested) and removed 13 (30 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 1770 atoms. Found 19 (41 requested) and removed 5 (30 requested) atoms. Cycle 19: After refmac, R = 0.2106 (Rfree = 0.000) for 1783 atoms. Found 13 (41 requested) and removed 14 (30 requested) atoms. Cycle 20: After refmac, R = 0.2078 (Rfree = 0.000) for 1781 atoms. Found 20 (40 requested) and removed 11 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.24 2.12 NCS extension: 5 residues added (12 deleted due to clashes), 1795 seeds are put forward Round 1: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 2: 188 peptides, 5 chains. Longest chain 49 peptides. Score 0.900 Round 3: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 4: 186 peptides, 6 chains. Longest chain 49 peptides. Score 0.888 Round 5: 186 peptides, 5 chains. Longest chain 49 peptides. Score 0.897 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 1770 restraints for refining 1769 atoms. 228 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2296 (Rfree = 0.000) for 1769 atoms. Found 17 (38 requested) and removed 24 (30 requested) atoms. Cycle 22: After refmac, R = 0.2171 (Rfree = 0.000) for 1762 atoms. Found 20 (37 requested) and removed 6 (30 requested) atoms. Cycle 23: After refmac, R = 0.2115 (Rfree = 0.000) for 1775 atoms. Found 13 (37 requested) and removed 9 (30 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 1778 atoms. Found 14 (36 requested) and removed 9 (30 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 1781 atoms. Found 14 (35 requested) and removed 8 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 2.12 NCS extension: 0 residues added, 1787 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, 5 chains. Longest chain 49 peptides. Score 0.899 Round 4: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 5: 185 peptides, 7 chains. Longest chain 50 peptides. Score 0.877 Taking the results from Round 4 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 1776 restraints for refining 1769 atoms. 234 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2297 (Rfree = 0.000) for 1769 atoms. Found 25 (34 requested) and removed 23 (30 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 1771 atoms. Found 18 (32 requested) and removed 9 (30 requested) atoms. Cycle 28: After refmac, R = 0.2106 (Rfree = 0.000) for 1779 atoms. Found 21 (32 requested) and removed 7 (30 requested) atoms. Cycle 29: After refmac, R = 0.2049 (Rfree = 0.000) for 1792 atoms. Found 15 (33 requested) and removed 10 (30 requested) atoms. Cycle 30: After refmac, R = 0.2031 (Rfree = 0.000) for 1795 atoms. Found 18 (32 requested) and removed 14 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.25 2.13 NCS extension: 6 residues added (11 deleted due to clashes), 1806 seeds are put forward Round 1: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 2: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 3: 185 peptides, 7 chains. Longest chain 49 peptides. Score 0.877 Round 4: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Round 5: 186 peptides, 6 chains. Longest chain 49 peptides. Score 0.888 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 1769 restraints for refining 1769 atoms. 227 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2254 (Rfree = 0.000) for 1769 atoms. Found 30 (30 requested) and removed 25 (30 requested) atoms. Cycle 32: After refmac, R = 0.2156 (Rfree = 0.000) for 1772 atoms. Found 18 (30 requested) and removed 10 (30 requested) atoms. Cycle 33: After refmac, R = 0.2076 (Rfree = 0.000) for 1780 atoms. Found 16 (30 requested) and removed 9 (30 requested) atoms. Cycle 34: After refmac, R = 0.2039 (Rfree = 0.000) for 1787 atoms. Found 19 (30 requested) and removed 12 (30 requested) atoms. Cycle 35: After refmac, R = 0.2023 (Rfree = 0.000) for 1792 atoms. Found 19 (30 requested) and removed 13 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.24 2.12 NCS extension: 4 residues added (13 deleted due to clashes), 1803 seeds are put forward Round 1: 187 peptides, 4 chains. Longest chain 54 peptides. Score 0.907 Round 2: 186 peptides, 6 chains. Longest chain 49 peptides. Score 0.888 Round 3: 188 peptides, 4 chains. Longest chain 49 peptides. Score 0.908 Round 4: 181 peptides, 7 chains. Longest chain 48 peptides. Score 0.871 Round 5: 181 peptides, 6 chains. Longest chain 49 peptides. Score 0.881 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 1751 restraints for refining 1769 atoms. 209 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2267 (Rfree = 0.000) for 1769 atoms. Found 30 (30 requested) and removed 18 (30 requested) atoms. Cycle 37: After refmac, R = 0.2147 (Rfree = 0.000) for 1779 atoms. Found 16 (30 requested) and removed 11 (30 requested) atoms. Cycle 38: After refmac, R = 0.2076 (Rfree = 0.000) for 1782 atoms. Found 18 (30 requested) and removed 9 (30 requested) atoms. Cycle 39: After refmac, R = 0.2031 (Rfree = 0.000) for 1791 atoms. Found 18 (30 requested) and removed 7 (30 requested) atoms. Cycle 40: After refmac, R = 0.1990 (Rfree = 0.000) for 1800 atoms. Found 14 (30 requested) and removed 15 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.25 2.13 NCS extension: 0 residues added, 1799 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, 4 chains. Longest chain 49 peptides. Score 0.908 Round 5: 187 peptides, 5 chains. Longest chain 49 peptides. Score 0.899 Taking the results from Round 4 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 1760 restraints for refining 1769 atoms. 218 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2282 (Rfree = 0.000) for 1769 atoms. Found 30 (30 requested) and removed 24 (30 requested) atoms. Cycle 42: After refmac, R = 0.2161 (Rfree = 0.000) for 1774 atoms. Found 24 (30 requested) and removed 12 (30 requested) atoms. Cycle 43: After refmac, R = 0.2084 (Rfree = 0.000) for 1785 atoms. Found 22 (30 requested) and removed 12 (30 requested) atoms. Cycle 44: After refmac, R = 0.2042 (Rfree = 0.000) for 1794 atoms. Found 23 (30 requested) and removed 12 (30 requested) atoms. Cycle 45: After refmac, R = 0.2021 (Rfree = 0.000) for 1805 atoms. Found 19 (30 requested) and removed 16 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.13 NCS extension: 0 residues added, 1808 seeds are put forward Round 1: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 2: 186 peptides, 5 chains. Longest chain 49 peptides. Score 0.897 Round 3: 187 peptides, 4 chains. Longest chain 49 peptides. Score 0.907 Round 4: 185 peptides, 6 chains. Longest chain 49 peptides. Score 0.887 Round 5: 186 peptides, 5 chains. Longest chain 49 peptides. Score 0.897 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 183, Estimated correctness of the model 99.1 % 4 chains (183 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 62 A 3 chains (196 residues) following loop building 3 chains (196 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 17355 reflections ( 98.91 % complete ) and 1646 restraints for refining 1598 atoms. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2913 (Rfree = 0.000) for 1598 atoms. Found 10 (27 requested) and removed 0 (27 requested) atoms. Cycle 47: After refmac, R = 0.2727 (Rfree = 0.000) for 1598 atoms. Found 0 (27 requested) and removed 0 (27 requested) atoms. Cycle 48: After refmac, R = 0.2612 (Rfree = 0.000) for 1598 atoms. Found 2 (27 requested) and removed 1 (27 requested) atoms. Cycle 49: After refmac, R = 0.2546 (Rfree = 0.000) for 1598 atoms. Found 1 (27 requested) and removed 0 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:01:11 GMT 2018 Job finished. TimeTaking 28.58 Used memory is bytes: 15835696