Sun 23 Dec 22:22:59 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-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 22:23:08 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.4-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 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-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-3.4-parrot-hancs.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 2182 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3283 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2940 (Rfree = 0.000) for 2182 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 2236 seeds are put forward NCS extension: 0 residues added, 2236 seeds are put forward Round 1: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.445 Round 2: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.523 Round 3: 157 peptides, 18 chains. Longest chain 24 peptides. Score 0.617 Round 4: 156 peptides, 19 chains. Longest chain 18 peptides. Score 0.595 Round 5: 170 peptides, 18 chains. Longest chain 22 peptides. Score 0.665 Taking the results from Round 5 Chains 19, Residues 152, Estimated correctness of the model 48.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3576 restraints for refining 1790 atoms. 2917 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2673 (Rfree = 0.000) for 1790 atoms. Found 8 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2545 (Rfree = 0.000) for 1772 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 3: After refmac, R = 0.2486 (Rfree = 0.000) for 1763 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.2444 (Rfree = 0.000) for 1756 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2505 (Rfree = 0.000) for 1750 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 1846 seeds are put forward Round 1: 149 peptides, 20 chains. Longest chain 21 peptides. Score 0.547 Round 2: 164 peptides, 17 chains. Longest chain 17 peptides. Score 0.660 Round 3: 169 peptides, 15 chains. Longest chain 26 peptides. Score 0.708 Round 4: 171 peptides, 17 chains. Longest chain 21 peptides. Score 0.684 Round 5: 178 peptides, 18 chains. Longest chain 22 peptides. Score 0.691 Taking the results from Round 3 Chains 15, Residues 154, Estimated correctness of the model 59.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3875 restraints for refining 1790 atoms. 3274 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2655 (Rfree = 0.000) for 1790 atoms. Found 12 (13 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.2483 (Rfree = 0.000) for 1785 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2430 (Rfree = 0.000) for 1776 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2374 (Rfree = 0.000) for 1771 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2261 (Rfree = 0.000) for 1763 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1845 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 1859 seeds are put forward Round 1: 150 peptides, 20 chains. Longest chain 16 peptides. Score 0.552 Round 2: 157 peptides, 20 chains. Longest chain 14 peptides. Score 0.581 Round 3: 154 peptides, 19 chains. Longest chain 21 peptides. Score 0.587 Round 4: 177 peptides, 18 chains. Longest chain 19 peptides. Score 0.688 Round 5: 182 peptides, 18 chains. Longest chain 34 peptides. Score 0.704 Taking the results from Round 5 Chains 18, Residues 164, Estimated correctness of the model 58.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3772 restraints for refining 1789 atoms. 3134 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2465 (Rfree = 0.000) for 1789 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 12: After refmac, R = 0.2318 (Rfree = 0.000) for 1789 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2321 (Rfree = 0.000) for 1782 atoms. Found 3 (11 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2301 (Rfree = 0.000) for 1779 atoms. Found 2 (11 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 1774 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 2.99 Search for helices and strands: 0 residues in 0 chains, 1833 seeds are put forward NCS extension: 39 residues added (11 deleted due to clashes), 1872 seeds are put forward Round 1: 150 peptides, 19 chains. Longest chain 16 peptides. Score 0.571 Round 2: 160 peptides, 14 chains. Longest chain 41 peptides. Score 0.695 Round 3: 168 peptides, 17 chains. Longest chain 28 peptides. Score 0.674 Round 4: 170 peptides, 15 chains. Longest chain 54 peptides. Score 0.711 Round 5: 171 peptides, 19 chains. Longest chain 25 peptides. Score 0.652 Taking the results from Round 4 Chains 16, Residues 155, Estimated correctness of the model 60.7 % 1 chains (49 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3203 restraints for refining 1790 atoms. 2358 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2732 (Rfree = 0.000) for 1790 atoms. Found 10 (10 requested) and removed 17 (6 requested) atoms. Cycle 17: After refmac, R = 0.2497 (Rfree = 0.000) for 1772 atoms. Found 8 (10 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2410 (Rfree = 0.000) for 1766 atoms. Found 2 (10 requested) and removed 9 (6 requested) atoms. Cycle 19: After refmac, R = 0.2259 (Rfree = 0.000) for 1755 atoms. Found 5 (10 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2476 (Rfree = 0.000) for 1751 atoms. Found 9 (9 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 2.94 Search for helices and strands: 0 residues in 0 chains, 1807 seeds are put forward NCS extension: 121 residues added (12 deleted due to clashes), 1928 seeds are put forward Round 1: 157 peptides, 21 chains. Longest chain 26 peptides. Score 0.562 Round 2: 170 peptides, 19 chains. Longest chain 40 peptides. Score 0.648 Round 3: 165 peptides, 18 chains. Longest chain 23 peptides. Score 0.647 Round 4: 167 peptides, 20 chains. Longest chain 19 peptides. Score 0.621 Round 5: 171 peptides, 21 chains. Longest chain 19 peptides. Score 0.619 Taking the results from Round 2 Chains 19, Residues 151, Estimated correctness of the model 43.6 % 1 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3272 restraints for refining 1790 atoms. 