Mon 24 Dec 07:48:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oyo-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:48:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-parrot-noncs/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 270 and 0 Target number of residues in the AU: 270 Target solvent content: 0.6507 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-3.6-parrot-noncs.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: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 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: 83.295 3.600 Wilson plot Bfac: 78.05 4986 reflections ( 99.82 % complete ) and 0 restraints for refining 3478 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3258 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2942 (Rfree = 0.000) for 3478 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 3559 seeds are put forward NCS extension: 0 residues added, 3559 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 10 peptides. Score 0.274 Round 2: 187 peptides, 31 chains. Longest chain 13 peptides. Score 0.431 Round 3: 203 peptides, 34 chains. Longest chain 13 peptides. Score 0.443 Round 4: 208 peptides, 32 chains. Longest chain 16 peptides. Score 0.490 Round 5: 205 peptides, 30 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 5 Chains 31, Residues 175, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6191 restraints for refining 2843 atoms. 5379 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2361 (Rfree = 0.000) for 2843 atoms. Found 8 (18 requested) and removed 25 (9 requested) atoms. Cycle 2: After refmac, R = 0.2280 (Rfree = 0.000) for 2774 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2202 (Rfree = 0.000) for 2746 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2160 (Rfree = 0.000) for 2725 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.2093 (Rfree = 0.000) for 2714 atoms. Found 3 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 2850 seeds are put forward Round 1: 204 peptides, 35 chains. Longest chain 12 peptides. Score 0.431 Round 2: 219 peptides, 32 chains. Longest chain 24 peptides. Score 0.527 Round 3: 226 peptides, 31 chains. Longest chain 24 peptides. Score 0.563 Round 4: 217 peptides, 24 chains. Longest chain 29 peptides. Score 0.628 Round 5: 209 peptides, 29 chains. Longest chain 16 peptides. Score 0.537 Taking the results from Round 4 Chains 28, Residues 193, Estimated correctness of the model 25.3 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6038 restraints for refining 2843 atoms. 5153 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2213 (Rfree = 0.000) for 2843 atoms. Found 14 (18 requested) and removed 15 (9 requested) atoms. Cycle 7: After refmac, R = 0.2138 (Rfree = 0.000) for 2814 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 8: After refmac, R = 0.2205 (Rfree = 0.000) for 2802 atoms. Found 14 (18 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2144 (Rfree = 0.000) for 2793 atoms. Found 15 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.1881 (Rfree = 0.000) for 2789 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 2924 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2950 seeds are put forward Round 1: 187 peptides, 32 chains. Longest chain 11 peptides. Score 0.416 Round 2: 201 peptides, 28 chains. Longest chain 19 peptides. Score 0.526 Round 3: 215 peptides, 29 chains. Longest chain 14 peptides. Score 0.556 Round 4: 226 peptides, 30 chains. Longest chain 17 peptides. Score 0.576 Round 5: 215 peptides, 28 chains. Longest chain 14 peptides. Score 0.570 Taking the results from Round 4 Chains 30, Residues 196, Estimated correctness of the model 5.1 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6285 restraints for refining 2843 atoms. 5501 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2253 (Rfree = 0.000) for 2843 atoms. Found 9 (18 requested) and removed 22 (9 requested) atoms. Cycle 12: After refmac, R = 0.2043 (Rfree = 0.000) for 2817 atoms. Found 15 (18 requested) and removed 18 (9 requested) atoms. Cycle 13: After refmac, R = 0.1931 (Rfree = 0.000) for 2801 atoms. Found 17 (18 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1893 (Rfree = 0.000) for 2790 atoms. Found 6 (17 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.1591 (Rfree = 0.000) for 2777 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2919 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 2947 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 18 peptides. Score 0.410 Round 2: 223 peptides, 34 chains. Longest chain 21 peptides. Score 0.511 Round 3: 204 peptides, 29 chains. Longest chain 21 peptides. Score 0.521 Round 4: 217 peptides, 31 chains. Longest chain 18 peptides. Score 0.535 Round 5: 206 peptides, 30 chains. Longest chain 12 peptides. Score 0.513 Taking the results from Round 4 Chains 32, Residues 186, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6240 restraints for refining 2843 atoms. 5483 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1976 (Rfree = 0.000) for 2843 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. Cycle 17: After refmac, R = 0.1908 (Rfree = 0.000) for 2824 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.1798 (Rfree = 0.000) for 2820 atoms. Found 10 (18 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.1703 (Rfree = 0.000) for 2811 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. Cycle 20: After refmac, R = 0.1474 (Rfree = 0.000) for 2793 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 2906 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2925 seeds are put forward Round 1: 198 peptides, 36 chains. Longest chain 12 peptides. Score 0.393 Round 2: 215 peptides, 33 chains. Longest chain 21 peptides. Score 0.499 Round 3: 215 peptides, 33 chains. Longest chain 21 peptides. Score 0.499 Round 4: 225 peptides, 31 chains. Longest chain 22 peptides. Score 0.560 Round 5: 213 peptides, 31 chains. Longest chain 14 peptides. Score 0.522 Taking the results from Round 4 Chains 32, Residues 194, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6263 restraints for refining 2843 atoms. 