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 2b8m-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.6-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/2b8m-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.6-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/2b8m-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-3.6-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 83 and 0 Target number of residues in the AU: 83 Target solvent content: 0.6063 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 117 Adjusted target solvent content: 0.45 Input MTZ file: 2b8m-3.6-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: 152 Cell parameters: 50.280 50.280 78.170 90.000 90.000 120.000 Input sequence file: 2b8m-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 936 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.086 3.602 Wilson plot Bfac: 54.90 1463 reflections ( 99.19 % complete ) and 0 restraints for refining 1046 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3144 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2287 (Rfree = 0.000) for 1046 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 4.00 Search for helices and strands: 0 residues in 0 chains, 1058 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.339 Round 2: 63 peptides, 8 chains. Longest chain 11 peptides. Score 0.599 Round 3: 64 peptides, 8 chains. Longest chain 14 peptides. Score 0.610 Round 4: 77 peptides, 9 chains. Longest chain 18 peptides. Score 0.688 Round 5: 84 peptides, 8 chains. Longest chain 19 peptides. Score 0.772 Taking the results from Round 5 Chains 8, Residues 76, Estimated correctness of the model 69.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1769 restraints for refining 848 atoms. 1473 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2610 (Rfree = 0.000) for 848 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 2: After refmac, R = 0.2530 (Rfree = 0.000) for 830 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.2386 (Rfree = 0.000) for 821 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2325 (Rfree = 0.000) for 816 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2306 (Rfree = 0.000) for 807 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.472 Round 2: 66 peptides, 9 chains. Longest chain 12 peptides. Score 0.584 Round 3: 76 peptides, 9 chains. Longest chain 15 peptides. Score 0.680 Round 4: 74 peptides, 6 chains. Longest chain 31 peptides. Score 0.770 Round 5: 77 peptides, 11 chains. Longest chain 16 peptides. Score 0.607 Taking the results from Round 4 Chains 6, Residues 68, Estimated correctness of the model 68.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1890 restraints for refining 842 atoms. 1624 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2728 (Rfree = 0.000) for 842 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 7: After refmac, R = 0.2536 (Rfree = 0.000) for 834 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2475 (Rfree = 0.000) for 825 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2421 (Rfree = 0.000) for 821 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 10: After refmac, R = 0.2396 (Rfree = 0.000) for 814 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 833 seeds are put forward Round 1: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.488 Round 2: 68 peptides, 9 chains. Longest chain 17 peptides. Score 0.605 Round 3: 73 peptides, 9 chains. Longest chain 13 peptides. Score 0.653 Round 4: 68 peptides, 7 chains. Longest chain 19 peptides. Score 0.690 Round 5: 68 peptides, 9 chains. Longest chain 17 peptides. Score 0.605 Taking the results from Round 4 Chains 7, Residues 61, Estimated correctness of the model 46.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1881 restraints for refining 837 atoms. 1644 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2687 (Rfree = 0.000) for 837 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 12: After refmac, R = 0.2477 (Rfree = 0.000) for 831 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2439 (Rfree = 0.000) for 828 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2415 (Rfree = 0.000) for 825 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2378 (Rfree = 0.000) for 822 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 845 seeds are put forward Round 1: 59 peptides, 8 chains. Longest chain 16 peptides. Score 0.556 Round 2: 72 peptides, 8 chains. Longest chain 14 peptides. Score 0.685 Round 3: 72 peptides, 9 chains. Longest chain 14 peptides. Score 0.644 Round 4: 64 peptides, 8 chains. Longest chain 13 peptides. Score 0.610 Round 5: 68 peptides, 8 chains. Longest chain 17 peptides. Score 0.649 Taking the results from Round 2 Chains 8, Residues 64, Estimated correctness of the model 44.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1862 restraints for refining 823 atoms. 1614 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2564 (Rfree = 0.000) for 823 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 17: After refmac, R = 0.2325 (Rfree = 0.000) for 823 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2276 (Rfree = 0.000) for 820 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2221 (Rfree = 0.000) for 817 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2200 (Rfree = 0.000) for 816 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 833 seeds are put forward Round 1: 63 peptides, 10 chains. Longest chain 11 peptides. Score 0.500 Round 2: 61 peptides, 7 chains. Longest chain 16 peptides. Score 0.626 Round 3: 57 peptides, 8 chains. Longest chain 11 peptides. Score 0.533 Round 4: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.528 Round 5: 72 peptides, 11 chains. Longest chain 12 peptides. Score 0.554 Taking the results from Round 2 Chains 7, Residues 54, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1916 restraints for refining 831 atoms. 