null Sun 23 Dec 23:47:59 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 2oyo-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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/2oyo-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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 23:48:04 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/2oyo-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.8-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 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-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.8-parrot-mrncs.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 = 0.3275 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2958 (Rfree = 0.000) for 3457 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 3549 seeds are put forward NCS extension: 0 residues added, 3549 seeds are put forward Round 1: 153 peptides, 28 chains. Longest chain 11 peptides. Score 0.350 Round 2: 193 peptides, 29 chains. Longest chain 16 peptides. Score 0.484 Round 3: 196 peptides, 29 chains. Longest chain 13 peptides. Score 0.494 Round 4: 191 peptides, 26 chains. Longest chain 17 peptides. Score 0.522 Round 5: 200 peptides, 29 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 4 Chains 27, Residues 165, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6548 restraints for refining 2830 atoms. 5824 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2214 (Rfree = 0.000) for 2830 atoms. Found 9 (15 requested) and removed 18 (7 requested) atoms. Cycle 2: After refmac, R = 0.2078 (Rfree = 0.000) for 2784 atoms. Found 9 (15 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.2005 (Rfree = 0.000) for 2756 atoms. Found 4 (15 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.1948 (Rfree = 0.000) for 2728 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.1983 (Rfree = 0.000) for 2717 atoms. Found 8 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2848 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 2865 seeds are put forward Round 1: 175 peptides, 33 chains. Longest chain 11 peptides. Score 0.353 Round 2: 207 peptides, 31 chains. Longest chain 13 peptides. Score 0.502 Round 3: 215 peptides, 29 chains. Longest chain 15 peptides. Score 0.556 Round 4: 210 peptides, 24 chains. Longest chain 18 peptides. Score 0.609 Round 5: 195 peptides, 26 chains. Longest chain 18 peptides. Score 0.535 Taking the results from Round 4 Chains 26, Residues 186, Estimated correctness of the model 3.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6105 restraints for refining 2835 atoms. 5276 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2150 (Rfree = 0.000) for 2835 atoms. Found 7 (15 requested) and removed 25 (7 requested) atoms. Cycle 7: After refmac, R = 0.2214 (Rfree = 0.000) for 2792 atoms. Found 5 (15 requested) and removed 29 (7 requested) atoms. Cycle 8: After refmac, R = 0.1807 (Rfree = 0.000) for 2750 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.1787 (Rfree = 0.000) for 2728 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.1740 (Rfree = 0.000) for 2717 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2837 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2852 seeds are put forward Round 1: 161 peptides, 27 chains. Longest chain 11 peptides. Score 0.399 Round 2: 174 peptides, 26 chains. Longest chain 12 peptides. Score 0.464 Round 3: 189 peptides, 27 chains. Longest chain 13 peptides. Score 0.501 Round 4: 185 peptides, 24 chains. Longest chain 13 peptides. Score 0.532 Round 5: 174 peptides, 26 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 4 Chains 25, Residues 161, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6475 restraints for refining 2835 atoms. 5819 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2031 (Rfree = 0.000) for 2835 atoms. Found 2 (15 requested) and removed 24 (7 requested) atoms. Cycle 12: After refmac, R = 0.2040 (Rfree = 0.000) for 2790 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.1905 (Rfree = 0.000) for 2774 atoms. Found 9 (15 requested) and removed 16 (7 requested) atoms. Cycle 14: After refmac, R = 0.1920 (Rfree = 0.000) for 2759 atoms. Found 13 (15 requested) and removed 15 (7 requested) atoms. Cycle 15: After refmac, R = 0.1783 (Rfree = 0.000) for 2742 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 2892 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2905 seeds are put forward Round 1: 149 peptides, 30 chains. Longest chain 9 peptides. Score 0.298 Round 2: 165 peptides, 26 chains. Longest chain 12 peptides. Score 0.431 Round 3: 173 peptides, 26 chains. Longest chain 13 peptides. Score 0.460 Round 4: 166 peptides, 25 chains. Longest chain 13 peptides. Score 0.451 Round 5: 173 peptides, 28 chains. Longest chain 14 peptides. Score 0.428 Taking the results from Round 3 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6205 restraints for refining 2814 atoms. 5569 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1926 (Rfree = 0.000) for 2814 atoms. Found 7 (15 requested) and removed 17 (7 requested) atoms. Cycle 17: After refmac, R = 0.2064 (Rfree = 0.000) for 2793 atoms. Found 13 (15 requested) and removed 20 (7 requested) atoms. Cycle 18: After refmac, R = 0.1792 (Rfree = 0.000) for 2775 atoms. Found 11 (15 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.1929 (Rfree = 0.000) for 2770 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 20: After refmac, R = 0.1681 (Rfree = 0.000) for 2756 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 2861 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2877 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 9 peptides. Score 0.288 Round 2: 162 peptides, 30 chains. Longest chain 12 peptides. Score 0.352 Round 3: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.437 Round 4: 173 peptides, 27 chains. Longest chain 15 peptides. Score 0.444 Round 5: 167 peptides, 27 chains. Longest chain 10 peptides. Score 0.422 Taking the results from Round 4 Chains 27, Residues 146, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6524 restraints for refining 2835 atoms. 