Tue 25 Dec 19:27:57 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 1vkn-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkn-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-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/1vkn-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-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 ============================================================ Tue 25 Dec 19:28:07 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/1vkn-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkn-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 1002 and 0 Target number of residues in the AU: 1002 Target solvent content: 0.6305 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.75 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: 93.562 3.400 Wilson plot Bfac: 66.71 19863 reflections ( 98.93 % complete ) and 0 restraints for refining 12451 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2984 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2466 (Rfree = 0.000) for 12451 atoms. Found 94 (94 requested) and removed 77 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 12700 seeds are put forward NCS extension: 0 residues added, 12700 seeds are put forward Round 1: 690 peptides, 117 chains. Longest chain 20 peptides. Score 0.430 Round 2: 837 peptides, 108 chains. Longest chain 24 peptides. Score 0.602 Round 3: 851 peptides, 101 chains. Longest chain 22 peptides. Score 0.638 Round 4: 898 peptides, 108 chains. Longest chain 24 peptides. Score 0.649 Round 5: 913 peptides, 104 chains. Longest chain 25 peptides. Score 0.672 Taking the results from Round 5 Chains 114, Residues 809, Estimated correctness of the model 50.4 % 14 chains (161 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 20675 restraints for refining 10208 atoms. 17003 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2201 (Rfree = 0.000) for 10208 atoms. Found 63 (77 requested) and removed 81 (38 requested) atoms. Cycle 2: After refmac, R = 0.2072 (Rfree = 0.000) for 10044 atoms. Found 39 (76 requested) and removed 59 (38 requested) atoms. Cycle 3: After refmac, R = 0.2023 (Rfree = 0.000) for 9965 atoms. Found 37 (75 requested) and removed 46 (37 requested) atoms. Cycle 4: After refmac, R = 0.1956 (Rfree = 0.000) for 9923 atoms. Found 28 (75 requested) and removed 43 (37 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1919 (Rfree = 0.000) for 9878 atoms. Found 27 (74 requested) and removed 45 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 10173 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 10188 seeds are put forward Round 1: 796 peptides, 111 chains. Longest chain 28 peptides. Score 0.557 Round 2: 868 peptides, 100 chains. Longest chain 40 peptides. Score 0.653 Round 3: 888 peptides, 102 chains. Longest chain 38 peptides. Score 0.661 Round 4: 904 peptides, 97 chains. Longest chain 31 peptides. Score 0.688 Round 5: 907 peptides, 99 chains. Longest chain 39 peptides. Score 0.683 Taking the results from Round 4 Chains 106, Residues 807, Estimated correctness of the model 54.7 % 12 chains (194 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 19863 reflections ( 98.93 % complete ) and 20692 restraints for refining 10211 atoms. 16847 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2213 (Rfree = 0.000) for 10211 atoms. Found 67 (77 requested) and removed 73 (38 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2076 (Rfree = 0.000) for 10140 atoms. Found 43 (77 requested) and removed 51 (38 requested) atoms. Cycle 8: After refmac, R = 0.2016 (Rfree = 0.000) for 10094 atoms. Found 40 (76 requested) and removed 44 (38 requested) atoms. Cycle 9: After refmac, R = 0.1929 (Rfree = 0.000) for 10068 atoms. Found 22 (76 requested) and removed 46 (38 requested) atoms. Cycle 10: After refmac, R = 0.1907 (Rfree = 0.000) for 10021 atoms. Found 23 (75 requested) and removed 49 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 10349 seeds are put forward NCS extension: 18 residues added (21 deleted due to clashes), 10367 seeds are put forward Round 1: 805 peptides, 120 chains. Longest chain 24 peptides. Score 0.529 Round 2: 867 peptides, 110 chains. Longest chain 30 peptides. Score 0.619 Round 3: 894 peptides, 107 chains. Longest chain 37 peptides. Score 0.649 Round 4: 906 peptides, 109 chains. Longest chain 28 peptides. Score 0.651 Round 5: 903 peptides, 105 chains. Longest chain 36 peptides. Score 0.662 Taking the results from Round 5 Chains 109, Residues 798, Estimated correctness of the model 47.6 % 10 chains (108 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 21855 restraints for refining 10213 atoms. 