null Mon 24 Dec 00:30:45 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-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 ============================================================ Mon 24 Dec 00:30:49 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-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 210 and 0 Target number of residues in the AU: 210 Target solvent content: 0.6243 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-3.4-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-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.80 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 3.400 Wilson plot Bfac: 63.50 4439 reflections ( 98.89 % complete ) and 0 restraints for refining 2193 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3306 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2850 (Rfree = 0.000) for 2193 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 2.99 Search for helices and strands: 0 residues in 0 chains, 2250 seeds are put forward NCS extension: 0 residues added, 2250 seeds are put forward Round 1: 140 peptides, 21 chains. Longest chain 16 peptides. Score 0.486 Round 2: 154 peptides, 22 chains. Longest chain 13 peptides. Score 0.530 Round 3: 166 peptides, 20 chains. Longest chain 20 peptides. Score 0.617 Round 4: 172 peptides, 18 chains. Longest chain 23 peptides. Score 0.671 Round 5: 178 peptides, 19 chains. Longest chain 28 peptides. Score 0.676 Taking the results from Round 5 Chains 19, Residues 159, Estimated correctness of the model 51.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3688 restraints for refining 1788 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2669 (Rfree = 0.000) for 1788 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 2: After refmac, R = 0.2553 (Rfree = 0.000) for 1766 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2418 (Rfree = 0.000) for 1755 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2389 (Rfree = 0.000) for 1745 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2373 (Rfree = 0.000) for 1737 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward NCS extension: 33 residues added (7 deleted due to clashes), 1852 seeds are put forward Round 1: 155 peptides, 17 chains. Longest chain 32 peptides. Score 0.627 Round 2: 166 peptides, 16 chains. Longest chain 49 peptides. Score 0.683 Round 3: 170 peptides, 15 chains. Longest chain 41 peptides. Score 0.711 Round 4: 166 peptides, 16 chains. Longest chain 43 peptides. Score 0.683 Round 5: 168 peptides, 17 chains. Longest chain 33 peptides. Score 0.674 Taking the results from Round 3 Chains 15, Residues 155, Estimated correctness of the model 60.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3671 restraints for refining 1790 atoms. 3066 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2588 (Rfree = 0.000) for 1790 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 7: After refmac, R = 0.2405 (Rfree = 0.000) for 1785 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2347 (Rfree = 0.000) for 1782 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2301 (Rfree = 0.000) for 1774 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2332 (Rfree = 0.000) for 1769 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.00 Search for helices and strands: 0 residues in 0 chains, 1844 seeds are put forward NCS extension: 55 residues added (18 deleted due to clashes), 1899 seeds are put forward Round 1: 140 peptides, 23 chains. Longest chain 13 peptides. Score 0.443 Round 2: 161 peptides, 21 chains. Longest chain 21 peptides. Score 0.579 Round 3: 163 peptides, 22 chains. Longest chain 17 peptides. Score 0.569 Round 4: 169 peptides, 22 chains. Longest chain 18 peptides. Score 0.593 Round 5: 181 peptides, 20 chains. Longest chain 28 peptides. Score 0.670 Taking the results from Round 5 Chains 20, Residues 161, Estimated correctness of the model 49.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3726 restraints for refining 1790 atoms. 3102 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2729 (Rfree = 0.000) for 1790 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.2489 (Rfree = 0.000) for 1780 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2415 (Rfree = 0.000) for 1771 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2424 (Rfree = 0.000) for 1766 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2406 (Rfree = 0.000) for 1764 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 1835 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 1872 seeds are put forward Round 1: 153 peptides, 24 chains. Longest chain 19 peptides. Score 0.485 Round 2: 145 peptides, 18 chains. Longest chain 20 peptides. Score 0.569 Round 3: 151 peptides, 20 chains. Longest chain 18 peptides. Score 0.556 Round 4: 159 peptides, 19 chains. Longest chain 18 peptides. Score 0.607 Round 5: 166 peptides, 21 chains. Longest chain 19 peptides. Score 0.599 Taking the results from Round 4 Chains 19, Residues 140, Estimated correctness of the model 30.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3874 restraints for refining 1790 atoms. 3333 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2632 (Rfree = 0.000) for 1790 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.2607 (Rfree = 0.000) for 1786 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.2529 (Rfree = 0.000) for 1785 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2387 (Rfree = 0.000) for 1779 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.2397 (Rfree = 0.000) for 1768 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1846 seeds are put forward Round 1: 142 peptides, 24 chains. Longest chain 19 peptides. Score 0.431 Round 2: 149 peptides, 19 chains. Longest chain 18 peptides. Score 0.567 Round 3: 143 peptides, 17 chains. Longest chain 18 peptides. Score 0.580 Round 4: 144 peptides, 16 chains. Longest chain 24 peptides. Score 0.603 Round 5: 155 peptides, 21 chains. Longest chain 15 peptides. Score 0.554 Taking the results from Round 4 Chains 16, Residues 128, Estimated correctness of the model 29.