Sun 23 Dec 23:45:52 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-mrncs ############### 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 23:45:56 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-4.0-parrot-mrncs/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 300 and 0 Target number of residues in the AU: 300 Target solvent content: 0.6683 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-4.0-parrot-mrncs.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: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3520 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.066 4.001 Wilson plot Bfac: 90.57 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4445 reflections ( 98.32 % complete ) and 0 restraints for refining 3917 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3546 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3389 (Rfree = 0.000) for 3917 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 4010 seeds are put forward NCS extension: 0 residues added, 4010 seeds are put forward Round 1: 152 peptides, 32 chains. Longest chain 8 peptides. Score 0.263 Round 2: 214 peptides, 36 chains. Longest chain 11 peptides. Score 0.420 Round 3: 229 peptides, 38 chains. Longest chain 16 peptides. Score 0.440 Round 4: 239 peptides, 33 chains. Longest chain 16 peptides. Score 0.534 Round 5: 229 peptides, 30 chains. Longest chain 20 peptides. Score 0.543 Taking the results from Round 5 Chains 30, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 7367 restraints for refining 3176 atoms. 6601 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2847 (Rfree = 0.000) for 3176 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 2: After refmac, R = 0.2493 (Rfree = 0.000) for 3110 atoms. Found 3 (15 requested) and removed 12 (7 requested) atoms. Cycle 3: After refmac, R = 0.2420 (Rfree = 0.000) for 3069 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2830 (Rfree = 0.000) for 3033 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2694 (Rfree = 0.000) for 3005 atoms. Found 8 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 3120 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 3151 seeds are put forward Round 1: 169 peptides, 32 chains. Longest chain 9 peptides. Score 0.326 Round 2: 211 peptides, 37 chains. Longest chain 11 peptides. Score 0.397 Round 3: 202 peptides, 30 chains. Longest chain 14 peptides. Score 0.465 Round 4: 209 peptides, 34 chains. Longest chain 12 peptides. Score 0.432 Round 5: 206 peptides, 29 chains. Longest chain 15 peptides. Score 0.490 Taking the results from Round 5 Chains 29, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6884 restraints for refining 2998 atoms. 6205 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2877 (Rfree = 0.000) for 2998 atoms. Found 14 (14 requested) and removed 33 (7 requested) atoms. Cycle 7: After refmac, R = 0.2637 (Rfree = 0.000) for 2945 atoms. Found 12 (14 requested) and removed 20 (7 requested) atoms. Cycle 8: After refmac, R = 0.2560 (Rfree = 0.000) for 2904 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 9: After refmac, R = 0.2682 (Rfree = 0.000) for 2873 atoms. Found 4 (13 requested) and removed 19 (6 requested) atoms. Cycle 10: After refmac, R = 0.2743 (Rfree = 0.000) for 2837 atoms. Found 4 (13 requested) and removed 29 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 2931 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2948 seeds are put forward Round 1: 148 peptides, 33 chains. Longest chain 9 peptides. Score 0.232 Round 2: 185 peptides, 36 chains. Longest chain 9 peptides. Score 0.322 Round 3: 202 peptides, 38 chains. Longest chain 11 peptides. Score 0.352 Round 4: 185 peptides, 34 chains. Longest chain 10 peptides. Score 0.352 Round 5: 173 peptides, 29 chains. Longest chain 11 peptides. Score 0.385 Taking the results from Round 5 Chains 29, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6917 restraints for refining 2987 atoms. 6370 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2923 (Rfree = 0.000) for 2987 atoms. Found 14 (14 requested) and removed 301 (7 requested) atoms. Cycle 12: After refmac, R = 0.2896 (Rfree = 0.000) for 2679 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 13: After refmac, R = 0.2971 (Rfree = 0.000) for 2659 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 14: After refmac, R = 0.2798 (Rfree = 0.000) for 2642 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.2587 (Rfree = 0.000) for 2637 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.77 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2760 seeds are put forward Round 1: 144 peptides, 29 chains. Longest chain 9 peptides. Score 0.281 Round 2: 183 peptides, 31 chains. Longest chain 13 peptides. Score 0.390 Round 3: 178 peptides, 28 chains. Longest chain 18 peptides. Score 0.417 Round 4: 198 peptides, 31 chains. Longest chain 15 peptides. Score 0.439 Round 5: 188 peptides, 29 chains. Longest chain 18 peptides. Score 0.435 Taking the results from Round 4 Chains 31, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6290 restraints for refining 2847 atoms. 5653 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2713 (Rfree = 0.000) for 2847 atoms. Found 12 (13 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.2657 (Rfree = 0.000) for 2824 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 18: After refmac, R = 0.2541 (Rfree = 0.000) for 2803 atoms. Found 12 (13 requested) and removed 14 (6 requested) atoms. Cycle 19: After refmac, R = 0.2511 (Rfree = 0.000) for 2788 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.2031 (Rfree = 0.000) for 2770 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 2869 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2887 seeds are put forward Round 1: 145 peptides, 31 chains. Longest chain 8 peptides. Score 0.252 Round 2: 150 peptides, 29 chains. Longest chain 12 peptides. Score 0.303 Round 3: 164 peptides, 27 chains. Longest chain 15 peptides. Score 0.384 Round 4: 169 peptides, 26 chains. Longest chain 13 peptides. Score 0.416 Round 5: 174 peptides, 29 chains. Longest chain 9 peptides. Score 0.389 Taking the results from Round 4 Chains 26, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6857 restraints for refining 2966 atoms. 