Sun 23 Dec 22:23:08 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-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 22:23:17 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-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 218 and 0 Target number of residues in the AU: 218 Target solvent content: 0.6100 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 56.63 5298 reflections ( 99.07 % complete ) and 0 restraints for refining 2191 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3180 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3098 (Rfree = 0.000) for 2191 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 2.78 Search for helices and strands: 0 residues in 0 chains, 2234 seeds are put forward NCS extension: 0 residues added, 2234 seeds are put forward Round 1: 133 peptides, 22 chains. Longest chain 16 peptides. Score 0.430 Round 2: 166 peptides, 22 chains. Longest chain 18 peptides. Score 0.581 Round 3: 177 peptides, 21 chains. Longest chain 17 peptides. Score 0.641 Round 4: 188 peptides, 22 chains. Longest chain 21 peptides. Score 0.663 Round 5: 182 peptides, 16 chains. Longest chain 22 peptides. Score 0.732 Taking the results from Round 5 Chains 18, Residues 166, Estimated correctness of the model 71.7 % 2 chains (28 residues) have been docked in sequence Building loops using Loopy2018 18 chains (166 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3397 restraints for refining 1796 atoms. 2616 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2846 (Rfree = 0.000) for 1796 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.2721 (Rfree = 0.000) for 1768 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 3: After refmac, R = 0.2654 (Rfree = 0.000) for 1759 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2516 (Rfree = 0.000) for 1747 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2488 (Rfree = 0.000) for 1738 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 2.81 Search for helices and strands: 0 residues in 0 chains, 1806 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 1830 seeds are put forward Round 1: 172 peptides, 21 chains. Longest chain 21 peptides. Score 0.622 Round 2: 194 peptides, 19 chains. Longest chain 28 peptides. Score 0.725 Round 3: 185 peptides, 21 chains. Longest chain 19 peptides. Score 0.668 Round 4: 176 peptides, 20 chains. Longest chain 18 peptides. Score 0.653 Round 5: 190 peptides, 18 chains. Longest chain 22 peptides. Score 0.727 Taking the results from Round 5 Chains 18, Residues 172, Estimated correctness of the model 70.7 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3713 restraints for refining 1796 atoms. 2970 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2685 (Rfree = 0.000) for 1796 atoms. Found 13 (14 requested) and removed 10 (8 requested) atoms. Cycle 7: After refmac, R = 0.2692 (Rfree = 0.000) for 1794 atoms. Found 13 (14 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.2705 (Rfree = 0.000) for 1790 atoms. Found 14 (14 requested) and removed 19 (8 requested) atoms. Cycle 9: After refmac, R = 0.2568 (Rfree = 0.000) for 1783 atoms. Found 13 (13 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2492 (Rfree = 0.000) for 1782 atoms. Found 13 (13 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 2.82 Search for helices and strands: 0 residues in 0 chains, 1848 seeds are put forward NCS extension: 10 residues added (6 deleted due to clashes), 1858 seeds are put forward Round 1: 174 peptides, 21 chains. Longest chain 19 peptides. Score 0.630 Round 2: 181 peptides, 18 chains. Longest chain 21 peptides. Score 0.701 Round 3: 183 peptides, 17 chains. Longest chain 21 peptides. Score 0.721 Round 4: 197 peptides, 16 chains. Longest chain 26 peptides. Score 0.771 Round 5: 191 peptides, 16 chains. Longest chain 32 peptides. Score 0.756 Taking the results from Round 4 Chains 16, Residues 181, Estimated correctness of the model 78.8 % 2 chains (47 residues) have been docked in sequence Building loops using Loopy2018 16 chains (181 residues) following loop building 2 chains (47 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5298 reflections ( 99.07 % complete ) and 3175 restraints for refining 1797 atoms. 