null Mon 24 Dec 07:58:08 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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 07:58:13 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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 205 and 0 Target number of residues in the AU: 205 Target solvent content: 0.6332 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 68.10 3754 reflections ( 98.69 % complete ) and 0 restraints for refining 2167 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3516 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2763 (Rfree = 0.000) for 2167 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2217 seeds are put forward NCS extension: 0 residues added, 2217 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.342 Round 2: 146 peptides, 24 chains. Longest chain 12 peptides. Score 0.451 Round 3: 142 peptides, 20 chains. Longest chain 16 peptides. Score 0.516 Round 4: 138 peptides, 19 chains. Longest chain 16 peptides. Score 0.518 Round 5: 158 peptides, 19 chains. Longest chain 16 peptides. Score 0.603 Taking the results from Round 5 Chains 19, Residues 139, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3911 restraints for refining 1784 atoms. 3374 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2589 (Rfree = 0.000) for 1784 atoms. Found 8 (11 requested) and removed 13 (5 requested) atoms. Cycle 2: After refmac, R = 0.2423 (Rfree = 0.000) for 1764 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2372 (Rfree = 0.000) for 1750 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2324 (Rfree = 0.000) for 1744 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2316 (Rfree = 0.000) for 1736 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 1810 seeds are put forward Round 1: 150 peptides, 23 chains. Longest chain 15 peptides. Score 0.492 Round 2: 167 peptides, 21 chains. Longest chain 17 peptides. Score 0.603 Round 3: 157 peptides, 19 chains. Longest chain 18 peptides. Score 0.599 Round 4: 169 peptides, 19 chains. Longest chain 21 peptides. Score 0.645 Round 5: 163 peptides, 19 chains. Longest chain 21 peptides. Score 0.623 Taking the results from Round 4 Chains 19, Residues 150, Estimated correctness of the model 31.4 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3650 restraints for refining 1784 atoms. 3011 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2553 (Rfree = 0.000) for 1784 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 7: After refmac, R = 0.2403 (Rfree = 0.000) for 1773 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2331 (Rfree = 0.000) for 1765 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2300 (Rfree = 0.000) for 1757 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2326 (Rfree = 0.000) for 1754 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 1853 seeds are put forward Round 1: 131 peptides, 21 chains. Longest chain 11 peptides. Score 0.442 Round 2: 144 peptides, 18 chains. Longest chain 19 peptides. Score 0.565 Round 3: 160 peptides, 19 chains. Longest chain 18 peptides. Score 0.611 Round 4: 157 peptides, 21 chains. Longest chain 18 peptides. Score 0.562 Round 5: 157 peptides, 20 chains. Longest chain 18 peptides. Score 0.581 Taking the results from Round 3 Chains 19, Residues 141, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3880 restraints for refining 1784 atoms. 3335 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2502 (Rfree = 0.000) for 1784 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. Cycle 12: After refmac, R = 0.2240 (Rfree = 0.000) for 1784 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2204 (Rfree = 0.000) for 1776 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2199 (Rfree = 0.000) for 1772 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2238 (Rfree = 0.000) for 1768 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1842 seeds are put forward Round 1: 134 peptides, 23 chains. Longest chain 13 peptides. Score 0.412 Round 2: 140 peptides, 19 chains. Longest chain 27 peptides. Score 0.527 Round 3: 142 peptides, 19 chains. Longest chain 16 peptides. Score 0.536 Round 4: 147 peptides, 19 chains. Longest chain 23 peptides. Score 0.558 Round 5: 143 peptides, 21 chains. Longest chain 12 peptides. Score 0.500 Taking the results from Round 4 Chains 19, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3962 restraints for refining 1784 atoms. 3469 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2640 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 17: After refmac, R = 0.2556 (Rfree = 0.000) for 1783 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2382 (Rfree = 0.000) for 1784 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2201 (Rfree = 0.000) for 1776 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.2254 (Rfree = 0.000) for 1767 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 1848 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 1880 seeds are put forward Round 1: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.370 Round 2: 141 peptides, 20 chains. Longest chain 15 peptides. Score 0.511 Round 3: 131 peptides, 19 chains. Longest chain 14 peptides. Score 0.485 Round 4: 141 peptides, 21 chains. Longest chain 21 peptides. Score 0.491 Round 5: 127 peptides, 15 chains. Longest chain 24 peptides. Score 0.550 Taking the results from Round 5 Chains 15, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4074 restraints for refining 1784 atoms. 