Sun 23 Dec 22:23:10 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ets-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ets-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-3.2-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 22:23:19 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-3.2-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 117 and 0 Target number of residues in the AU: 117 Target solvent content: 0.6278 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 64.84 2931 reflections ( 99.80 % complete ) and 0 restraints for refining 1149 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3811 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3511 (Rfree = 0.000) for 1149 atoms. Found 9 (10 requested) and removed 21 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.83 Search for helices and strands: 0 residues in 0 chains, 1154 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.227 Round 2: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.248 Round 3: 65 peptides, 12 chains. Longest chain 7 peptides. Score 0.352 Round 4: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.337 Round 5: 69 peptides, 12 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 5 Chains 12, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2193 restraints for refining 935 atoms. 1977 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3359 (Rfree = 0.000) for 935 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 2: After refmac, R = 0.3175 (Rfree = 0.000) for 920 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.3144 (Rfree = 0.000) for 910 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.2754 (Rfree = 0.000) for 907 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2870 (Rfree = 0.000) for 899 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.85 Search for helices and strands: 0 residues in 0 chains, 951 seeds are put forward Round 1: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.298 Round 2: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.413 Round 3: 54 peptides, 7 chains. Longest chain 12 peptides. Score 0.459 Round 4: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.426 Round 5: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.471 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2086 restraints for refining 906 atoms. 1860 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2935 (Rfree = 0.000) for 906 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2898 (Rfree = 0.000) for 902 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 8: After refmac, R = 0.2796 (Rfree = 0.000) for 901 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2838 (Rfree = 0.000) for 899 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2762 (Rfree = 0.000) for 894 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.77 Search for helices and strands: 0 residues in 0 chains, 935 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.298 Round 2: 64 peptides, 11 chains. Longest chain 12 peptides. Score 0.384 Round 3: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.391 Round 4: 77 peptides, 13 chains. Longest chain 9 peptides. Score 0.425 Round 5: 75 peptides, 11 chains. Longest chain 11 peptides. Score 0.484 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 6.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2148 restraints for refining 935 atoms. 1903 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2900 (Rfree = 0.000) for 935 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2724 (Rfree = 0.000) for 930 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2690 (Rfree = 0.000) for 926 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2550 (Rfree = 0.000) for 924 atoms. Found 0 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2561 (Rfree = 0.000) for 916 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.81 Search for helices and strands: 0 residues in 0 chains, 950 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.361 Round 2: 71 peptides, 10 chains. Longest chain 16 peptides. Score 0.488 Round 3: 70 peptides, 11 chains. Longest chain 11 peptides. Score 0.440 Round 4: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.384 Round 5: 67 peptides, 10 chains. Longest chain 16 peptides. Score 0.453 Taking the results from Round 2 Chains 10, Residues 61, Estimated correctness of the model 7.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2193 restraints for refining 935 atoms. 1959 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2874 (Rfree = 0.000) for 935 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2864 (Rfree = 0.000) for 929 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2729 (Rfree = 0.000) for 927 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2622 (Rfree = 0.000) for 925 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2669 (Rfree = 0.000) for 922 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 971 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.352 Round 2: 62 peptides, 8 chains. Longest chain 13 peptides. Score 0.489 Round 3: 67 peptides, 9 chains. Longest chain 13 peptides. Score 0.493 Round 4: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.426 Round 5: 68 peptides, 10 chains. Longest chain 17 peptides. Score 0.462 Taking the results from Round 3 Chains 9, Residues 58, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2200 restraints for refining 935 atoms. 1977 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2667 (Rfree = 0.000) for 935 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 22: After refmac, R = 0.2628 (Rfree = 0.000) for 930 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2497 (Rfree = 0.000) for 926 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2508 (Rfree = 0.000) for 921 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2900 (Rfree = 0.000) for 918 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.76 Search for helices and strands: 0 residues in 0 chains, 970 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.334 Round 2: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.422 Round 3: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.416 Round 4: 56 peptides, 8 chains. Longest chain 11 peptides. Score 0.435 Round 5: 57 peptides, 7 chains. Longest chain 12 peptides. Score 0.486 Taking the results from Round 5 Chains 7, Residues 50, Estimated correctness of the model 6.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2181 restraints for refining 935 atoms. 1988 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2728 (Rfree = 0.000) for 935 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2570 (Rfree = 0.000) for 936 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.2489 (Rfree = 0.000) for 935 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2450 (Rfree = 0.000) for 931 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2456 (Rfree = 0.000) for 926 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.78 Search for helices and strands: 0 residues in 0 chains, 973 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.267 Round 2: 59 peptides, 10 chains. Longest chain 8 peptides. Score 0.378 Round 3: 63 peptides, 10 chains. Longest chain 11 peptides. Score 0.416 Round 4: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.400 Round 5: 69 peptides, 12 chains. Longest chain 8 peptides. Score 0.391 Taking the results from Round 3 Chains 10, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2205 restraints for refining 935 atoms. 2003 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2509 (Rfree = 0.000) for 935 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2454 (Rfree = 0.000) for 924 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2499 (Rfree = 0.000) for 918 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2423 (Rfree = 0.000) for 916 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2450 (Rfree = 0.000) for 911 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 2.76 Search for helices and strands: 0 residues in 0 chains, 958 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.331 Round 2: 63 peptides, 10 chains. Longest chain 13 peptides. Score 0.416 Round 3: 73 peptides, 11 chains. Longest chain 12 peptides. Score 0.467 Round 4: 74 peptides, 11 chains. Longest chain 15 peptides. Score 0.476 Round 5: 65 peptides, 9 chains. Longest chain 14 peptides. Score 0.475 Taking the results from Round 4 Chains 11, Residues 63, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2111 restraints for refining 935 atoms. 1870 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2692 (Rfree = 0.000) for 935 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2467 (Rfree = 0.000) for 928 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.2494 (Rfree = 0.000) for 919 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.2447 (Rfree = 0.000) for 914 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2517 (Rfree = 0.000) for 910 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 2.77 Search for helices and strands: 0 residues in 0 chains, 948 seeds are put forward Round 1: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.401 Round 2: 73 peptides, 9 chains. Longest chain 19 peptides. Score 0.542 Round 3: 63 peptides, 9 chains. Longest chain 11 peptides. Score 0.458 Round 4: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.378 Round 5: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 2 Chains 9, Residues 64, Estimated correctness of the model 24.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2931 reflections ( 99.80 % complete ) and 2054 restraints for refining 929 atoms. 1807 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2536 (Rfree = 0.000) for 929 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2469 (Rfree = 0.000) for 927 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2416 (Rfree = 0.000) for 924 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2349 (Rfree = 0.000) for 919 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2364 (Rfree = 0.000) for 916 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.76 Search for helices and strands: 0 residues in 0 chains, 959 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.295 Round 2: 67 peptides, 12 chains. Longest chain 9 peptides. Score 0.371 Round 3: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.303 Round 4: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.384 Round 5: 67 peptides, 10 chains. Longest chain 19 peptides. Score 0.453 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 57, 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. 2931 reflections ( 99.80 % complete ) and 2132 restraints for refining 935 atoms. 1914 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2523 (Rfree = 0.000) for 935 atoms. Found 0 (8 requested) and removed 3 (4 requested) atoms. Cycle 47: After refmac, R = 0.2503 (Rfree = 0.000) for 932 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2521 (Rfree = 0.000) for 928 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2470 (Rfree = 0.000) for 924 atoms. TimeTaking 26.53