null 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 1vr5-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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/1vr5-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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 22:23:07 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/1vr5-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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 971 and 0 Target number of residues in the AU: 971 Target solvent content: 0.6646 Checking the provided sequence file Detected sequence length: 547 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1094 Adjusted target solvent content: 0.62 Input MTZ file: 1vr5-4.0-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.95 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: 115.780 4.000 Wilson plot Bfac: 88.19 13747 reflections ( 99.52 % complete ) and 0 restraints for refining 9716 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3305 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3198 (Rfree = 0.000) for 9716 atoms. Found 46 (46 requested) and removed 42 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 3.24 Search for helices and strands: 0 residues in 0 chains, 9902 seeds are put forward NCS extension: 0 residues added, 9902 seeds are put forward Round 1: 529 peptides, 94 chains. Longest chain 16 peptides. Score 0.353 Round 2: 661 peptides, 87 chains. Longest chain 22 peptides. Score 0.516 Round 3: 672 peptides, 80 chains. Longest chain 24 peptides. Score 0.553 Round 4: 672 peptides, 78 chains. Longest chain 25 peptides. Score 0.561 Round 5: 691 peptides, 79 chains. Longest chain 49 peptides. Score 0.573 Taking the results from Round 5 Chains 84, Residues 612, Estimated correctness of the model 0.0 % 8 chains (92 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16582 restraints for refining 7898 atoms. 13858 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2581 (Rfree = 0.000) for 7898 atoms. Found 37 (37 requested) and removed 63 (18 requested) atoms. Cycle 2: After refmac, R = 0.2327 (Rfree = 0.000) for 7704 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 3: After refmac, R = 0.2175 (Rfree = 0.000) for 7648 atoms. Found 29 (36 requested) and removed 37 (18 requested) atoms. Cycle 4: After refmac, R = 0.2054 (Rfree = 0.000) for 7602 atoms. Found 30 (36 requested) and removed 33 (18 requested) atoms. Cycle 5: After refmac, R = 0.2059 (Rfree = 0.000) for 7577 atoms. Found 33 (36 requested) and removed 40 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.17 Search for helices and strands: 0 residues in 0 chains, 7846 seeds are put forward NCS extension: 64 residues added (3 deleted due to clashes), 7910 seeds are put forward Round 1: 647 peptides, 91 chains. Longest chain 24 peptides. Score 0.486 Round 2: 714 peptides, 85 chains. Longest chain 26 peptides. Score 0.569 Round 3: 696 peptides, 77 chains. Longest chain 30 peptides. Score 0.584 Round 4: 691 peptides, 78 chains. Longest chain 24 peptides. Score 0.577 Round 5: 698 peptides, 74 chains. Longest chain 29 peptides. Score 0.597 Taking the results from Round 5 Chains 79, Residues 624, Estimated correctness of the model 0.0 % 6 chains (71 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16637 restraints for refining 7903 atoms. 13944 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2319 (Rfree = 0.000) for 7903 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 7: After refmac, R = 0.2084 (Rfree = 0.000) for 7824 atoms. Found 21 (37 requested) and removed 32 (18 requested) atoms. Cycle 8: After refmac, R = 0.2007 (Rfree = 0.000) for 7773 atoms. Found 17 (37 requested) and removed 32 (18 requested) atoms. Cycle 9: After refmac, R = 0.1933 (Rfree = 0.000) for 7726 atoms. Found 24 (36 requested) and removed 22 (18 requested) atoms. Cycle 10: After refmac, R = 0.1973 (Rfree = 0.000) for 7701 atoms. Found 29 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.18 Search for helices and strands: 0 residues in 0 chains, 7966 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7986 seeds are put forward Round 1: 622 peptides, 88 chains. Longest chain 22 peptides. Score 0.475 Round 2: 690 peptides, 85 chains. Longest chain 25 peptides. Score 0.549 Round 3: 696 peptides, 83 chains. Longest chain 20 peptides. Score 0.562 Round 4: 695 peptides, 80 chains. Longest chain 34 peptides. Score 0.572 Round 5: 693 peptides, 82 chains. Longest chain 23 peptides. Score 0.563 Taking the results from Round 4 Chains 83, Residues 615, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17242 restraints for refining 7902 atoms. 