null Sun 23 Dec 22:22:43 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 2ets-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ets-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ets-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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/2ets-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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 22:22:53 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/2ets-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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 114 and 0 Target number of residues in the AU: 114 Target solvent content: 0.6373 Checking the provided sequence file Detected sequence length: 128 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 128 Adjusted target solvent content: 0.59 Input MTZ file: 2ets-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: 155 Cell parameters: 93.473 93.473 101.164 90.000 90.000 120.000 Input sequence file: 2ets-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1024 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 Loops will be built when appropriate and at the last cycle Resolution range: 63.206 3.401 Wilson plot Bfac: 69.97 2458 reflections ( 99.76 % complete ) and 0 restraints for refining 1133 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3833 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3652 (Rfree = 0.000) for 1133 atoms. Found 6 (8 requested) and removed 21 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 1144 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.239 Round 2: 50 peptides, 10 chains. Longest chain 9 peptides. Score 0.284 Round 3: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.342 Round 4: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.440 Round 5: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.391 Taking the results from Round 4 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2094 restraints for refining 931 atoms. 1869 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2980 (Rfree = 0.000) for 931 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 2: After refmac, R = 0.2828 (Rfree = 0.000) for 907 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 3: After refmac, R = 0.2674 (Rfree = 0.000) for 889 atoms. Found 1 (6 requested) and removed 21 (3 requested) atoms. Cycle 4: After refmac, R = 0.2672 (Rfree = 0.000) for 868 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 5: After refmac, R = 0.2555 (Rfree = 0.000) for 853 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 2.98 Search for helices and strands: 0 residues in 0 chains, 908 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.273 Round 2: 53 peptides, 9 chains. Longest chain 8 peptides. Score 0.361 Round 3: 50 peptides, 8 chains. Longest chain 9 peptides. Score 0.376 Round 4: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.372 Round 5: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.382 Taking the results from Round 5 Chains 9, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2167 restraints for refining 903 atoms. 1992 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2841 (Rfree = 0.000) for 903 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 7: After refmac, R = 0.2624 (Rfree = 0.000) for 899 atoms. Found 1 (6 requested) and removed 9 (3 requested) atoms. Cycle 8: After refmac, R = 0.2463 (Rfree = 0.000) for 891 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2440 (Rfree = 0.000) for 887 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2395 (Rfree = 0.000) for 884 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 915 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.247 Round 2: 53 peptides, 8 chains. Longest chain 11 peptides. Score 0.406 Round 3: 53 peptides, 8 chains. Longest chain 16 peptides. Score 0.406 Round 4: 59 peptides, 9 chains. Longest chain 12 peptides. Score 0.420 Round 5: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 4 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2185 restraints for refining 931 atoms. 1994 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2956 (Rfree = 0.000) for 931 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 12: After refmac, R = 0.2690 (Rfree = 0.000) for 921 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2715 (Rfree = 0.000) for 917 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.2567 (Rfree = 0.000) for 916 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2409 (Rfree = 0.000) for 914 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.03 Search for helices and strands: 0 residues in 0 chains, 949 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.269 Round 2: 73 peptides, 12 chains. Longest chain 17 peptides. Score 0.428 Round 3: 63 peptides, 11 chains. Longest chain 16 peptides. Score 0.374 Round 4: 60 peptides, 10 chains. Longest chain 14 peptides. Score 0.388 Round 5: 64 peptides, 11 chains. Longest chain 13 peptides. Score 0.384 Taking the results from Round 2 Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2089 restraints for refining 930 atoms. 1857 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3078 (Rfree = 0.000) for 930 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2667 (Rfree = 0.000) for 921 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2625 (Rfree = 0.000) for 917 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2535 (Rfree = 0.000) for 914 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2488 (Rfree = 0.000) for 914 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.94 Search for helices and strands: 0 residues in 0 chains, 952 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.290 Round 2: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.374 Round 3: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.409 Round 4: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.381 Round 5: 70 peptides, 11 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 5 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2095 restraints for refining 931 atoms. 1870 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3117 (Rfree = 0.000) for 931 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. Cycle 22: After refmac, R = 0.2663 (Rfree = 0.000) for 927 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.2794 (Rfree = 0.000) for 926 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2622 (Rfree = 0.000) for 922 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2515 (Rfree = 0.000) for 919 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 964 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.284 Round 2: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.388 Round 3: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.337 Round 4: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.378 Round 5: 62 peptides, 10 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2131 restraints for refining 931 atoms. 1933 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2954 (Rfree = 0.000) for 931 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.2743 (Rfree = 0.000) for 927 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 28: After refmac, R = 0.2790 (Rfree = 0.000) for 919 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.2670 (Rfree = 0.000) for 920 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2462 (Rfree = 0.000) for 918 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 2.98 Search for helices and strands: 0 residues in 0 chains, 957 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.327 Round 2: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.381 Round 3: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.462 Round 4: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.471 Round 5: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.391 Taking the results from Round 4 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2115 restraints for refining 931 atoms. 1889 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2814 (Rfree = 0.000) for 931 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2613 (Rfree = 0.000) for 924 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.2576 (Rfree = 0.000) for 920 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2551 (Rfree = 0.000) for 916 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2529 (Rfree = 0.000) for 912 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 2.97 Search for helices and strands: 0 residues in 0 chains, 937 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 9 peptides. Score 0.260 Round 2: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.372 Round 3: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.401 Round 4: 60 peptides, 9 chains. Longest chain 12 peptides. Score 0.430 Round 5: 63 peptides, 9 chains. Longest chain 11 peptides. Score 0.458 Taking the results from Round 5 Chains 9, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2117 restraints for refining 931 atoms. 1910 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2685 (Rfree = 0.000) for 931 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.2516 (Rfree = 0.000) for 929 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2474 (Rfree = 0.000) for 926 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2452 (Rfree = 0.000) for 922 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2452 (Rfree = 0.000) for 917 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 2.98 Search for helices and strands: 0 residues in 0 chains, 940 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 7 peptides. Score 0.214 Round 2: 45 peptides, 8 chains. Longest chain 10 peptides. Score 0.324 Round 3: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.313 Round 4: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.364 Round 5: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2458 reflections ( 99.76 % complete ) and 2111 restraints for refining 931 atoms. 1913 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2794 (Rfree = 0.000) for 931 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2597 (Rfree = 0.000) for 925 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2526 (Rfree = 0.000) for 927 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2472 (Rfree = 0.000) for 922 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2438 (Rfree = 0.000) for 919 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 954 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.229 Round 2: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.241 Round 3: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.294 Round 4: 42 peptides, 8 chains. Longest chain 7 peptides. Score 0.290 Round 5: 46 peptides, 7 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 39, 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 2ets-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2458 reflections ( 99.76 % complete ) and 2141 restraints for refining 921 atoms. 1992 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2673 (Rfree = 0.000) for 921 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2575 (Rfree = 0.000) for 917 atoms. Found 0 (6 requested) and removed 1 (3 requested) atoms. Cycle 48: After refmac, R = 0.2547 (Rfree = 0.000) for 916 atoms. Found 0 (6 requested) and removed 2 (3 requested) atoms. Cycle 49: After refmac, R = 0.2531 (Rfree = 0.000) for 914 atoms. Found 0 (6 requested) and removed 0 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:48:29 GMT 2018 Job finished. TimeTaking 25.76 Used memory is bytes: 5721976