Mon 24 Dec 07:26:24 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 2i8d-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-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/2i8d-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-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 07:26:28 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/2i8d-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-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 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-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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-3.8-parrot-noncs.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 2166 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3573 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3362 (Rfree = 0.000) for 2166 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 0 residues added, 2215 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 17 peptides. Score 0.380 Round 2: 130 peptides, 22 chains. Longest chain 13 peptides. Score 0.414 Round 3: 134 peptides, 21 chains. Longest chain 15 peptides. Score 0.457 Round 4: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.450 Round 5: 133 peptides, 17 chains. Longest chain 18 peptides. Score 0.536 Taking the results from Round 5 Chains 17, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4004 restraints for refining 1780 atoms. 3557 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2917 (Rfree = 0.000) for 1780 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 2: After refmac, R = 0.2660 (Rfree = 0.000) for 1761 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2516 (Rfree = 0.000) for 1748 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 4: After refmac, R = 0.2605 (Rfree = 0.000) for 1730 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 5: After refmac, R = 0.2725 (Rfree = 0.000) for 1718 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 1816 seeds are put forward Round 1: 125 peptides, 19 chains. Longest chain 16 peptides. Score 0.456 Round 2: 141 peptides, 18 chains. Longest chain 17 peptides. Score 0.552 Round 3: 147 peptides, 18 chains. Longest chain 20 peptides. Score 0.577 Round 4: 140 peptides, 18 chains. Longest chain 18 peptides. Score 0.547 Round 5: 156 peptides, 21 chains. Longest chain 21 peptides. Score 0.558 Taking the results from Round 3 Chains 19, Residues 129, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3789 restraints for refining 1780 atoms. 3228 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2664 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2357 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.2371 (Rfree = 0.000) for 1755 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 9: After refmac, R = 0.2211 (Rfree = 0.000) for 1742 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 10: After refmac, R = 0.2194 (Rfree = 0.000) for 1734 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward NCS extension: 0 residues added, 1793 seeds are put forward Round 1: 124 peptides, 18 chains. Longest chain 23 peptides. Score 0.473 Round 2: 117 peptides, 17 chains. Longest chain 15 peptides. Score 0.460 Round 3: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.408 Round 4: 124 peptides, 18 chains. Longest chain 17 peptides. Score 0.473 Round 5: 116 peptides, 12 chains. Longest chain 20 peptides. Score 0.564 Taking the results from Round 5 Chains 12, Residues 104, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3793 restraints for refining 1780 atoms. 3310 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2637 (Rfree = 0.000) for 1780 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2390 (Rfree = 0.000) for 1767 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2336 (Rfree = 0.000) for 1762 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2413 (Rfree = 0.000) for 1756 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2114 (Rfree = 0.000) for 1755 atoms. Found 4 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 1812 seeds are put forward NCS extension: 0 residues added, 1812 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 17 peptides. Score 0.322 Round 2: 122 peptides, 17 chains. Longest chain 14 peptides. Score 0.485 Round 3: 117 peptides, 20 chains. Longest chain 12 peptides. Score 0.391 Round 4: 132 peptides, 19 chains. Longest chain 16 peptides. Score 0.490 Round 5: 134 peptides, 20 chains. Longest chain 13 peptides. Score 0.478 Taking the results from Round 4 Chains 21, Residues 113, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3952 restraints for refining 1780 atoms. 3457 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2595 (Rfree = 0.000) for 1780 atoms. Found 8 (9 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.2744 (Rfree = 0.000) for 1762 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 18: After refmac, R = 0.2578 (Rfree = 0.000) for 1750 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 19: After refmac, R = 0.2368 (Rfree = 0.000) for 1738 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.2488 (Rfree = 0.000) for 1735 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 1789 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1803 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 8 peptides. Score 0.339 Round 2: 110 peptides, 18 chains. Longest chain 14 peptides. Score 0.400 Round 3: 116 peptides, 16 chains. Longest chain 12 peptides. Score 0.477 Round 4: 119 peptides, 16 chains. Longest chain 15 peptides. Score 0.492 Round 5: 110 peptides, 16 chains. Longest chain 11 peptides. Score 0.447 Taking the results from Round 4 Chains 16, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4037 restraints for refining 1780 atoms. 