18410 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2209 (Rfree = 0.000) for 10213 atoms. Found 64 (77 requested) and removed 66 (38 requested) atoms. Cycle 12: After refmac, R = 0.2050 (Rfree = 0.000) for 10178 atoms. Found 34 (77 requested) and removed 47 (38 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2017 (Rfree = 0.000) for 10141 atoms. Found 36 (76 requested) and removed 45 (38 requested) atoms. Cycle 14: After refmac, R = 0.1993 (Rfree = 0.000) for 10120 atoms. Found 31 (76 requested) and removed 45 (38 requested) atoms. Cycle 15: After refmac, R = 0.1957 (Rfree = 0.000) for 10098 atoms. Found 28 (76 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10381 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 10396 seeds are put forward Round 1: 759 peptides, 114 chains. Longest chain 23 peptides. Score 0.511 Round 2: 878 peptides, 105 chains. Longest chain 40 peptides. Score 0.644 Round 3: 892 peptides, 108 chains. Longest chain 32 peptides. Score 0.644 Round 4: 876 peptides, 110 chains. Longest chain 30 peptides. Score 0.626 Round 5: 899 peptides, 115 chains. Longest chain 31 peptides. Score 0.626 Taking the results from Round 3 Chains 113, Residues 784, Estimated correctness of the model 42.4 % 12 chains (188 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 20780 restraints for refining 10212 atoms. 17042 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2100 (Rfree = 0.000) for 10212 atoms. Found 60 (77 requested) and removed 66 (38 requested) atoms. Cycle 17: After refmac, R = 0.1980 (Rfree = 0.000) for 10160 atoms. Found 32 (77 requested) and removed 47 (38 requested) atoms. Cycle 18: After refmac, R = 0.1902 (Rfree = 0.000) for 10123 atoms. Found 29 (76 requested) and removed 42 (38 requested) atoms. Cycle 19: After refmac, R = 0.1857 (Rfree = 0.000) for 10102 atoms. Found 28 (76 requested) and removed 42 (38 requested) atoms. Cycle 20: After refmac, R = 0.1819 (Rfree = 0.000) for 10078 atoms. Found 24 (76 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10396 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 10419 seeds are put forward Round 1: 740 peptides, 119 chains. Longest chain 21 peptides. Score 0.472 Round 2: 799 peptides, 98 chains. Longest chain 32 peptides. Score 0.608 Round 3: 821 peptides, 101 chains. Longest chain 40 peptides. Score 0.615 Round 4: 816 peptides, 101 chains. Longest chain 30 peptides. Score 0.611 Round 5: 831 peptides, 101 chains. Longest chain 24 peptides. Score 0.622 Taking the results from Round 5 Chains 103, Residues 730, Estimated correctness of the model 35.7 % 7 chains (52 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22862 restraints for refining 10213 atoms. 19892 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2044 (Rfree = 0.000) for 10213 atoms. Found 61 (77 requested) and removed 51 (38 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1912 (Rfree = 0.000) for 10190 atoms. Found 33 (77 requested) and removed 47 (38 requested) atoms. Cycle 23: After refmac, R = 0.1832 (Rfree = 0.000) for 10160 atoms. Found 36 (76 requested) and removed 43 (38 requested) atoms. Cycle 24: After refmac, R = 0.1762 (Rfree = 0.000) for 10141 atoms. Found 26 (76 requested) and removed 43 (38 requested) atoms. Cycle 25: After refmac, R = 0.1761 (Rfree = 0.000) for 10109 atoms. Found 27 (76 requested) and removed 44 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10412 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 10433 seeds are put forward Round 1: 717 peptides, 116 chains. Longest chain 27 peptides. Score 0.462 Round 2: 788 peptides, 103 chains. Longest chain 27 peptides. Score 0.580 Round 3: 802 peptides, 107 chains. Longest chain 35 peptides. Score 0.577 Round 4: 801 peptides, 101 chains. Longest chain 35 peptides. Score 0.599 Round 5: 809 peptides, 101 chains. Longest chain 26 peptides. Score 0.605 Taking the results from Round 5 Chains 106, Residues 708, Estimated correctness of the model 30.3 % 7 chains (104 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22013 restraints for refining 10211 atoms. 18907 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2025 (Rfree = 0.000) for 10211 atoms. Found 67 (77 requested) and removed 56 (38 requested) atoms. Cycle 27: After refmac, R = 0.1907 (Rfree = 0.000) for 10184 atoms. Found 24 (77 requested) and removed 44 (38 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 10149 atoms. Found 22 (76 requested) and removed 42 (38 requested) atoms. Cycle 29: After refmac, R = 0.1806 (Rfree = 0.000) for 10107 atoms. Found 31 (76 requested) and removed 44 (38 requested) atoms. Cycle 30: After refmac, R = 0.1783 (Rfree = 0.000) for 10082 atoms. Found 23 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10387 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 10400 seeds are put forward Round 1: 676 peptides, 103 chains. Longest chain 27 peptides. Score 0.478 Round 2: 767 peptides, 106 chains. Longest chain 29 peptides. Score 0.551 Round 3: 737 peptides, 97 chains. Longest chain 36 peptides. Score 0.560 Round 4: 770 peptides, 96 chains. Longest chain 30 peptides. Score 0.592 Round 5: 769 peptides, 98 chains. Longest chain 31 peptides. Score 0.583 Taking the results from Round 4 Chains 97, Residues 674, Estimated correctness of the model 26.0 % 8 chains (87 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22659 restraints for refining 10212 atoms. 