14725 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2341 (Rfree = 0.000) for 7902 atoms. Found 31 (37 requested) and removed 34 (18 requested) atoms. Cycle 12: After refmac, R = 0.2169 (Rfree = 0.000) for 7821 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 13: After refmac, R = 0.2144 (Rfree = 0.000) for 7765 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 14: After refmac, R = 0.2092 (Rfree = 0.000) for 7715 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Cycle 15: After refmac, R = 0.2011 (Rfree = 0.000) for 7679 atoms. Found 36 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.14 Search for helices and strands: 0 residues in 0 chains, 8003 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8028 seeds are put forward Round 1: 605 peptides, 104 chains. Longest chain 15 peptides. Score 0.388 Round 2: 680 peptides, 80 chains. Longest chain 24 peptides. Score 0.560 Round 3: 647 peptides, 81 chains. Longest chain 23 peptides. Score 0.527 Round 4: 678 peptides, 83 chains. Longest chain 27 peptides. Score 0.547 Round 5: 662 peptides, 80 chains. Longest chain 22 peptides. Score 0.545 Taking the results from Round 2 Chains 87, Residues 600, Estimated correctness of the model 0.0 % 9 chains (111 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16476 restraints for refining 7902 atoms. 13693 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2171 (Rfree = 0.000) for 7902 atoms. Found 36 (37 requested) and removed 31 (18 requested) atoms. Cycle 17: After refmac, R = 0.1986 (Rfree = 0.000) for 7853 atoms. Found 22 (37 requested) and removed 30 (18 requested) atoms. Cycle 18: After refmac, R = 0.1942 (Rfree = 0.000) for 7825 atoms. Found 31 (37 requested) and removed 27 (18 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 7811 atoms. Found 29 (37 requested) and removed 27 (18 requested) atoms. Cycle 20: After refmac, R = 0.1800 (Rfree = 0.000) for 7787 atoms. Found 24 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.23 Search for helices and strands: 0 residues in 0 chains, 8072 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8093 seeds are put forward Round 1: 587 peptides, 92 chains. Longest chain 28 peptides. Score 0.423 Round 2: 647 peptides, 84 chains. Longest chain 28 peptides. Score 0.515 Round 3: 671 peptides, 87 chains. Longest chain 28 peptides. Score 0.525 Round 4: 671 peptides, 81 chains. Longest chain 20 peptides. Score 0.548 Round 5: 679 peptides, 84 chains. Longest chain 19 peptides. Score 0.543 Taking the results from Round 4 Chains 85, Residues 590, Estimated correctness of the model 0.0 % 8 chains (61 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17034 restraints for refining 7902 atoms. 14520 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2351 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Cycle 22: After refmac, R = 0.2125 (Rfree = 0.000) for 7781 atoms. Found 22 (37 requested) and removed 32 (18 requested) atoms. Cycle 23: After refmac, R = 0.2039 (Rfree = 0.000) for 7724 atoms. Found 34 (36 requested) and removed 29 (18 requested) atoms. Cycle 24: After refmac, R = 0.1968 (Rfree = 0.000) for 7698 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 25: After refmac, R = 0.1856 (Rfree = 0.000) for 7685 atoms. Found 30 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.19 Search for helices and strands: 0 residues in 0 chains, 7945 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 7971 seeds are put forward Round 1: 576 peptides, 93 chains. Longest chain 14 peptides. Score 0.408 Round 2: 640 peptides, 87 chains. Longest chain 18 peptides. Score 0.496 Round 3: 657 peptides, 85 chains. Longest chain 27 peptides. Score 0.520 Round 4: 653 peptides, 85 chains. Longest chain 24 peptides. Score 0.517 Round 5: 665 peptides, 87 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 3 Chains 85, Residues 572, Estimated correctness of the model 0.0 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17291 restraints for refining 7903 atoms. 14872 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2061 (Rfree = 0.000) for 7903 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 27: After refmac, R = 0.1919 (Rfree = 0.000) for 7862 atoms. Found 25 (37 requested) and removed 31 (18 requested) atoms. Cycle 28: After refmac, R = 0.1866 (Rfree = 0.000) for 7838 atoms. Found 22 (37 requested) and removed 27 (18 requested) atoms. Cycle 29: After refmac, R = 0.1798 (Rfree = 0.000) for 7811 atoms. Found 22 (37 requested) and removed 25 (18 requested) atoms. Cycle 30: After refmac, R = 0.1775 (Rfree = 0.000) for 7799 atoms. Found 28 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.20 Search for helices and strands: 0 residues in 0 chains, 8051 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 8090 seeds are put forward Round 1: 512 peptides, 90 chains. Longest chain 14 peptides. Score 0.353 Round 2: 566 peptides, 86 chains. Longest chain 21 peptides. Score 0.429 Round 3: 581 peptides, 84 chains. Longest chain 20 peptides. Score 0.453 Round 4: 594 peptides, 87 chains. Longest chain 18 peptides. Score 0.453 Round 5: 627 peptides, 82 chains. Longest chain 20 peptides. Score 0.505 Taking the results from Round 5 Chains 87, Residues 545, Estimated correctness of the model 0.0 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17752 restraints for refining 7902 atoms. 