2488 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2414 (Rfree = 0.000) for 1790 atoms. Found 8 (9 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.2223 (Rfree = 0.000) for 1775 atoms. Found 7 (9 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2135 (Rfree = 0.000) for 1773 atoms. Found 3 (9 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2100 (Rfree = 0.000) for 1768 atoms. Found 3 (9 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2062 (Rfree = 0.000) for 1761 atoms. Found 1 (9 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 47 residues added (9 deleted due to clashes), 1881 seeds are put forward Round 1: 151 peptides, 20 chains. Longest chain 21 peptides. Score 0.556 Round 2: 152 peptides, 23 chains. Longest chain 18 peptides. Score 0.501 Round 3: 156 peptides, 19 chains. Longest chain 21 peptides. Score 0.595 Round 4: 163 peptides, 19 chains. Longest chain 22 peptides. Score 0.623 Round 5: 153 peptides, 18 chains. Longest chain 22 peptides. Score 0.602 Taking the results from Round 4 Chains 20, Residues 144, Estimated correctness of the model 36.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3590 restraints for refining 1790 atoms. 2928 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2473 (Rfree = 0.000) for 1790 atoms. Found 9 (9 requested) and removed 11 (6 requested) atoms. Cycle 27: After refmac, R = 0.2262 (Rfree = 0.000) for 1785 atoms. Found 4 (9 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2164 (Rfree = 0.000) for 1781 atoms. Found 2 (9 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2186 (Rfree = 0.000) for 1776 atoms. Found 6 (9 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2176 (Rfree = 0.000) for 1776 atoms. Found 1 (9 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.00 Search for helices and strands: 0 residues in 0 chains, 1847 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 1873 seeds are put forward Round 1: 123 peptides, 17 chains. Longest chain 18 peptides. Score 0.490 Round 2: 139 peptides, 17 chains. Longest chain 16 peptides. Score 0.563 Round 3: 144 peptides, 18 chains. Longest chain 20 peptides. Score 0.565 Round 4: 135 peptides, 19 chains. Longest chain 13 peptides. Score 0.504 Round 5: 140 peptides, 18 chains. Longest chain 21 peptides. Score 0.547 Taking the results from Round 3 Chains 18, Residues 126, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 4000 restraints for refining 1790 atoms. 3514 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2407 (Rfree = 0.000) for 1790 atoms. Found 6 (9 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.2249 (Rfree = 0.000) for 1786 atoms. Found 6 (9 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.2202 (Rfree = 0.000) for 1781 atoms. Found 4 (9 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2216 (Rfree = 0.000) for 1777 atoms. Found 1 (9 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2202 (Rfree = 0.000) for 1772 atoms. Found 1 (9 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1862 seeds are put forward Round 1: 123 peptides, 19 chains. Longest chain 15 peptides. Score 0.445 Round 2: 140 peptides, 20 chains. Longest chain 22 peptides. Score 0.507 Round 3: 149 peptides, 21 chains. Longest chain 22 peptides. Score 0.527 Round 4: 144 peptides, 17 chains. Longest chain 22 peptides. Score 0.584 Round 5: 143 peptides, 17 chains. Longest chain 21 peptides. Score 0.580 Taking the results from Round 4 Chains 19, Residues 127, Estimated correctness of the model 23.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3696 restraints for refining 1790 atoms. 3119 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2632 (Rfree = 0.000) for 1790 atoms. Found 9 (9 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.2423 (Rfree = 0.000) for 1782 atoms. Found 3 (9 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2381 (Rfree = 0.000) for 1774 atoms. Found 3 (9 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2376 (Rfree = 0.000) for 1769 atoms. Found 0 (9 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2387 (Rfree = 0.000) for 1763 atoms. Found 1 (9 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 1861 seeds are put forward Round 1: 126 peptides, 22 chains. Longest chain 14 peptides. Score 0.393 Round 2: 125 peptides, 20 chains. Longest chain 15 peptides. Score 0.433 Round 3: 144 peptides, 19 chains. Longest chain 16 peptides. Score 0.545 Round 4: 138 peptides, 18 chains. Longest chain 16 peptides. Score 0.538 Round 5: 140 peptides, 17 chains. Longest chain 17 peptides. Score 0.567 Taking the results from Round 5 Chains 17, Residues 123, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4439 reflections ( 98.89 % complete ) and 3934 restraints for refining 1790 atoms. 3459 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2599 (Rfree = 0.000) for 1790 atoms. Found 9 (9 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2459 (Rfree = 0.000) for 1788 atoms. Found 5 (9 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2388 (Rfree = 0.000) for 1786 atoms. Found 2 (9 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2365 (Rfree = 0.000) for 1778 atoms. Found 1 (9 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2370 (Rfree = 0.000) for 1771 atoms. Found 1 (9 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 1848 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1863 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 12 peptides. Score 0.402 Round 2: 151 peptides, 20 chains. Longest chain 19 peptides. Score 0.556 Round 3: 145 peptides, 18 chains. Longest chain 15 peptides. Score 0.569 Round 4: 151 peptides, 21 chains. Longest chain 15 peptides. Score 0.536 Round 5: 138 peptides, 20 chains. Longest chain 13 peptides. Score 0.497 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 127, Estimated correctness of the model 18.2 % 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 3945 restraints for refining 1790 atoms. 3455 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2602 (Rfree = 0.000) for 1790 atoms. Found 0 (9 requested) and removed 2 (6 requested) atoms. Cycle 47: After refmac, R = 0.2530 (Rfree = 0.000) for 1787 atoms. Found 0 (9 requested) and removed 3 (6 requested) atoms. Cycle 48: After refmac, R = 0.2557 (Rfree = 0.000) for 1784 atoms. Found 0 (9 requested) and removed 0 (6 requested) atoms. Cycle 49: After refmac, R = 0.2544 (Rfree = 0.000) for 1784 atoms. Found 0 (9 requested) and removed 0 (6 requested) atoms. Writing output files ... TimeTaking 32.48