null Sun 23 Dec 22:22:46 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 2i8d-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-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/2i8d-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-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 22:22:56 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/2i8d-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6529 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-4.0-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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-4.0-parrot-hancs.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 4.000 Wilson plot Bfac: 79.92 2744 reflections ( 98.21 % complete ) and 0 restraints for refining 2172 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3527 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3385 (Rfree = 0.000) for 2172 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.44 Search for helices and strands: 0 residues in 0 chains, 2220 seeds are put forward NCS extension: 0 residues added, 2220 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.271 Round 2: 126 peptides, 17 chains. Longest chain 15 peptides. Score 0.504 Round 3: 134 peptides, 19 chains. Longest chain 13 peptides. Score 0.499 Round 4: 142 peptides, 17 chains. Longest chain 20 peptides. Score 0.575 Round 5: 136 peptides, 17 chains. Longest chain 16 peptides. Score 0.550 Taking the results from Round 4 Chains 17, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3988 restraints for refining 1776 atoms. 3505 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2935 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2888 (Rfree = 0.000) for 1733 atoms. Found 4 (8 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.2733 (Rfree = 0.000) for 1706 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2793 (Rfree = 0.000) for 1688 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 5: After refmac, R = 0.2613 (Rfree = 0.000) for 1673 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 1761 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1776 seeds are put forward Round 1: 124 peptides, 19 chains. Longest chain 14 peptides. Score 0.450 Round 2: 129 peptides, 18 chains. Longest chain 11 peptides. Score 0.497 Round 3: 137 peptides, 18 chains. Longest chain 12 peptides. Score 0.534 Round 4: 139 peptides, 16 chains. Longest chain 16 peptides. Score 0.582 Round 5: 133 peptides, 16 chains. Longest chain 15 peptides. Score 0.557 Taking the results from Round 4 Chains 16, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4023 restraints for refining 1774 atoms. 3547 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2860 (Rfree = 0.000) for 1774 atoms. Found 8 (8 requested) and removed 27 (4 requested) atoms. Cycle 7: After refmac, R = 0.2497 (Rfree = 0.000) for 1727 atoms. Found 6 (8 requested) and removed 18 (4 requested) atoms. Cycle 8: After refmac, R = 0.2308 (Rfree = 0.000) for 1699 atoms. Found 6 (8 requested) and removed 16 (4 requested) atoms. Cycle 9: After refmac, R = 0.2322 (Rfree = 0.000) for 1681 atoms. Found 7 (8 requested) and removed 14 (4 requested) atoms. Cycle 10: After refmac, R = 0.2354 (Rfree = 0.000) for 1659 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 1736 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1753 seeds are put forward Round 1: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.373 Round 2: 126 peptides, 22 chains. Longest chain 9 peptides. Score 0.393 Round 3: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.430 Round 4: 122 peptides, 18 chains. Longest chain 13 peptides. Score 0.463 Round 5: 121 peptides, 16 chains. Longest chain 13 peptides. Score 0.502 Taking the results from Round 5 Chains 16, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4037 restraints for refining 1777 atoms. 3633 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3138 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.2614 (Rfree = 0.000) for 1743 atoms. Found 7 (8 requested) and removed 17 (4 requested) atoms. Cycle 13: After refmac, R = 0.2250 (Rfree = 0.000) for 1716 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2248 (Rfree = 0.000) for 1707 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.1809 (Rfree = 0.000) for 1699 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 1768 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1782 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.352 Round 2: 114 peptides, 18 chains. Longest chain 11 peptides. Score 0.422 Round 3: 114 peptides, 18 chains. Longest chain 12 peptides. Score 0.422 Round 4: 120 peptides, 18 chains. Longest chain 14 peptides. Score 0.453 Round 5: 125 peptides, 17 chains. Longest chain 14 peptides. Score 0.499 Taking the results from Round 5 Chains 17, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4058 restraints for refining 1777 atoms. 3643 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2584 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.2496 (Rfree = 0.000) for 1760 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 18: After refmac, R = 0.2266 (Rfree = 0.000) for 1741 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 19: After refmac, R = 0.2516 (Rfree = 0.000) for 1730 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.2272 (Rfree = 0.000) for 1720 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 1768 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1788 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.305 Round 2: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.382 Round 3: 115 peptides, 18 chains. Longest chain 14 peptides. Score 0.427 Round 4: 114 peptides, 18 chains. Longest chain 12 peptides. Score 0.422 Round 5: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 3 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3987 restraints for refining 1776 atoms. 