5487 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1941 (Rfree = 0.000) for 2843 atoms. Found 14 (18 requested) and removed 24 (9 requested) atoms. Cycle 22: After refmac, R = 0.1903 (Rfree = 0.000) for 2826 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Cycle 23: After refmac, R = 0.1798 (Rfree = 0.000) for 2821 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. Cycle 24: After refmac, R = 0.1782 (Rfree = 0.000) for 2811 atoms. Found 11 (18 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.1682 (Rfree = 0.000) for 2805 atoms. Found 13 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 2924 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2936 seeds are put forward Round 1: 178 peptides, 35 chains. Longest chain 12 peptides. Score 0.331 Round 2: 199 peptides, 31 chains. Longest chain 14 peptides. Score 0.475 Round 3: 197 peptides, 27 chains. Longest chain 23 peptides. Score 0.527 Round 4: 191 peptides, 28 chains. Longest chain 12 peptides. Score 0.492 Round 5: 198 peptides, 28 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 3 Chains 28, Residues 170, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4986 reflections ( 99.82 % complete ) and 6392 restraints for refining 2843 atoms. 5707 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1951 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.1871 (Rfree = 0.000) for 2838 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.1839 (Rfree = 0.000) for 2835 atoms. Found 14 (18 requested) and removed 12 (9 requested) atoms. Cycle 29: After refmac, R = 0.1571 (Rfree = 0.000) for 2829 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 2817 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 0 residues added, 2942 seeds are put forward Round 1: 133 peptides, 25 chains. Longest chain 11 peptides. Score 0.320 Round 2: 161 peptides, 22 chains. Longest chain 14 peptides. Score 0.481 Round 3: 163 peptides, 24 chains. Longest chain 13 peptides. Score 0.456 Round 4: 171 peptides, 24 chains. Longest chain 15 peptides. Score 0.485 Round 5: 163 peptides, 23 chains. Longest chain 16 peptides. Score 0.472 Taking the results from Round 4 Chains 25, Residues 147, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6468 restraints for refining 2843 atoms. 5823 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 2843 atoms. Found 15 (18 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2156 (Rfree = 0.000) for 2836 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 33: After refmac, R = 0.2105 (Rfree = 0.000) for 2836 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 34: After refmac, R = 0.2047 (Rfree = 0.000) for 2835 atoms. Found 14 (18 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.2426 (Rfree = 0.000) for 2834 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2978 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2981 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 10 peptides. Score 0.328 Round 2: 173 peptides, 28 chains. Longest chain 12 peptides. Score 0.428 Round 3: 174 peptides, 29 chains. Longest chain 14 peptides. Score 0.415 Round 4: 166 peptides, 28 chains. Longest chain 10 peptides. Score 0.401 Round 5: 173 peptides, 27 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 5 Chains 28, Residues 146, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6468 restraints for refining 2843 atoms. 5836 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2104 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 37: After refmac, R = 0.2058 (Rfree = 0.000) for 2834 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.1816 (Rfree = 0.000) for 2819 atoms. Found 5 (18 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.1850 (Rfree = 0.000) for 2805 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1687 (Rfree = 0.000) for 2796 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 2925 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2937 seeds are put forward Round 1: 142 peptides, 28 chains. Longest chain 9 peptides. Score 0.304 Round 2: 171 peptides, 31 chains. Longest chain 9 peptides. Score 0.370 Round 3: 175 peptides, 30 chains. Longest chain 15 peptides. Score 0.403 Round 4: 176 peptides, 32 chains. Longest chain 11 peptides. Score 0.373 Round 5: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 5 Chains 30, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6711 restraints for refining 2843 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1865 (Rfree = 0.000) for 2843 atoms. Found 15 (18 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.1825 (Rfree = 0.000) for 2841 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1830 (Rfree = 0.000) for 2832 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.1570 (Rfree = 0.000) for 2825 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1586 (Rfree = 0.000) for 2817 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2932 seeds are put forward Round 1: 133 peptides, 27 chains. Longest chain 9 peptides. Score 0.283 Round 2: 150 peptides, 25 chains. Longest chain 11 peptides. Score 0.390 Round 3: 152 peptides, 28 chains. Longest chain 13 peptides. Score 0.346 Round 4: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.355 Round 5: 156 peptides, 28 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 125, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4986 reflections ( 99.82 % complete ) and 6625 restraints for refining 2843 atoms. 6124 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1791 (Rfree = 0.000) for 2843 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1842 (Rfree = 0.000) for 2828 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1756 (Rfree = 0.000) for 2818 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1778 (Rfree = 0.000) for 2801 atoms. TimeTaking 39.2