2230 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2694 (Rfree = 0.000) for 1797 atoms. Found 13 (13 requested) and removed 10 (8 requested) atoms. Cycle 12: After refmac, R = 0.2444 (Rfree = 0.000) for 1795 atoms. Found 12 (12 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2573 (Rfree = 0.000) for 1792 atoms. Found 12 (12 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.2488 (Rfree = 0.000) for 1787 atoms. Found 12 (12 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2471 (Rfree = 0.000) for 1782 atoms. Found 12 (12 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 2.80 Search for helices and strands: 0 residues in 0 chains, 1850 seeds are put forward NCS extension: 0 residues added, 1850 seeds are put forward Round 1: 171 peptides, 17 chains. Longest chain 19 peptides. Score 0.684 Round 2: 184 peptides, 19 chains. Longest chain 21 peptides. Score 0.695 Round 3: 182 peptides, 15 chains. Longest chain 35 peptides. Score 0.745 Round 4: 192 peptides, 13 chains. Longest chain 34 peptides. Score 0.795 Round 5: 188 peptides, 11 chains. Longest chain 32 peptides. Score 0.809 Taking the results from Round 5 Chains 15, Residues 177, Estimated correctness of the model 84.8 % 3 chains (55 residues) have been docked in sequence Building loops using Loopy2018 15 chains (177 residues) following loop building 3 chains (55 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3115 restraints for refining 1796 atoms. 2168 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2856 (Rfree = 0.000) for 1796 atoms. Found 6 (11 requested) and removed 18 (8 requested) atoms. Cycle 17: After refmac, R = 0.2805 (Rfree = 0.000) for 1781 atoms. Found 11 (11 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.2815 (Rfree = 0.000) for 1775 atoms. Found 10 (10 requested) and removed 16 (7 requested) atoms. Cycle 19: After refmac, R = 0.2594 (Rfree = 0.000) for 1769 atoms. Found 10 (10 requested) and removed 11 (7 requested) atoms. Cycle 20: After refmac, R = 0.2582 (Rfree = 0.000) for 1762 atoms. Found 9 (9 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 2.85 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 1860 seeds are put forward Round 1: 181 peptides, 19 chains. Longest chain 25 peptides. Score 0.686 Round 2: 194 peptides, 18 chains. Longest chain 29 peptides. Score 0.738 Round 3: 179 peptides, 20 chains. Longest chain 17 peptides. Score 0.664 Round 4: 175 peptides, 15 chains. Longest chain 21 peptides. Score 0.726 Round 5: 184 peptides, 15 chains. Longest chain 41 peptides. Score 0.751 Taking the results from Round 5 Chains 16, Residues 169, Estimated correctness of the model 75.2 % 3 chains (64 residues) have been docked in sequence Building loops using Loopy2018 16 chains (169 residues) following loop building 3 chains (64 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3098 restraints for refining 1797 atoms. 2146 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2708 (Rfree = 0.000) for 1797 atoms. Found 10 (10 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2465 (Rfree = 0.000) for 1792 atoms. Found 5 (9 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2349 (Rfree = 0.000) for 1785 atoms. Found 4 (9 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.2222 (Rfree = 0.000) for 1779 atoms. Found 5 (8 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2331 (Rfree = 0.000) for 1773 atoms. Found 6 (8 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.82 Search for helices and strands: 0 residues in 0 chains, 1856 seeds are put forward NCS extension: 22 residues added (15 deleted due to clashes), 1878 seeds are put forward Round 1: 161 peptides, 15 chains. Longest chain 24 peptides. Score 0.682 Round 2: 174 peptides, 16 chains. Longest chain 26 peptides. Score 0.708 Round 3: 182 peptides, 16 chains. Longest chain 43 peptides. Score 0.732 Round 4: 171 peptides, 18 chains. Longest chain 22 peptides. Score 0.668 Round 5: 185 peptides, 18 chains. Longest chain 35 peptides. Score 0.713 Taking the results from Round 3 Chains 16, Residues 166, Estimated correctness of the model 71.7 % 2 chains (60 residues) have been docked in sequence Building loops using Loopy2018 16 chains (166 residues) following loop building 2 chains (60 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3174 restraints for refining 1797 atoms. 2248 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2625 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.2472 (Rfree = 0.000) for 1784 atoms. Found 8 (8 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2420 (Rfree = 0.000) for 1779 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.2395 (Rfree = 0.000) for 1776 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.2413 (Rfree = 0.000) for 1773 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 2.86 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 63 residues added (17 deleted due to clashes), 1886 seeds are put forward Round 1: 172 peptides, 20 chains. Longest chain 29 peptides. Score 0.639 Round 2: 187 peptides, 17 chains. Longest chain 33 peptides. Score 0.732 Round 3: 181 peptides, 18 chains. Longest chain 40 peptides. Score 0.701 Round 4: 186 peptides, 20 chains. Longest chain 23 peptides. Score 0.687 Round 5: 189 peptides, 20 chains. Longest chain 30 peptides. Score 0.696 Taking the results from Round 2 Chains 19, Residues 170, Estimated correctness of the model 71.7 % 2 chains (42 residues) have been docked in sequence Building loops using Loopy2018 19 chains (170 residues) following loop building 2 chains (42 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3265 restraints for refining 1797 atoms. 