Sun 23 Dec 22:22:56 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ets-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ets-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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/2ets-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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 22:23:05 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-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 109 and 0 Target number of residues in the AU: 109 Target solvent content: 0.6532 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-3.6-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: 155 Cell parameters: 93.473 93.473 101.164 90.000 90.000 120.000 Input sequence file: 2ets-3.6-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 3.601 Wilson plot Bfac: 79.15 2071 reflections ( 99.71 % complete ) and 0 restraints for refining 1142 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3973 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3846 (Rfree = 0.000) for 1142 atoms. Found 4 (7 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.14 Search for helices and strands: 0 residues in 0 chains, 1162 seeds are put forward Round 1: 34 peptides, 6 chains. Longest chain 11 peptides. Score 0.300 Round 2: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.258 Round 3: 55 peptides, 10 chains. Longest chain 11 peptides. Score 0.337 Round 4: 68 peptides, 11 chains. Longest chain 18 peptides. Score 0.422 Round 5: 59 peptides, 10 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2094 restraints for refining 928 atoms. 1877 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3342 (Rfree = 0.000) for 928 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 2: After refmac, R = 0.3008 (Rfree = 0.000) for 909 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 3: After refmac, R = 0.2960 (Rfree = 0.000) for 902 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.3032 (Rfree = 0.000) for 896 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 5: After refmac, R = 0.2598 (Rfree = 0.000) for 892 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.07 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 7 peptides. Score 0.247 Round 2: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.334 Round 3: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.368 Round 4: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.444 Round 5: 65 peptides, 10 chains. Longest chain 10 peptides. Score 0.435 Taking the results from Round 4 Chains 10, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2092 restraints for refining 906 atoms. 1878 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2869 (Rfree = 0.000) for 906 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 7: After refmac, R = 0.2616 (Rfree = 0.000) for 893 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2608 (Rfree = 0.000) for 887 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2221 (Rfree = 0.000) for 886 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2317 (Rfree = 0.000) for 885 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.19 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward Round 1: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.372 Round 2: 52 peptides, 8 chains. Longest chain 10 peptides. Score 0.396 Round 3: 61 peptides, 9 chains. Longest chain 15 peptides. Score 0.439 Round 4: 56 peptides, 7 chains. Longest chain 13 peptides. Score 0.477 Round 5: 51 peptides, 7 chains. Longest chain 17 peptides. Score 0.431 Taking the results from Round 4 Chains 7, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2061 restraints for refining 912 atoms. 1872 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2789 (Rfree = 0.000) for 912 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 12: After refmac, R = 0.2654 (Rfree = 0.000) for 904 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.2702 (Rfree = 0.000) for 899 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 14: After refmac, R = 0.2528 (Rfree = 0.000) for 896 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2544 (Rfree = 0.000) for 895 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.14 Search for helices and strands: 0 residues in 0 chains, 938 seeds are put forward Round 1: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.345 Round 2: 58 peptides, 8 chains. Longest chain 13 peptides. Score 0.453 Round 3: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.384 Round 4: 58 peptides, 8 chains. Longest chain 12 peptides. Score 0.453 Round 5: 55 peptides, 6 chains. Longest chain 15 peptides. Score 0.510 Taking the results from Round 5 Chains 6, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2127 restraints for refining 928 atoms. 1937 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2475 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 17: After refmac, R = 0.2436 (Rfree = 0.000) for 927 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2587 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2554 (Rfree = 0.000) for 924 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 20: After refmac, R = 0.2251 (Rfree = 0.000) for 924 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.11 Search for helices and strands: 0 residues in 0 chains, 957 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.327 Round 2: 50 peptides, 7 chains. Longest chain 12 peptides. Score 0.421 Round 3: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.411 Round 4: 50 peptides, 8 chains. Longest chain 11 peptides. Score 0.376 Round 5: 62 peptides, 9 chains. Longest chain 10 peptides. Score 0.448 Taking the results from Round 5 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2069 restraints for refining 928 atoms. 