19755 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1928 (Rfree = 0.000) for 10212 atoms. Found 70 (77 requested) and removed 54 (38 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1829 (Rfree = 0.000) for 10197 atoms. Found 44 (77 requested) and removed 49 (38 requested) atoms. Cycle 33: After refmac, R = 0.1783 (Rfree = 0.000) for 10171 atoms. Found 53 (76 requested) and removed 52 (38 requested) atoms. Cycle 34: After refmac, R = 0.1727 (Rfree = 0.000) for 10160 atoms. Found 46 (76 requested) and removed 47 (38 requested) atoms. Cycle 35: After refmac, R = 0.1690 (Rfree = 0.000) for 10149 atoms. Found 45 (76 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10484 seeds are put forward NCS extension: 23 residues added (8 deleted due to clashes), 10507 seeds are put forward Round 1: 665 peptides, 117 chains. Longest chain 16 peptides. Score 0.403 Round 2: 743 peptides, 102 chains. Longest chain 20 peptides. Score 0.545 Round 3: 754 peptides, 100 chains. Longest chain 23 peptides. Score 0.563 Round 4: 757 peptides, 98 chains. Longest chain 35 peptides. Score 0.573 Round 5: 727 peptides, 104 chains. Longest chain 24 peptides. Score 0.522 Taking the results from Round 4 Chains 99, Residues 659, Estimated correctness of the model 19.6 % 9 chains (90 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22540 restraints for refining 10213 atoms. 19660 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1930 (Rfree = 0.000) for 10213 atoms. Found 60 (77 requested) and removed 46 (38 requested) atoms. Cycle 37: After refmac, R = 0.1816 (Rfree = 0.000) for 10172 atoms. Found 29 (77 requested) and removed 40 (38 requested) atoms. Cycle 38: After refmac, R = 0.1794 (Rfree = 0.000) for 10136 atoms. Found 38 (76 requested) and removed 43 (38 requested) atoms. Cycle 39: After refmac, R = 0.1726 (Rfree = 0.000) for 10120 atoms. Found 40 (76 requested) and removed 42 (38 requested) atoms. Cycle 40: After refmac, R = 0.1713 (Rfree = 0.000) for 10098 atoms. Found 38 (76 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 10382 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 10413 seeds are put forward Round 1: 636 peptides, 106 chains. Longest chain 22 peptides. Score 0.423 Round 2: 732 peptides, 106 chains. Longest chain 26 peptides. Score 0.519 Round 3: 725 peptides, 100 chains. Longest chain 20 peptides. Score 0.537 Round 4: 722 peptides, 95 chains. Longest chain 30 peptides. Score 0.554 Round 5: 735 peptides, 99 chains. Longest chain 31 peptides. Score 0.550 Taking the results from Round 4 Chains 100, Residues 627, Estimated correctness of the model 13.0 % 7 chains (93 residues) have been docked in sequence ------------------------------------------------------ 19863 reflections ( 98.93 % complete ) and 22660 restraints for refining 10212 atoms. 19921 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1836 (Rfree = 0.000) for 10212 atoms. Found 74 (77 requested) and removed 51 (38 requested) atoms. Cycle 42: After refmac, R = 0.1729 (Rfree = 0.000) for 10213 atoms. Found 35 (77 requested) and removed 42 (38 requested) atoms. Cycle 43: After refmac, R = 0.1650 (Rfree = 0.000) for 10188 atoms. Found 35 (77 requested) and removed 40 (38 requested) atoms. Cycle 44: After refmac, R = 0.1608 (Rfree = 0.000) for 10164 atoms. Found 33 (76 requested) and removed 42 (38 requested) atoms. Cycle 45: After refmac, R = 0.1580 (Rfree = 0.000) for 10142 atoms. Found 42 (76 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10390 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10410 seeds are put forward Round 1: 572 peptides, 101 chains. Longest chain 13 peptides. Score 0.377 Round 2: 672 peptides, 97 chains. Longest chain 21 peptides. Score 0.500 Round 3: 670 peptides, 102 chains. Longest chain 18 peptides. Score 0.476 Round 4: 658 peptides, 92 chains. Longest chain 21 peptides. Score 0.508 Round 5: 651 peptides, 97 chains. Longest chain 21 peptides. Score 0.479 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 92, Residues 566, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 92 chains (566 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19863 reflections ( 98.93 % complete ) and 23817 restraints for refining 10212 atoms. 21609 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1733 (Rfree = 0.000) for 10212 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.1688 (Rfree = 0.000) for 10150 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.1626 (Rfree = 0.000) for 10098 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1594 (Rfree = 0.000) for 10049 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:49:23 GMT 2018 Job finished. TimeTaking 141.43