null Tue 25 Dec 19:27:57 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 2oyo-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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/2oyo-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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 ============================================================ Tue 25 Dec 19:28:07 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/2oyo-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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 260 and 0 Target number of residues in the AU: 260 Target solvent content: 0.6636 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-3.8-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: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.85 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 3.800 Wilson plot Bfac: 87.04 4247 reflections ( 99.79 % complete ) and 0 restraints for refining 3457 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3307 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3077 (Rfree = 0.000) for 3457 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.78 Search for helices and strands: 0 residues in 0 chains, 3572 seeds are put forward NCS extension: 0 residues added, 3572 seeds are put forward Round 1: 125 peptides, 25 chains. Longest chain 10 peptides. Score 0.285 Round 2: 162 peptides, 23 chains. Longest chain 17 peptides. Score 0.469 Round 3: 165 peptides, 21 chains. Longest chain 21 peptides. Score 0.511 Round 4: 172 peptides, 21 chains. Longest chain 23 peptides. Score 0.535 Round 5: 180 peptides, 23 chains. Longest chain 18 peptides. Score 0.531 Taking the results from Round 4 Chains 23, Residues 151, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6512 restraints for refining 2836 atoms. 5829 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2423 (Rfree = 0.000) for 2836 atoms. Found 10 (15 requested) and removed 12 (7 requested) atoms. Cycle 2: After refmac, R = 0.2521 (Rfree = 0.000) for 2798 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. Cycle 3: After refmac, R = 0.2454 (Rfree = 0.000) for 2773 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2314 (Rfree = 0.000) for 2746 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.1934 (Rfree = 0.000) for 2734 atoms. Found 3 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2862 seeds are put forward Round 1: 166 peptides, 31 chains. Longest chain 10 peptides. Score 0.351 Round 2: 196 peptides, 31 chains. Longest chain 14 peptides. Score 0.464 Round 3: 182 peptides, 26 chains. Longest chain 13 peptides. Score 0.492 Round 4: 190 peptides, 27 chains. Longest chain 14 peptides. Score 0.504 Round 5: 189 peptides, 28 chains. Longest chain 15 peptides. Score 0.486 Taking the results from Round 4 Chains 27, Residues 163, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6312 restraints for refining 2752 atoms. 5645 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2153 (Rfree = 0.000) for 2752 atoms. Found 4 (15 requested) and removed 27 (7 requested) atoms. Cycle 7: After refmac, R = 0.2038 (Rfree = 0.000) for 2708 atoms. Found 6 (15 requested) and removed 16 (7 requested) atoms. Cycle 8: After refmac, R = 0.2031 (Rfree = 0.000) for 2689 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 9: After refmac, R = 0.1991 (Rfree = 0.000) for 2675 atoms. Found 7 (14 requested) and removed 17 (7 requested) atoms. Cycle 10: After refmac, R = 0.1743 (Rfree = 0.000) for 2659 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2809 seeds are put forward Round 1: 182 peptides, 34 chains. Longest chain 14 peptides. Score 0.364 Round 2: 191 peptides, 31 chains. Longest chain 14 peptides. Score 0.446 Round 3: 203 peptides, 26 chains. Longest chain 21 peptides. Score 0.561 Round 4: 196 peptides, 27 chains. Longest chain 16 peptides. Score 0.524 Round 5: 203 peptides, 28 chains. Longest chain 18 peptides. Score 0.532 Taking the results from Round 3 Chains 30, Residues 177, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 5990 restraints for refining 2789 atoms. 5220 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1990 (Rfree = 0.000) for 2789 atoms. Found 6 (15 requested) and removed 26 (7 requested) atoms. Cycle 12: After refmac, R = 0.2023 (Rfree = 0.000) for 2748 atoms. Found 7 (15 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.1969 (Rfree = 0.000) for 2728 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 14: After refmac, R = 0.1868 (Rfree = 0.000) for 2716 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 15: After refmac, R = 0.1838 (Rfree = 0.000) for 2695 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 2843 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2859 seeds are put forward Round 1: 181 peptides, 34 chains. Longest chain 11 peptides. Score 0.360 Round 2: 199 peptides, 33 chains. Longest chain 16 peptides. Score 0.444 Round 3: 221 peptides, 33 chains. Longest chain 24 peptides. Score 0.519 Round 4: 209 peptides, 31 chains. Longest chain 14 peptides. Score 0.509 Round 5: 207 peptides, 31 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 3 Chains 35, Residues 188, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6233 restraints for refining 2825 atoms. 5452 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1933 (Rfree = 0.000) for 2825 atoms. Found 7 (15 requested) and removed 20 (7 requested) atoms. Cycle 17: After refmac, R = 0.1937 (Rfree = 0.000) for 2788 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 18: After refmac, R = 0.1913 (Rfree = 0.000) for 2777 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.1775 (Rfree = 0.000) for 2774 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 20: After refmac, R = 0.1762 (Rfree = 0.000) for 2764 atoms. Found 12 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 2892 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2903 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 10 peptides. Score 0.292 Round 2: 178 peptides, 27 chains. Longest chain 15 peptides. Score 0.462 Round 3: 174 peptides, 27 chains. Longest chain 12 peptides. Score 0.448 Round 4: 189 peptides, 29 chains. Longest chain 15 peptides. Score 0.470 Round 5: 195 peptides, 29 chains. Longest chain 15 peptides. Score 0.491 Taking the results from Round 5 Chains 29, Residues 166, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6318 restraints for refining 2835 atoms. 