15442 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2286 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 32: After refmac, R = 0.2087 (Rfree = 0.000) for 7847 atoms. Found 37 (37 requested) and removed 22 (18 requested) atoms. Cycle 33: After refmac, R = 0.1961 (Rfree = 0.000) for 7824 atoms. Found 28 (37 requested) and removed 27 (18 requested) atoms. Cycle 34: After refmac, R = 0.1896 (Rfree = 0.000) for 7796 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Cycle 35: After refmac, R = 0.1879 (Rfree = 0.000) for 7790 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.19 Search for helices and strands: 0 residues in 0 chains, 7994 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8014 seeds are put forward Round 1: 514 peptides, 91 chains. Longest chain 13 peptides. Score 0.351 Round 2: 557 peptides, 86 chains. Longest chain 17 peptides. Score 0.420 Round 3: 562 peptides, 83 chains. Longest chain 17 peptides. Score 0.439 Round 4: 570 peptides, 77 chains. Longest chain 19 peptides. Score 0.473 Round 5: 572 peptides, 80 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 4 Chains 80, Residues 493, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17768 restraints for refining 7900 atoms. 15721 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2057 (Rfree = 0.000) for 7900 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 37: After refmac, R = 0.1949 (Rfree = 0.000) for 7864 atoms. Found 30 (37 requested) and removed 25 (18 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 7841 atoms. Found 27 (37 requested) and removed 33 (18 requested) atoms. Cycle 39: After refmac, R = 0.1844 (Rfree = 0.000) for 7813 atoms. Found 30 (37 requested) and removed 30 (18 requested) atoms. Cycle 40: After refmac, R = 0.1819 (Rfree = 0.000) for 7800 atoms. Found 25 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.19 Search for helices and strands: 0 residues in 0 chains, 8039 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8052 seeds are put forward Round 1: 494 peptides, 91 chains. Longest chain 14 peptides. Score 0.328 Round 2: 556 peptides, 85 chains. Longest chain 17 peptides. Score 0.423 Round 3: 560 peptides, 87 chains. Longest chain 19 peptides. Score 0.419 Round 4: 564 peptides, 82 chains. Longest chain 19 peptides. Score 0.445 Round 5: 565 peptides, 80 chains. Longest chain 18 peptides. Score 0.455 Taking the results from Round 5 Chains 82, Residues 485, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 18038 restraints for refining 7902 atoms. 16045 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2369 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Cycle 42: After refmac, R = 0.2236 (Rfree = 0.000) for 7855 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 43: After refmac, R = 0.1950 (Rfree = 0.000) for 7825 atoms. Found 36 (37 requested) and removed 29 (18 requested) atoms. Cycle 44: After refmac, R = 0.1665 (Rfree = 0.000) for 7810 atoms. Found 6 (37 requested) and removed 22 (18 requested) atoms. Cycle 45: After refmac, R = 0.1742 (Rfree = 0.000) for 7786 atoms. Found 11 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.20 Search for helices and strands: 0 residues in 0 chains, 8003 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8026 seeds are put forward Round 1: 468 peptides, 86 chains. Longest chain 12 peptides. Score 0.323 Round 2: 541 peptides, 83 chains. Longest chain 19 peptides. Score 0.417 Round 3: 553 peptides, 82 chains. Longest chain 19 peptides. Score 0.434 Round 4: 552 peptides, 79 chains. Longest chain 17 peptides. Score 0.447 Round 5: 531 peptides, 77 chains. Longest chain 26 peptides. Score 0.435 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 473, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vr5-4_warpNtrace.pdb as input Building loops using Loopy2018 79 chains (473 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13747 reflections ( 99.52 % complete ) and 18182 restraints for refining 7902 atoms. 16321 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2466 (Rfree = 0.000) for 7902 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2098 (Rfree = 0.000) for 7821 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2047 (Rfree = 0.000) for 7769 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1995 (Rfree = 0.000) for 7728 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:06:11 GMT 2018 Job finished. TimeTaking 103.2 Used memory is bytes: 24659280