3641 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2594 (Rfree = 0.000) for 1780 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2607 (Rfree = 0.000) for 1766 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2482 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2352 (Rfree = 0.000) for 1755 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.1997 (Rfree = 0.000) for 1757 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1843 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.311 Round 2: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.367 Round 3: 127 peptides, 18 chains. Longest chain 20 peptides. Score 0.487 Round 4: 135 peptides, 18 chains. Longest chain 20 peptides. Score 0.525 Round 5: 119 peptides, 17 chains. Longest chain 19 peptides. Score 0.470 Taking the results from Round 4 Chains 18, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3996 restraints for refining 1780 atoms. 3546 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2316 (Rfree = 0.000) for 1780 atoms. Found 8 (9 requested) and removed 29 (4 requested) atoms. Cycle 27: After refmac, R = 0.2144 (Rfree = 0.000) for 1752 atoms. Found 4 (9 requested) and removed 31 (4 requested) atoms. Cycle 28: After refmac, R = 0.2089 (Rfree = 0.000) for 1721 atoms. Found 2 (9 requested) and removed 16 (4 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 1706 atoms. Found 0 (9 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.2079 (Rfree = 0.000) for 1693 atoms. Found 0 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 1728 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1748 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 8 peptides. Score 0.258 Round 2: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.343 Round 3: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.398 Round 4: 109 peptides, 17 chains. Longest chain 18 peptides. Score 0.419 Round 5: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.434 Taking the results from Round 5 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4043 restraints for refining 1779 atoms. 3680 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2305 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 32: After refmac, R = 0.2116 (Rfree = 0.000) for 1768 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2048 (Rfree = 0.000) for 1766 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2038 (Rfree = 0.000) for 1762 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2025 (Rfree = 0.000) for 1757 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 1812 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 1827 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.344 Round 2: 125 peptides, 20 chains. Longest chain 14 peptides. Score 0.433 Round 3: 118 peptides, 19 chains. Longest chain 10 peptides. Score 0.420 Round 4: 131 peptides, 21 chains. Longest chain 11 peptides. Score 0.442 Round 5: 133 peptides, 19 chains. Longest chain 15 peptides. Score 0.495 Taking the results from Round 5 Chains 19, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4020 restraints for refining 1780 atoms. 3583 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2411 (Rfree = 0.000) for 1780 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2261 (Rfree = 0.000) for 1771 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2436 (Rfree = 0.000) for 1765 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2205 (Rfree = 0.000) for 1762 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2201 (Rfree = 0.000) for 1758 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 1820 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1840 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.302 Round 2: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.424 Round 3: 118 peptides, 17 chains. Longest chain 13 peptides. Score 0.465 Round 4: 125 peptides, 20 chains. Longest chain 10 peptides. Score 0.433 Round 5: 124 peptides, 19 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 3 Chains 17, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4080 restraints for refining 1780 atoms. 3693 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2417 (Rfree = 0.000) for 1780 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2355 (Rfree = 0.000) for 1775 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2308 (Rfree = 0.000) for 1771 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2314 (Rfree = 0.000) for 1767 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2321 (Rfree = 0.000) for 1763 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 1804 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1819 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 7 peptides. Score 0.274 Round 2: 104 peptides, 18 chains. Longest chain 8 peptides. Score 0.367 Round 3: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.352 Round 4: 114 peptides, 20 chains. Longest chain 9 peptides. Score 0.375 Round 5: 110 peptides, 17 chains. Longest chain 9 peptides. Score 0.424 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 93, 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 4120 restraints for refining 1780 atoms. 3765 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2397 (Rfree = 0.000) for 1780 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2313 (Rfree = 0.000) for 1769 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2287 (Rfree = 0.000) for 1764 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2306 (Rfree = 0.000) for 1759 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 24.87