null Sun 23 Dec 23:45:55 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 2i8d-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-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/2i8d-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-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 23:46:00 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/2i8d-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6440 Checking the provided sequence file Detected sequence length: 123 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 246 Adjusted target solvent content: 0.56 Input MTZ file: 2i8d-3.8-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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.85 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: 55.142 3.801 Wilson plot Bfac: 74.39 3202 reflections ( 98.46 % complete ) and 0 restraints for refining 2190 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3461 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3360 (Rfree = 0.000) for 2190 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2236 seeds are put forward NCS extension: 0 residues added, 2236 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 8 peptides. Score 0.344 Round 2: 138 peptides, 23 chains. Longest chain 10 peptides. Score 0.433 Round 3: 142 peptides, 17 chains. Longest chain 19 peptides. Score 0.575 Round 4: 147 peptides, 18 chains. Longest chain 17 peptides. Score 0.577 Round 5: 159 peptides, 17 chains. Longest chain 22 peptides. Score 0.642 Taking the results from Round 5 Chains 20, Residues 142, Estimated correctness of the model 17.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3636 restraints for refining 1780 atoms. 2997 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2715 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2821 (Rfree = 0.000) for 1754 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.2302 (Rfree = 0.000) for 1738 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2379 (Rfree = 0.000) for 1715 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 5: After refmac, R = 0.2522 (Rfree = 0.000) for 1703 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.23 Search for helices and strands: 0 residues in 0 chains, 1772 seeds are put forward NCS extension: 0 residues added, 1772 seeds are put forward Round 1: 133 peptides, 22 chains. Longest chain 13 peptides. Score 0.430 Round 2: 141 peptides, 18 chains. Longest chain 23 peptides. Score 0.552 Round 3: 152 peptides, 17 chains. Longest chain 22 peptides. Score 0.616 Round 4: 145 peptides, 18 chains. Longest chain 15 peptides. Score 0.569 Round 5: 138 peptides, 17 chains. Longest chain 17 peptides. Score 0.558 Taking the results from Round 3 Chains 17, Residues 135, Estimated correctness of the model 6.1 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3764 restraints for refining 1780 atoms. 3189 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2780 (Rfree = 0.000) for 1780 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 7: After refmac, R = 0.2501 (Rfree = 0.000) for 1765 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2420 (Rfree = 0.000) for 1757 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2326 (Rfree = 0.000) for 1749 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2272 (Rfree = 0.000) for 1748 atoms. Found 0 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 1811 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 1849 seeds are put forward Round 1: 130 peptides, 23 chains. Longest chain 16 peptides. Score 0.391 Round 2: 143 peptides, 21 chains. Longest chain 17 peptides. Score 0.500 Round 3: 149 peptides, 20 chains. Longest chain 15 peptides. Score 0.547 Round 4: 157 peptides, 20 chains. Longest chain 25 peptides. Score 0.581 Round 5: 152 peptides, 17 chains. Longest chain 20 peptides. Score 0.616 Taking the results from Round 5 Chains 17, Residues 135, Estimated correctness of the model 6.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3940 restraints for refining 1779 atoms. 3417 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2628 (Rfree = 0.000) for 1779 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2466 (Rfree = 0.000) for 1770 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2400 (Rfree = 0.000) for 1763 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2409 (Rfree = 0.000) for 1755 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2413 (Rfree = 0.000) for 1750 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward NCS extension: 17 residues added (9 deleted due to clashes), 1830 seeds are put forward Round 1: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.384 Round 2: 136 peptides, 18 chains. Longest chain 15 peptides. Score 0.529 Round 3: 137 peptides, 18 chains. Longest chain 20 peptides. Score 0.534 Round 4: 136 peptides, 18 chains. Longest chain 16 peptides. Score 0.529 Round 5: 140 peptides, 17 chains. Longest chain 16 peptides. Score 0.567 Taking the results from Round 5 Chains 17, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4026 restraints for refining 1780 atoms. 3551 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2861 (Rfree = 0.000) for 1780 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2647 (Rfree = 0.000) for 1768 atoms. Found 5 (9 requested) and removed 11 (4 requested) atoms. Cycle 18: After refmac, R = 0.2403 (Rfree = 0.000) for 1756 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2353 (Rfree = 0.000) for 1748 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2202 (Rfree = 0.000) for 1743 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.23 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 1839 seeds are put forward Round 1: 106 peptides, 19 chains. Longest chain 8 peptides. Score 0.354 Round 2: 133 peptides, 19 chains. Longest chain 17 peptides. Score 0.495 Round 3: 134 peptides, 20 chains. Longest chain 17 peptides. Score 0.478 Round 4: 132 peptides, 18 chains. Longest chain 15 peptides. Score 0.511 Round 5: 130 peptides, 19 chains. Longest chain 19 peptides. Score 0.480 Taking the results from Round 4 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4029 restraints for refining 1780 atoms. 