5611 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1969 (Rfree = 0.000) for 2835 atoms. Found 7 (15 requested) and removed 17 (7 requested) atoms. Cycle 22: After refmac, R = 0.1753 (Rfree = 0.000) for 2811 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.1713 (Rfree = 0.000) for 2796 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 24: After refmac, R = 0.1715 (Rfree = 0.000) for 2783 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.1481 (Rfree = 0.000) for 2776 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2894 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2918 seeds are put forward Round 1: 157 peptides, 31 chains. Longest chain 9 peptides. Score 0.314 Round 2: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.403 Round 3: 188 peptides, 32 chains. Longest chain 11 peptides. Score 0.419 Round 4: 181 peptides, 27 chains. Longest chain 14 peptides. Score 0.473 Round 5: 182 peptides, 24 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 5 Chains 24, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6563 restraints for refining 2836 atoms. 5955 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2110 (Rfree = 0.000) for 2836 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. Cycle 27: After refmac, R = 0.1931 (Rfree = 0.000) for 2817 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.1614 (Rfree = 0.000) for 2809 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.1672 (Rfree = 0.000) for 2797 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1555 (Rfree = 0.000) for 2794 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 2912 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2935 seeds are put forward Round 1: 134 peptides, 28 chains. Longest chain 9 peptides. Score 0.269 Round 2: 160 peptides, 28 chains. Longest chain 16 peptides. Score 0.378 Round 3: 154 peptides, 25 chains. Longest chain 11 peptides. Score 0.406 Round 4: 157 peptides, 27 chains. Longest chain 13 peptides. Score 0.383 Round 5: 156 peptides, 26 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 3 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6723 restraints for refining 2836 atoms. 6232 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2016 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 32: After refmac, R = 0.1893 (Rfree = 0.000) for 2825 atoms. Found 14 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.1501 (Rfree = 0.000) for 2819 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.1543 (Rfree = 0.000) for 2811 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1375 (Rfree = 0.000) for 2806 atoms. Found 0 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2908 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2921 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 12 peptides. Score 0.280 Round 2: 154 peptides, 27 chains. Longest chain 12 peptides. Score 0.371 Round 3: 154 peptides, 25 chains. Longest chain 13 peptides. Score 0.406 Round 4: 137 peptides, 23 chains. Longest chain 13 peptides. Score 0.373 Round 5: 146 peptides, 24 chains. Longest chain 16 peptides. Score 0.391 Taking the results from Round 3 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6650 restraints for refining 2836 atoms. 6159 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1792 (Rfree = 0.000) for 2836 atoms. Found 11 (15 requested) and removed 17 (7 requested) atoms. Cycle 37: After refmac, R = 0.1720 (Rfree = 0.000) for 2816 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. Cycle 38: After refmac, R = 0.1682 (Rfree = 0.000) for 2810 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.1275 (Rfree = 0.000) for 2811 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.1241 (Rfree = 0.000) for 2799 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 2912 seeds are put forward NCS extension: 0 residues added, 2912 seeds are put forward Round 1: 131 peptides, 29 chains. Longest chain 8 peptides. Score 0.237 Round 2: 148 peptides, 28 chains. Longest chain 10 peptides. Score 0.329 Round 3: 150 peptides, 28 chains. Longest chain 10 peptides. Score 0.337 Round 4: 148 peptides, 25 chains. Longest chain 13 peptides. Score 0.382 Round 5: 143 peptides, 24 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 4 Chains 25, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6774 restraints for refining 2836 atoms. 6307 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1842 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 42: After refmac, R = 0.1717 (Rfree = 0.000) for 2829 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.1313 (Rfree = 0.000) for 2828 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1411 (Rfree = 0.000) for 2826 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1300 (Rfree = 0.000) for 2818 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2905 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2920 seeds are put forward Round 1: 126 peptides, 25 chains. Longest chain 13 peptides. Score 0.290 Round 2: 135 peptides, 24 chains. Longest chain 20 peptides. Score 0.347 Round 3: 144 peptides, 24 chains. Longest chain 26 peptides. Score 0.384 Round 4: 135 peptides, 22 chains. Longest chain 21 peptides. Score 0.383 Round 5: 136 peptides, 25 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 120, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4247 reflections ( 99.79 % complete ) and 6624 restraints for refining 2836 atoms. 6125 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1669 (Rfree = 0.000) for 2836 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 2821 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1685 (Rfree = 0.000) for 2807 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1565 (Rfree = 0.000) for 2797 atoms. Found 0 (15 requested) and removed 4 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:25:05 GMT 2018 Job finished. TimeTaking 57.13 Used memory is bytes: 8655656