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3866 restraints for refining 1790 atoms. 3370 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2476 (Rfree = 0.000) for 1790 atoms. Found 10 (12 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.2326 (Rfree = 0.000) for 1791 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.2651 (Rfree = 0.000) for 1783 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2179 (Rfree = 0.000) for 1783 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2198 (Rfree = 0.000) for 1778 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1854 seeds are put forward Round 1: 136 peptides, 22 chains. Longest chain 17 peptides. Score 0.445 Round 2: 151 peptides, 23 chains. Longest chain 14 peptides. Score 0.496 Round 3: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.523 Round 4: 148 peptides, 20 chains. Longest chain 16 peptides. Score 0.543 Round 5: 145 peptides, 21 chains. Longest chain 14 peptides. Score 0.509 Taking the results from Round 4 Chains 20, Residues 128, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3806 restraints for refining 1789 atoms. 3314 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2438 (Rfree = 0.000) for 1789 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2391 (Rfree = 0.000) for 1785 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 1778 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2180 (Rfree = 0.000) for 1772 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2186 (Rfree = 0.000) for 1767 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 1851 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1863 seeds are put forward Round 1: 126 peptides, 22 chains. Longest chain 16 peptides. Score 0.393 Round 2: 150 peptides, 20 chains. Longest chain 16 peptides. Score 0.552 Round 3: 156 peptides, 20 chains. Longest chain 16 peptides. Score 0.577 Round 4: 159 peptides, 19 chains. Longest chain 16 peptides. Score 0.607 Round 5: 148 peptides, 18 chains. Longest chain 17 peptides. Score 0.581 Taking the results from Round 4 Chains 19, Residues 140, Estimated correctness of the model 30.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3812 restraints for refining 1790 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2427 (Rfree = 0.000) for 1790 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.2257 (Rfree = 0.000) for 1795 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.2229 (Rfree = 0.000) for 1794 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2209 (Rfree = 0.000) for 1792 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2030 (Rfree = 0.000) for 1789 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 1860 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1877 seeds are put forward Round 1: 126 peptides, 19 chains. Longest chain 17 peptides. Score 0.461 Round 2: 137 peptides, 18 chains. Longest chain 20 peptides. Score 0.534 Round 3: 137 peptides, 18 chains. Longest chain 14 peptides. Score 0.534 Round 4: 133 peptides, 15 chains. Longest chain 22 peptides. Score 0.576 Round 5: 143 peptides, 17 chains. Longest chain 17 peptides. Score 0.580 Taking the results from Round 5 Chains 17, Residues 126, Estimated correctness of the model 22.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3723 restraints for refining 1790 atoms. 3153 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2513 (Rfree = 0.000) for 1790 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.2327 (Rfree = 0.000) for 1783 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2348 (Rfree = 0.000) for 1780 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.2229 (Rfree = 0.000) for 1773 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2259 (Rfree = 0.000) for 1768 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 1833 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1855 seeds are put forward Round 1: 114 peptides, 16 chains. Longest chain 17 peptides. Score 0.468 Round 2: 129 peptides, 19 chains. Longest chain 14 peptides. Score 0.475 Round 3: 125 peptides, 19 chains. Longest chain 14 peptides. Score 0.456 Round 4: 142 peptides, 18 chains. Longest chain 14 peptides. Score 0.556 Round 5: 124 peptides, 19 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 4 Chains 18, Residues 124, Estimated correctness of the model 13.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3891 restraints for refining 1790 atoms. 3413 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2490 (Rfree = 0.000) for 1790 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2372 (Rfree = 0.000) for 1785 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2316 (Rfree = 0.000) for 1781 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2254 (Rfree = 0.000) for 1778 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2220 (Rfree = 0.000) for 1772 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1828 seeds are put forward Round 1: 116 peptides, 22 chains. Longest chain 13 peptides. Score 0.338 Round 2: 125 peptides, 18 chains. Longest chain 14 peptides. Score 0.478 Round 3: 125 peptides, 17 chains. Longest chain 13 peptides. Score 0.499 Round 4: 123 peptides, 16 chains. Longest chain 15 peptides. Score 0.511 Round 5: 119 peptides, 17 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 107, 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. 4439 reflections ( 98.89 % complete ) and 3978 restraints for refining 1790 atoms. 3566 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2419 (Rfree = 0.000) for 1790 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2289 (Rfree = 0.000) for 1780 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2246 (Rfree = 0.000) for 1773 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2188 (Rfree = 0.000) for 1767 atoms. Found 0 (12 requested) and removed 5 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:55:17 GMT 2018 Job finished. TimeTaking 24.54 Used memory is bytes: 1188056