3617 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2697 (Rfree = 0.000) for 1776 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.2712 (Rfree = 0.000) for 1751 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 23: After refmac, R = 0.2447 (Rfree = 0.000) for 1739 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.2430 (Rfree = 0.000) for 1731 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2325 (Rfree = 0.000) for 1728 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 1810 seeds are put forward NCS extension: 0 residues added, 1810 seeds are put forward Round 1: 91 peptides, 15 chains. Longest chain 11 peptides. Score 0.368 Round 2: 108 peptides, 16 chains. Longest chain 12 peptides. Score 0.437 Round 3: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.397 Round 4: 110 peptides, 17 chains. Longest chain 10 peptides. Score 0.424 Round 5: 119 peptides, 17 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 5 Chains 17, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3938 restraints for refining 1777 atoms. 3547 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2649 (Rfree = 0.000) for 1777 atoms. Found 7 (8 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2441 (Rfree = 0.000) for 1756 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2213 (Rfree = 0.000) for 1749 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.1740 (Rfree = 0.000) for 1742 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2175 (Rfree = 0.000) for 1739 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.38 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1830 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 8 peptides. Score 0.277 Round 2: 120 peptides, 21 chains. Longest chain 9 peptides. Score 0.384 Round 3: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.407 Round 4: 123 peptides, 19 chains. Longest chain 11 peptides. Score 0.445 Round 5: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 4 Chains 19, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4024 restraints for refining 1777 atoms. 3627 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2324 (Rfree = 0.000) for 1777 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.2440 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 33: After refmac, R = 0.2310 (Rfree = 0.000) for 1749 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2154 (Rfree = 0.000) for 1743 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 35: After refmac, R = 0.2043 (Rfree = 0.000) for 1734 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 1796 seeds are put forward NCS extension: 0 residues added, 1796 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.271 Round 2: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.408 Round 3: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.376 Round 4: 106 peptides, 17 chains. Longest chain 13 peptides. Score 0.402 Round 5: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 2 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3959 restraints for refining 1777 atoms. 3616 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2522 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 37: After refmac, R = 0.2493 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 32 (4 requested) atoms. Cycle 38: After refmac, R = 0.2487 (Rfree = 0.000) for 1739 atoms. Found 8 (8 requested) and removed 28 (4 requested) atoms. Cycle 39: After refmac, R = 0.2177 (Rfree = 0.000) for 1712 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 40: After refmac, R = 0.2227 (Rfree = 0.000) for 1704 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.37 Search for helices and strands: 0 residues in 0 chains, 1752 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1768 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 6 peptides. Score 0.251 Round 2: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.319 Round 3: 119 peptides, 20 chains. Longest chain 18 peptides. Score 0.402 Round 4: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.399 Round 5: 99 peptides, 17 chains. Longest chain 15 peptides. Score 0.364 Taking the results from Round 3 Chains 20, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3788 restraints for refining 1767 atoms. 3412 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2190 (Rfree = 0.000) for 1767 atoms. Found 7 (8 requested) and removed 24 (4 requested) atoms. Cycle 42: After refmac, R = 0.2195 (Rfree = 0.000) for 1738 atoms. Found 7 (8 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.2016 (Rfree = 0.000) for 1730 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 44: After refmac, R = 0.2023 (Rfree = 0.000) for 1719 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 45: After refmac, R = 0.1914 (Rfree = 0.000) for 1712 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 1791 seeds are put forward NCS extension: 0 residues added, 1791 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.256 Round 2: 88 peptides, 18 chains. Longest chain 9 peptides. Score 0.273 Round 3: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.333 Round 4: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.307 Round 5: 90 peptides, 15 chains. Longest chain 12 peptides. Score 0.362 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 75, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2744 reflections ( 98.21 % complete ) and 4094 restraints for refining 1777 atoms. 3809 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2510 (Rfree = 0.000) for 1777 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2500 (Rfree = 0.000) for 1763 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2197 (Rfree = 0.000) for 1748 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2439 (Rfree = 0.000) for 1740 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:12 GMT 2018 Job finished. TimeTaking 30.43 Used memory is bytes: 10092120