3641 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2510 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 22: After refmac, R = 0.2202 (Rfree = 0.000) for 1779 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2087 (Rfree = 0.000) for 1773 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2031 (Rfree = 0.000) for 1768 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2009 (Rfree = 0.000) for 1764 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 0 residues added, 1823 seeds are put forward Round 1: 134 peptides, 24 chains. Longest chain 9 peptides. Score 0.390 Round 2: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.484 Round 3: 135 peptides, 21 chains. Longest chain 13 peptides. Score 0.462 Round 4: 137 peptides, 21 chains. Longest chain 18 peptides. Score 0.471 Round 5: 131 peptides, 19 chains. Longest chain 14 peptides. Score 0.485 Taking the results from Round 5 Chains 19, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4088 restraints for refining 1784 atoms. 3659 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2233 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 27: After refmac, R = 0.2002 (Rfree = 0.000) for 1782 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1885 (Rfree = 0.000) for 1774 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1891 (Rfree = 0.000) for 1767 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1826 (Rfree = 0.000) for 1763 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 1831 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1853 seeds are put forward Round 1: 121 peptides, 21 chains. Longest chain 9 peptides. Score 0.389 Round 2: 142 peptides, 20 chains. Longest chain 16 peptides. Score 0.516 Round 3: 143 peptides, 21 chains. Longest chain 10 peptides. Score 0.500 Round 4: 145 peptides, 21 chains. Longest chain 13 peptides. Score 0.509 Round 5: 136 peptides, 20 chains. Longest chain 15 peptides. Score 0.488 Taking the results from Round 2 Chains 20, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3924 restraints for refining 1784 atoms. 3456 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2121 (Rfree = 0.000) for 1784 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 32: After refmac, R = 0.2151 (Rfree = 0.000) for 1782 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2141 (Rfree = 0.000) for 1775 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2033 (Rfree = 0.000) for 1771 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2008 (Rfree = 0.000) for 1769 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 1828 seeds are put forward NCS extension: 0 residues added, 1828 seeds are put forward Round 1: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.382 Round 2: 134 peptides, 19 chains. Longest chain 17 peptides. Score 0.499 Round 3: 133 peptides, 18 chains. Longest chain 17 peptides. Score 0.516 Round 4: 133 peptides, 18 chains. Longest chain 20 peptides. Score 0.516 Round 5: 141 peptides, 18 chains. Longest chain 13 peptides. Score 0.552 Taking the results from Round 5 Chains 18, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4004 restraints for refining 1784 atoms. 3530 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2363 (Rfree = 0.000) for 1784 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2319 (Rfree = 0.000) for 1772 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2111 (Rfree = 0.000) for 1767 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2122 (Rfree = 0.000) for 1764 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1941 (Rfree = 0.000) for 1762 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 1829 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1842 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 8 peptides. Score 0.308 Round 2: 123 peptides, 21 chains. Longest chain 8 peptides. Score 0.400 Round 3: 138 peptides, 23 chains. Longest chain 10 peptides. Score 0.433 Round 4: 134 peptides, 20 chains. Longest chain 11 peptides. Score 0.478 Round 5: 139 peptides, 20 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 5 Chains 20, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4040 restraints for refining 1784 atoms. 3584 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2315 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2124 (Rfree = 0.000) for 1781 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2053 (Rfree = 0.000) for 1782 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2029 (Rfree = 0.000) for 1780 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1853 (Rfree = 0.000) for 1782 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 1837 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1862 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 12 peptides. Score 0.317 Round 2: 113 peptides, 20 chains. Longest chain 11 peptides. Score 0.369 Round 3: 120 peptides, 19 chains. Longest chain 12 peptides. Score 0.430 Round 4: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.409 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.404 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 101, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2i8d-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3754 reflections ( 98.69 % complete ) and 3991 restraints for refining 1784 atoms. 3580 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2069 (Rfree = 0.000) for 1784 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1933 (Rfree = 0.000) for 1769 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1897 (Rfree = 0.000) for 1759 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1885 (Rfree = 0.000) for 1753 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:26:49 GMT 2018 Job finished. TimeTaking 28.69 Used memory is bytes: 5614208