Sun 23 Dec 22:22:53 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ets-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ets-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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/2ets-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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 22:23:03 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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 102 and 0 Target number of residues in the AU: 102 Target solvent content: 0.6755 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-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: 155 Cell parameters: 93.473 93.473 101.164 90.000 90.000 120.000 Input sequence file: 2ets-4.0-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 4.002 Wilson plot Bfac: 96.99 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1526 reflections ( 99.61 % complete ) and 0 restraints for refining 1131 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.4105 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3734 (Rfree = 0.000) for 1131 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.96 3.51 Search for helices and strands: 0 residues in 0 chains, 1146 seeds are put forward Round 1: 26 peptides, 5 chains. Longest chain 7 peptides. Score 0.256 Round 2: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.271 Round 3: 41 peptides, 8 chains. Longest chain 6 peptides. Score 0.279 Round 4: 41 peptides, 5 chains. Longest chain 13 peptides. Score 0.425 Round 5: 44 peptides, 7 chains. Longest chain 11 peptides. Score 0.360 Taking the results from Round 4 Chains 5, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2309 restraints for refining 924 atoms. 2170 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3137 (Rfree = 0.000) for 924 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 2: After refmac, R = 0.2759 (Rfree = 0.000) for 914 atoms. Found 1 (4 requested) and removed 18 (2 requested) atoms. Cycle 3: After refmac, R = 0.2843 (Rfree = 0.000) for 891 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 4: After refmac, R = 0.2848 (Rfree = 0.000) for 885 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2510 (Rfree = 0.000) for 879 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.88 3.44 Search for helices and strands: 0 residues in 0 chains, 903 seeds are put forward Round 1: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.283 Round 2: 53 peptides, 9 chains. Longest chain 9 peptides. Score 0.361 Round 3: 50 peptides, 9 chains. Longest chain 13 peptides. Score 0.330 Round 4: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.292 Round 5: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 2 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2131 restraints for refining 879 atoms. 1964 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2651 (Rfree = 0.000) for 879 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 7: After refmac, R = 0.2510 (Rfree = 0.000) for 877 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 8: After refmac, R = 0.2486 (Rfree = 0.000) for 868 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2267 (Rfree = 0.000) for 864 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2362 (Rfree = 0.000) for 860 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.89 3.45 Search for helices and strands: 0 residues in 0 chains, 881 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.287 Round 2: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.313 Round 3: 48 peptides, 7 chains. Longest chain 11 peptides. Score 0.401 Round 4: 39 peptides, 6 chains. Longest chain 11 peptides. Score 0.356 Round 5: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 3 Chains 7, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2138 restraints for refining 899 atoms. 1981 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2414 (Rfree = 0.000) for 899 atoms. Found 2 (4 requested) and removed 10 (2 requested) atoms. Cycle 12: After refmac, R = 0.2299 (Rfree = 0.000) for 888 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.2456 (Rfree = 0.000) for 878 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.2160 (Rfree = 0.000) for 873 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2370 (Rfree = 0.000) for 868 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.93 3.48 Search for helices and strands: 0 residues in 0 chains, 900 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.313 Round 2: 50 peptides, 8 chains. Longest chain 12 peptides. Score 0.376 Round 3: 51 peptides, 7 chains. Longest chain 12 peptides. Score 0.431 Round 4: 57 peptides, 8 chains. Longest chain 14 peptides. Score 0.444 Round 5: 44 peptides, 7 chains. Longest chain 13 peptides. Score 0.360 Taking the results from Round 4 Chains 8, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2130 restraints for refining 925 atoms. 1942 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2991 (Rfree = 0.000) for 925 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 17: After refmac, R = 0.2689 (Rfree = 0.000) for 914 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2391 (Rfree = 0.000) for 913 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2727 (Rfree = 0.000) for 905 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2273 (Rfree = 0.000) for 905 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.93 3.48 Search for helices and strands: 0 residues in 0 chains, 937 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.276 Round 2: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.302 Round 3: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.317 Round 4: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.283 Round 5: 36 peptides, 6 chains. Longest chain 10 peptides. Score 0.323 Taking the results from Round 5 Chains 6, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2325 restraints for refining 925 atoms. 