1866 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2864 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2700 (Rfree = 0.000) for 923 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2622 (Rfree = 0.000) for 924 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 24: After refmac, R = 0.2341 (Rfree = 0.000) for 921 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.2367 (Rfree = 0.000) for 921 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.11 Search for helices and strands: 0 residues in 0 chains, 967 seeds are put forward Round 1: 45 peptides, 8 chains. Longest chain 11 peptides. Score 0.324 Round 2: 57 peptides, 10 chains. Longest chain 13 peptides. Score 0.358 Round 3: 64 peptides, 9 chains. Longest chain 20 peptides. Score 0.466 Round 4: 67 peptides, 10 chains. Longest chain 11 peptides. Score 0.453 Round 5: 54 peptides, 9 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 3 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2029 restraints for refining 928 atoms. 1818 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2656 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 27: After refmac, R = 0.2545 (Rfree = 0.000) for 925 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2431 (Rfree = 0.000) for 924 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.2421 (Rfree = 0.000) for 921 atoms. Found 3 (5 requested) and removed 6 (2 requested) atoms. Cycle 30: After refmac, R = 0.2244 (Rfree = 0.000) for 915 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.14 Search for helices and strands: 0 residues in 0 chains, 959 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 15 peptides. Score 0.378 Round 2: 63 peptides, 8 chains. Longest chain 22 peptides. Score 0.498 Round 3: 65 peptides, 10 chains. Longest chain 19 peptides. Score 0.435 Round 4: 56 peptides, 10 chains. Longest chain 15 peptides. Score 0.347 Round 5: 62 peptides, 10 chains. Longest chain 16 peptides. Score 0.407 Taking the results from Round 2 Chains 8, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2079 restraints for refining 928 atoms. 1867 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3048 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 32: After refmac, R = 0.2706 (Rfree = 0.000) for 929 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.2627 (Rfree = 0.000) for 927 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2547 (Rfree = 0.000) for 926 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 35: After refmac, R = 0.2412 (Rfree = 0.000) for 925 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.08 Search for helices and strands: 0 residues in 0 chains, 969 seeds are put forward Round 1: 53 peptides, 12 chains. Longest chain 8 peptides. Score 0.225 Round 2: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.287 Round 3: 47 peptides, 8 chains. Longest chain 16 peptides. Score 0.345 Round 4: 46 peptides, 8 chains. Longest chain 13 peptides. Score 0.334 Round 5: 51 peptides, 9 chains. Longest chain 13 peptides. Score 0.341 Taking the results from Round 3 Chains 8, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2159 restraints for refining 928 atoms. 2011 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3206 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.2780 (Rfree = 0.000) for 927 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.2409 (Rfree = 0.000) for 925 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2303 (Rfree = 0.000) for 924 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2328 (Rfree = 0.000) for 924 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.14 Search for helices and strands: 0 residues in 0 chains, 965 seeds are put forward Round 1: 38 peptides, 6 chains. Longest chain 14 peptides. Score 0.345 Round 2: 41 peptides, 7 chains. Longest chain 11 peptides. Score 0.328 Round 3: 48 peptides, 9 chains. Longest chain 11 peptides. Score 0.309 Round 4: 49 peptides, 8 chains. Longest chain 11 peptides. Score 0.366 Round 5: 48 peptides, 7 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 5 Chains 7, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2071 reflections ( 99.71 % complete ) and 2082 restraints for refining 928 atoms. 1925 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2888 (Rfree = 0.000) for 928 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 42: After refmac, R = 0.2937 (Rfree = 0.000) for 917 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2620 (Rfree = 0.000) for 914 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.2320 (Rfree = 0.000) for 914 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2510 (Rfree = 0.000) for 911 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.12 Search for helices and strands: 0 residues in 0 chains, 951 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.180 Round 2: 34 peptides, 7 chains. Longest chain 6 peptides. Score 0.247 Round 3: 35 peptides, 7 chains. Longest chain 8 peptides. Score 0.259 Round 4: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.306 Round 5: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.234 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 32, 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. 2071 reflections ( 99.71 % complete ) and 2188 restraints for refining 928 atoms. 2067 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3006 (Rfree = 0.000) for 928 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2927 (Rfree = 0.000) for 918 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2617 (Rfree = 0.000) for 912 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2482 (Rfree = 0.000) for 906 atoms. TimeTaking 25.75