1707 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2390 (Rfree = 0.000) for 831 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.2316 (Rfree = 0.000) for 826 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2274 (Rfree = 0.000) for 823 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.2252 (Rfree = 0.000) for 821 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2227 (Rfree = 0.000) for 821 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 845 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.450 Round 2: 64 peptides, 8 chains. Longest chain 16 peptides. Score 0.610 Round 3: 64 peptides, 7 chains. Longest chain 15 peptides. Score 0.654 Round 4: 55 peptides, 7 chains. Longest chain 11 peptides. Score 0.561 Round 5: 64 peptides, 9 chains. Longest chain 13 peptides. Score 0.562 Taking the results from Round 3 Chains 7, Residues 57, Estimated correctness of the model 34.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1812 restraints for refining 832 atoms. 1591 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2445 (Rfree = 0.000) for 832 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.2312 (Rfree = 0.000) for 829 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2261 (Rfree = 0.000) for 823 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.2234 (Rfree = 0.000) for 819 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2198 (Rfree = 0.000) for 818 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 833 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 11 peptides. Score 0.312 Round 2: 61 peptides, 9 chains. Longest chain 16 peptides. Score 0.528 Round 3: 64 peptides, 8 chains. Longest chain 19 peptides. Score 0.610 Round 4: 71 peptides, 7 chains. Longest chain 24 peptides. Score 0.714 Round 5: 62 peptides, 7 chains. Longest chain 16 peptides. Score 0.635 Taking the results from Round 4 Chains 7, Residues 64, Estimated correctness of the model 53.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1791 restraints for refining 827 atoms. 1542 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2591 (Rfree = 0.000) for 827 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.2478 (Rfree = 0.000) for 819 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.2497 (Rfree = 0.000) for 813 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2367 (Rfree = 0.000) for 812 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2334 (Rfree = 0.000) for 810 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 10 peptides. Score 0.346 Round 2: 70 peptides, 10 chains. Longest chain 14 peptides. Score 0.580 Round 3: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.492 Round 4: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.562 Round 5: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.508 Taking the results from Round 2 Chains 10, Residues 60, Estimated correctness of the model 6.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1833 restraints for refining 812 atoms. 1603 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2614 (Rfree = 0.000) for 812 atoms. Found 3 (3 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.2457 (Rfree = 0.000) for 808 atoms. Found 2 (3 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.2515 (Rfree = 0.000) for 804 atoms. Found 3 (3 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2439 (Rfree = 0.000) for 804 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2466 (Rfree = 0.000) for 802 atoms. Found 2 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.90 Search for helices and strands: 0 residues in 0 chains, 824 seeds are put forward Round 1: 42 peptides, 7 chains. Longest chain 11 peptides. Score 0.394 Round 2: 55 peptides, 6 chains. Longest chain 19 peptides. Score 0.611 Round 3: 57 peptides, 8 chains. Longest chain 15 peptides. Score 0.533 Round 4: 56 peptides, 6 chains. Longest chain 16 peptides. Score 0.622 Round 5: 57 peptides, 6 chains. Longest chain 16 peptides. Score 0.632 Taking the results from Round 5 Chains 6, Residues 51, Estimated correctness of the model 26.6 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 1463 reflections ( 99.19 % complete ) and 1839 restraints for refining 847 atoms. 1570 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2575 (Rfree = 0.000) for 847 atoms. Found 1 (3 requested) and removed 10 (2 requested) atoms. Cycle 42: After refmac, R = 0.2371 (Rfree = 0.000) for 837 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.2318 (Rfree = 0.000) for 834 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2279 (Rfree = 0.000) for 832 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2257 (Rfree = 0.000) for 830 atoms. Found 3 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 852 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 8 peptides. Score 0.277 Round 2: 60 peptides, 9 chains. Longest chain 13 peptides. Score 0.516 Round 3: 56 peptides, 9 chains. Longest chain 13 peptides. Score 0.466 Round 4: 57 peptides, 9 chains. Longest chain 13 peptides. Score 0.479 Round 5: 55 peptides, 8 chains. Longest chain 13 peptides. Score 0.509 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 51, 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 2b8m-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1463 reflections ( 99.19 % complete ) and 1982 restraints for refining 835 atoms. 1787 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2499 (Rfree = 0.000) for 835 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2399 (Rfree = 0.000) for 833 atoms. Found 0 (3 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2372 (Rfree = 0.000) for 831 atoms. Found 0 (3 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.2338 (Rfree = 0.000) for 830 atoms. Found 0 (3 requested) and removed 0 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:24 GMT 2018 Job finished. TimeTaking 22.43 Used memory is bytes: 785136