6311 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2421 (Rfree = 0.000) for 2966 atoms. Found 8 (14 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2600 (Rfree = 0.000) for 2925 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2495 (Rfree = 0.000) for 2905 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.2500 (Rfree = 0.000) for 2887 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.1915 (Rfree = 0.000) for 2875 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.76 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2971 seeds are put forward Round 1: 139 peptides, 31 chains. Longest chain 7 peptides. Score 0.229 Round 2: 174 peptides, 35 chains. Longest chain 12 peptides. Score 0.298 Round 3: 165 peptides, 29 chains. Longest chain 10 peptides. Score 0.358 Round 4: 176 peptides, 27 chains. Longest chain 18 peptides. Score 0.425 Round 5: 172 peptides, 29 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 4 Chains 27, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6410 restraints for refining 2933 atoms. 5841 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2609 (Rfree = 0.000) for 2933 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 27: After refmac, R = 0.2400 (Rfree = 0.000) for 2895 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2347 (Rfree = 0.000) for 2876 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.2301 (Rfree = 0.000) for 2862 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.1725 (Rfree = 0.000) for 2853 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 2935 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2958 seeds are put forward Round 1: 134 peptides, 28 chains. Longest chain 8 peptides. Score 0.258 Round 2: 149 peptides, 29 chains. Longest chain 9 peptides. Score 0.300 Round 3: 160 peptides, 26 chains. Longest chain 13 peptides. Score 0.386 Round 4: 150 peptides, 25 chains. Longest chain 13 peptides. Score 0.366 Round 5: 141 peptides, 23 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 3 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6305 restraints for refining 2898 atoms. 5795 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2338 (Rfree = 0.000) for 2898 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2373 (Rfree = 0.000) for 2868 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.2364 (Rfree = 0.000) for 2853 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.1957 (Rfree = 0.000) for 2836 atoms. Found 3 (13 requested) and removed 12 (6 requested) atoms. Cycle 35: After refmac, R = 0.1835 (Rfree = 0.000) for 2819 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2935 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 8 peptides. Score 0.282 Round 2: 141 peptides, 26 chains. Longest chain 13 peptides. Score 0.318 Round 3: 166 peptides, 30 chains. Longest chain 8 peptides. Score 0.346 Round 4: 165 peptides, 30 chains. Longest chain 10 peptides. Score 0.342 Round 5: 168 peptides, 28 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 5 Chains 28, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6399 restraints for refining 2860 atoms. 5867 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2544 (Rfree = 0.000) for 2860 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2423 (Rfree = 0.000) for 2840 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.2464 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2026 (Rfree = 0.000) for 2816 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.1907 (Rfree = 0.000) for 2810 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 2924 seeds are put forward NCS extension: 0 residues added, 2924 seeds are put forward Round 1: 147 peptides, 31 chains. Longest chain 8 peptides. Score 0.260 Round 2: 171 peptides, 31 chains. Longest chain 13 peptides. Score 0.348 Round 3: 159 peptides, 29 chains. Longest chain 12 peptides. Score 0.336 Round 4: 154 peptides, 26 chains. Longest chain 13 peptides. Score 0.365 Round 5: 145 peptides, 25 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 4 Chains 26, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4445 reflections ( 98.32 % complete ) and 6521 restraints for refining 2901 atoms. 6035 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2448 (Rfree = 0.000) for 2901 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 42: After refmac, R = 0.2363 (Rfree = 0.000) for 2891 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2228 (Rfree = 0.000) for 2892 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.2198 (Rfree = 0.000) for 2885 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 45: After refmac, R = 0.2163 (Rfree = 0.000) for 2879 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2981 seeds are put forward Round 1: 137 peptides, 31 chains. Longest chain 6 peptides. Score 0.221 Round 2: 175 peptides, 34 chains. Longest chain 12 peptides. Score 0.317 Round 3: 167 peptides, 30 chains. Longest chain 13 peptides. Score 0.349 Round 4: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.335 Round 5: 150 peptides, 27 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 137, 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 2od6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4445 reflections ( 98.32 % complete ) and 6666 restraints for refining 3004 atoms. 6148 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2373 (Rfree = 0.000) for 3004 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2154 (Rfree = 0.000) for 2984 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1999 (Rfree = 0.000) for 2965 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2044 (Rfree = 0.000) for 2954 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 33.37