null Sun 23 Dec 22:22:43 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 2ess-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ess-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-3.8-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/2ess-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-3.8-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 22:22:53 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/2ess-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ess-3.8-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 190 and 0 Target number of residues in the AU: 190 Target solvent content: 0.6690 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.57 Input MTZ file: 2ess-3.8-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: 152 Cell parameters: 91.150 91.150 64.770 90.000 90.000 120.000 Input sequence file: 2ess-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.962 3.801 Wilson plot Bfac: 91.49 3223 reflections ( 99.72 % complete ) and 0 restraints for refining 2210 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3827 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3538 (Rfree = 0.000) for 2210 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 2224 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.250 Round 2: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.322 Round 3: 118 peptides, 21 chains. Longest chain 12 peptides. Score 0.369 Round 4: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.350 Round 5: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 5 Chains 21, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4294 restraints for refining 1794 atoms. 3903 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2740 (Rfree = 0.000) for 1794 atoms. Found 1 (9 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.2701 (Rfree = 0.000) for 1747 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2595 (Rfree = 0.000) for 1727 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2277 (Rfree = 0.000) for 1715 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2218 (Rfree = 0.000) for 1707 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.43 Search for helices and strands: 0 residues in 0 chains, 1772 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 6 peptides. Score 0.256 Round 2: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.330 Round 3: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.349 Round 4: 105 peptides, 17 chains. Longest chain 10 peptides. Score 0.392 Round 5: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.406 Taking the results from Round 5 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4321 restraints for refining 1794 atoms. 3926 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2771 (Rfree = 0.000) for 1794 atoms. Found 6 (9 requested) and removed 14 (4 requested) atoms. Cycle 7: After refmac, R = 0.2608 (Rfree = 0.000) for 1768 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.2120 (Rfree = 0.000) for 1759 atoms. Found 1 (9 requested) and removed 9 (4 requested) atoms. Cycle 9: After refmac, R = 0.2067 (Rfree = 0.000) for 1740 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2049 (Rfree = 0.000) for 1734 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.309 Round 2: 113 peptides, 18 chains. Longest chain 9 peptides. Score 0.411 Round 3: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.420 Round 4: 109 peptides, 16 chains. Longest chain 10 peptides. Score 0.437 Round 5: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 4 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4257 restraints for refining 1793 atoms. 3901 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2575 (Rfree = 0.000) for 1793 atoms. Found 4 (9 requested) and removed 14 (4 requested) atoms. Cycle 12: After refmac, R = 0.2531 (Rfree = 0.000) for 1771 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2576 (Rfree = 0.000) for 1754 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2500 (Rfree = 0.000) for 1739 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2386 (Rfree = 0.000) for 1730 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 1793 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.262 Round 2: 114 peptides, 22 chains. Longest chain 8 peptides. Score 0.323 Round 3: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.347 Round 4: 107 peptides, 17 chains. Longest chain 15 peptides. Score 0.403 Round 5: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 4 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4303 restraints for refining 1794 atoms. 3960 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2458 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.2594 (Rfree = 0.000) for 1773 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2496 (Rfree = 0.000) for 1760 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2405 (Rfree = 0.000) for 1755 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2381 (Rfree = 0.000) for 1748 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 1797 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 6 peptides. Score 0.246 Round 2: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.339 Round 3: 103 peptides, 17 chains. Longest chain 14 peptides. Score 0.382 Round 4: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.376 Round 5: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 5 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4112 restraints for refining 1769 atoms. 3751 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2494 (Rfree = 0.000) for 1769 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.2490 (Rfree = 0.000) for 1748 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.2416 (Rfree = 0.000) for 1735 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2308 (Rfree = 0.000) for 1725 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.1927 (Rfree = 0.000) for 1716 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 1766 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 10 peptides. Score 0.245 Round 2: 109 peptides, 21 chains. Longest chain 12 peptides. Score 0.319 Round 3: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.326 Round 4: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.321 Round 5: 103 peptides, 20 chains. Longest chain 9 peptides. Score 0.309 Taking the results from Round 3 Chains 20, Residues 86, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4006 restraints for refining 1763 atoms. 3652 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2678 (Rfree = 0.000) for 1763 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 27: After refmac, R = 0.2413 (Rfree = 0.000) for 1742 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.2273 (Rfree = 0.000) for 1727 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 1725 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2003 (Rfree = 0.000) for 1722 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 1760 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 10 peptides. Score 0.267 Round 2: 103 peptides, 17 chains. Longest chain 12 peptides. Score 0.382 Round 3: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.390 Round 4: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.390 Round 5: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.398 Taking the results from Round 5 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4151 restraints for refining 1793 atoms. 3793 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2522 (Rfree = 0.000) for 1793 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.2224 (Rfree = 0.000) for 1775 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.2287 (Rfree = 0.000) for 1764 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2124 (Rfree = 0.000) for 1762 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2211 (Rfree = 0.000) for 1759 atoms. Found 6 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 1796 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 6 peptides. Score 0.220 Round 2: 85 peptides, 15 chains. Longest chain 14 peptides. Score 0.330 Round 3: 82 peptides, 14 chains. Longest chain 13 peptides. Score 0.338 Round 4: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.338 Round 5: 93 peptides, 15 chains. Longest chain 14 peptides. Score 0.375 Taking the results from Round 5 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4249 restraints for refining 1794 atoms. 3952 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2561 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 37: After refmac, R = 0.2482 (Rfree = 0.000) for 1782 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2051 (Rfree = 0.000) for 1779 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1940 (Rfree = 0.000) for 1773 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1876 (Rfree = 0.000) for 1766 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 1788 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 6 peptides. Score 0.200 Round 2: 109 peptides, 23 chains. Longest chain 7 peptides. Score 0.271 Round 3: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.321 Round 4: 97 peptides, 16 chains. Longest chain 14 peptides. Score 0.373 Round 5: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.351 Taking the results from Round 4 Chains 16, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3223 reflections ( 99.72 % complete ) and 4245 restraints for refining 1793 atoms. 3937 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2407 (Rfree = 0.000) for 1793 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2468 (Rfree = 0.000) for 1785 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2467 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2453 (Rfree = 0.000) for 1776 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.1995 (Rfree = 0.000) for 1773 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 1811 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.269 Round 2: 83 peptides, 16 chains. Longest chain 11 peptides. Score 0.292 Round 3: 81 peptides, 12 chains. Longest chain 14 peptides. Score 0.384 Round 4: 79 peptides, 12 chains. Longest chain 11 peptides. Score 0.373 Round 5: 70 peptides, 12 chains. Longest chain 8 peptides. Score 0.320 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 69, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2ess-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3223 reflections ( 99.72 % complete ) and 4203 restraints for refining 1793 atoms. 3907 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2239 (Rfree = 0.000) for 1793 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2294 (Rfree = 0.000) for 1781 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2337 (Rfree = 0.000) for 1773 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2102 (Rfree = 0.000) for 1767 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:01 GMT 2018 Job finished. TimeTaking 33.29 Used memory is bytes: 19290600