3591 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2517 (Rfree = 0.000) for 1780 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 1771 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2344 (Rfree = 0.000) for 1768 atoms. Found 0 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.2305 (Rfree = 0.000) for 1758 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2238 (Rfree = 0.000) for 1753 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.26 Search for helices and strands: 0 residues in 0 chains, 1811 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1831 seeds are put forward Round 1: 125 peptides, 22 chains. Longest chain 16 peptides. Score 0.388 Round 2: 133 peptides, 17 chains. Longest chain 17 peptides. Score 0.536 Round 3: 138 peptides, 18 chains. Longest chain 16 peptides. Score 0.538 Round 4: 135 peptides, 18 chains. Longest chain 15 peptides. Score 0.525 Round 5: 132 peptides, 19 chains. Longest chain 12 peptides. Score 0.490 Taking the results from Round 3 Chains 18, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4022 restraints for refining 1779 atoms. 3560 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2492 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2279 (Rfree = 0.000) for 1777 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2190 (Rfree = 0.000) for 1769 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 1763 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2124 (Rfree = 0.000) for 1759 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1840 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 13 peptides. Score 0.301 Round 2: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.381 Round 3: 113 peptides, 17 chains. Longest chain 14 peptides. Score 0.440 Round 4: 116 peptides, 18 chains. Longest chain 11 peptides. Score 0.432 Round 5: 115 peptides, 15 chains. Longest chain 23 peptides. Score 0.495 Taking the results from Round 5 Chains 15, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4167 restraints for refining 1780 atoms. 3782 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2590 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2325 (Rfree = 0.000) for 1782 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2261 (Rfree = 0.000) for 1776 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2207 (Rfree = 0.000) for 1771 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2187 (Rfree = 0.000) for 1760 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 1842 seeds are put forward Round 1: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.343 Round 2: 109 peptides, 15 chains. Longest chain 14 peptides. Score 0.465 Round 3: 112 peptides, 15 chains. Longest chain 15 peptides. Score 0.480 Round 4: 105 peptides, 13 chains. Longest chain 13 peptides. Score 0.491 Round 5: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 4 Chains 13, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4086 restraints for refining 1779 atoms. 3731 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2368 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2260 (Rfree = 0.000) for 1780 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2154 (Rfree = 0.000) for 1775 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.2123 (Rfree = 0.000) for 1771 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2109 (Rfree = 0.000) for 1768 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 1815 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1830 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.337 Round 2: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.442 Round 3: 112 peptides, 14 chains. Longest chain 15 peptides. Score 0.502 Round 4: 129 peptides, 17 chains. Longest chain 16 peptides. Score 0.518 Round 5: 105 peptides, 14 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 4 Chains 17, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3926 restraints for refining 1780 atoms. 3495 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2309 (Rfree = 0.000) for 1780 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 42: After refmac, R = 0.2165 (Rfree = 0.000) for 1774 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.2124 (Rfree = 0.000) for 1772 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2089 (Rfree = 0.000) for 1771 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.2060 (Rfree = 0.000) for 1768 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1846 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.275 Round 2: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.406 Round 3: 110 peptides, 17 chains. Longest chain 10 peptides. Score 0.424 Round 4: 108 peptides, 16 chains. Longest chain 13 peptides. Score 0.437 Round 5: 110 peptides, 16 chains. Longest chain 10 peptides. Score 0.447 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2i8d-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3202 reflections ( 98.46 % complete ) and 4041 restraints for refining 1779 atoms. 3681 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2306 (Rfree = 0.000) for 1779 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2241 (Rfree = 0.000) for 1771 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2199 (Rfree = 0.000) for 1766 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2187 (Rfree = 0.000) for 1762 atoms. Found 0 (9 requested) and removed 3 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:14:06 GMT 2018 Job finished. TimeTaking 28.19 Used memory is bytes: 5954552