2387 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2599 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 18 (8 requested) atoms. Cycle 32: After refmac, R = 0.2386 (Rfree = 0.000) for 1785 atoms. Found 7 (8 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.2312 (Rfree = 0.000) for 1779 atoms. Found 4 (7 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.2244 (Rfree = 0.000) for 1775 atoms. Found 4 (7 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.2390 (Rfree = 0.000) for 1770 atoms. Found 7 (7 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.91 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1848 seeds are put forward Round 1: 145 peptides, 18 chains. Longest chain 21 peptides. Score 0.569 Round 2: 160 peptides, 15 chains. Longest chain 24 peptides. Score 0.679 Round 3: 165 peptides, 15 chains. Longest chain 30 peptides. Score 0.695 Round 4: 167 peptides, 19 chains. Longest chain 21 peptides. Score 0.638 Round 5: 164 peptides, 19 chains. Longest chain 21 peptides. Score 0.626 Taking the results from Round 3 Chains 15, Residues 150, Estimated correctness of the model 64.1 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3549 restraints for refining 1797 atoms. 2819 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2508 (Rfree = 0.000) for 1797 atoms. Found 7 (8 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.2562 (Rfree = 0.000) for 1789 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2341 (Rfree = 0.000) for 1787 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2244 (Rfree = 0.000) for 1784 atoms. Found 5 (8 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2128 (Rfree = 0.000) for 1781 atoms. Found 5 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.81 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 1869 seeds are put forward Round 1: 149 peptides, 17 chains. Longest chain 22 peptides. Score 0.604 Round 2: 165 peptides, 16 chains. Longest chain 24 peptides. Score 0.679 Round 3: 162 peptides, 19 chains. Longest chain 22 peptides. Score 0.619 Round 4: 160 peptides, 17 chains. Longest chain 21 peptides. Score 0.646 Round 5: 146 peptides, 13 chains. Longest chain 32 peptides. Score 0.663 Taking the results from Round 2 Chains 17, Residues 149, Estimated correctness of the model 60.6 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3304 restraints for refining 1797 atoms. 2488 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2580 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 16 (8 requested) atoms. Cycle 42: After refmac, R = 0.2488 (Rfree = 0.000) for 1787 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2352 (Rfree = 0.000) for 1777 atoms. Found 4 (8 requested) and removed 13 (8 requested) atoms. Cycle 44: After refmac, R = 0.2421 (Rfree = 0.000) for 1767 atoms. Found 7 (7 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.2297 (Rfree = 0.000) for 1759 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 2.83 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 1845 seeds are put forward Round 1: 154 peptides, 18 chains. Longest chain 21 peptides. Score 0.606 Round 2: 178 peptides, 17 chains. Longest chain 37 peptides. Score 0.706 Round 3: 161 peptides, 13 chains. Longest chain 38 peptides. Score 0.713 Round 4: 168 peptides, 13 chains. Longest chain 46 peptides. Score 0.734 Round 5: 168 peptides, 16 chains. Longest chain 31 peptides. Score 0.689 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 155, Estimated correctness of the model 72.1 % 2 chains (63 residues) have been docked in sequence Sequence coverage is 40 % Consider running further cycles of model building using 2i8d-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 49 A and 57 A 11 chains (158 residues) following loop building 1 chains (70 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5298 reflections ( 99.07 % complete ) and 3043 restraints for refining 1797 atoms. 2090 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2499 (Rfree = 0.000) for 1797 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2323 (Rfree = 0.000) for 1784 atoms. Found 0 (8 requested) and removed 6 (8 requested) atoms. Cycle 48: After refmac, R = 0.2535 (Rfree = 0.000) for 1774 atoms. Found 0 (7 requested) and removed 5 (7 requested) atoms. Cycle 49: After refmac, R = 0.2274 (Rfree = 0.000) for 1766 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 42.59