2211 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2697 (Rfree = 0.000) for 925 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2518 (Rfree = 0.000) for 919 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2325 (Rfree = 0.000) for 913 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2341 (Rfree = 0.000) for 910 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2110 (Rfree = 0.000) for 907 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.89 3.45 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward Round 1: 35 peptides, 6 chains. Longest chain 11 peptides. Score 0.311 Round 2: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.287 Round 3: 45 peptides, 9 chains. Longest chain 9 peptides. Score 0.276 Round 4: 44 peptides, 7 chains. Longest chain 10 peptides. Score 0.360 Round 5: 45 peptides, 6 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 5 Chains 6, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2266 restraints for refining 925 atoms. 2116 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2750 (Rfree = 0.000) for 925 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 27: After refmac, R = 0.2325 (Rfree = 0.000) for 919 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2190 (Rfree = 0.000) for 912 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2104 (Rfree = 0.000) for 905 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2211 (Rfree = 0.000) for 903 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.45 Search for helices and strands: 0 residues in 0 chains, 941 seeds are put forward Round 1: 42 peptides, 7 chains. Longest chain 14 peptides. Score 0.339 Round 2: 45 peptides, 7 chains. Longest chain 18 peptides. Score 0.371 Round 3: 42 peptides, 7 chains. Longest chain 10 peptides. Score 0.339 Round 4: 39 peptides, 7 chains. Longest chain 12 peptides. Score 0.306 Round 5: 44 peptides, 8 chains. Longest chain 10 peptides. Score 0.313 Taking the results from Round 2 Chains 7, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2166 restraints for refining 912 atoms. 2021 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2242 (Rfree = 0.000) for 912 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.2259 (Rfree = 0.000) for 909 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2116 (Rfree = 0.000) for 903 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2059 (Rfree = 0.000) for 898 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 35: After refmac, R = 0.2081 (Rfree = 0.000) for 893 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 3.41 Search for helices and strands: 0 residues in 0 chains, 919 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.256 Round 2: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.294 Round 3: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.341 Round 4: 50 peptides, 8 chains. Longest chain 15 peptides. Score 0.376 Round 5: 52 peptides, 8 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 5 Chains 8, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2198 restraints for refining 919 atoms. 2030 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2515 (Rfree = 0.000) for 919 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.2540 (Rfree = 0.000) for 916 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 38: After refmac, R = 0.2268 (Rfree = 0.000) for 914 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2163 (Rfree = 0.000) for 906 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2321 (Rfree = 0.000) for 902 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.89 3.45 Search for helices and strands: 0 residues in 0 chains, 920 seeds are put forward Round 1: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.243 Round 2: 48 peptides, 9 chains. Longest chain 10 peptides. Score 0.309 Round 3: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.351 Round 4: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.316 Round 5: 55 peptides, 9 chains. Longest chain 10 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 ------------------------------------------------------ 1526 reflections ( 99.61 % complete ) and 2170 restraints for refining 907 atoms. 1995 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2620 (Rfree = 0.000) for 907 atoms. Found 3 (4 requested) and removed 9 (2 requested) atoms. Cycle 42: After refmac, R = 0.2516 (Rfree = 0.000) for 897 atoms. Found 0 (4 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2308 (Rfree = 0.000) for 890 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2085 (Rfree = 0.000) for 888 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2025 (Rfree = 0.000) for 884 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 3.44 Search for helices and strands: 0 residues in 0 chains, 902 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.227 Round 2: 40 peptides, 8 chains. Longest chain 8 peptides. Score 0.267 Round 3: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.290 Round 4: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.320 Round 5: 48 peptides, 8 chains. Longest chain 11 peptides. Score 0.355 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 40, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1526 reflections ( 99.61 % complete ) and 2267 restraints for refining 921 atoms. 2115 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2472 (Rfree = 0.000) for 921 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2276 (Rfree = 0.000) for 916 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2208 (Rfree = 0.000) for 911 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2096 (Rfree = 0.000) for 907 atoms. TimeTaking 24.82