5923 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2128 (Rfree = 0.000) for 2835 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.1919 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.1830 (Rfree = 0.000) for 2818 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.1569 (Rfree = 0.000) for 2811 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.1676 (Rfree = 0.000) for 2806 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2963 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 10 peptides. Score 0.285 Round 2: 158 peptides, 29 chains. Longest chain 13 peptides. Score 0.353 Round 3: 158 peptides, 27 chains. Longest chain 13 peptides. Score 0.387 Round 4: 163 peptides, 28 chains. Longest chain 12 peptides. Score 0.390 Round 5: 159 peptides, 27 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 27, Residues 132, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6656 restraints for refining 2835 atoms. 6122 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1956 (Rfree = 0.000) for 2835 atoms. Found 14 (15 requested) and removed 13 (7 requested) atoms. Cycle 27: After refmac, R = 0.1924 (Rfree = 0.000) for 2830 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 28: After refmac, R = 0.1790 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.1689 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 30: After refmac, R = 0.1612 (Rfree = 0.000) for 2820 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2945 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 8 peptides. Score 0.274 Round 2: 143 peptides, 28 chains. Longest chain 11 peptides. Score 0.308 Round 3: 150 peptides, 30 chains. Longest chain 8 peptides. Score 0.302 Round 4: 153 peptides, 28 chains. Longest chain 10 peptides. Score 0.350 Round 5: 155 peptides, 25 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Chains 25, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6755 restraints for refining 2835 atoms. 6260 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1781 (Rfree = 0.000) for 2835 atoms. Found 9 (15 requested) and removed 16 (7 requested) atoms. Cycle 32: After refmac, R = 0.1766 (Rfree = 0.000) for 2820 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 33: After refmac, R = 0.1555 (Rfree = 0.000) for 2816 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1621 (Rfree = 0.000) for 2816 atoms. Found 11 (15 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1185 (Rfree = 0.000) for 2809 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2944 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 7 peptides. Score 0.225 Round 2: 139 peptides, 28 chains. Longest chain 12 peptides. Score 0.291 Round 3: 148 peptides, 28 chains. Longest chain 9 peptides. Score 0.329 Round 4: 135 peptides, 26 chains. Longest chain 10 peptides. Score 0.310 Round 5: 137 peptides, 26 chains. Longest chain 11 peptides. Score 0.319 Taking the results from Round 3 Chains 28, Residues 120, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6707 restraints for refining 2836 atoms. 6230 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1645 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.1611 (Rfree = 0.000) for 2835 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.1662 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.1219 (Rfree = 0.000) for 2835 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1298 (Rfree = 0.000) for 2830 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2926 seeds are put forward NCS extension: 0 residues added, 2926 seeds are put forward Round 1: 108 peptides, 25 chains. Longest chain 6 peptides. Score 0.206 Round 2: 124 peptides, 24 chains. Longest chain 9 peptides. Score 0.300 Round 3: 134 peptides, 25 chains. Longest chain 13 peptides. Score 0.324 Round 4: 138 peptides, 24 chains. Longest chain 14 peptides. Score 0.359 Round 5: 128 peptides, 21 chains. Longest chain 12 peptides. Score 0.372 Taking the results from Round 5 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4247 reflections ( 99.79 % complete ) and 6867 restraints for refining 2835 atoms. 6460 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1748 (Rfree = 0.000) for 2835 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 42: After refmac, R = 0.1669 (Rfree = 0.000) for 2828 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1646 (Rfree = 0.000) for 2829 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1429 (Rfree = 0.000) for 2830 atoms. Found 10 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1470 (Rfree = 0.000) for 2828 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2967 seeds are put forward Round 1: 114 peptides, 26 chains. Longest chain 8 peptides. Score 0.216 Round 2: 130 peptides, 26 chains. Longest chain 10 peptides. Score 0.289 Round 3: 126 peptides, 25 chains. Longest chain 10 peptides. Score 0.290 Round 4: 135 peptides, 25 chains. Longest chain 10 peptides. Score 0.329 Round 5: 120 peptides, 24 chains. Longest chain 10 peptides. Score 0.282 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 110, 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 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4247 reflections ( 99.79 % complete ) and 6803 restraints for refining 2836 atoms. 6388 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1801 (Rfree = 0.000) for 2836 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1682 (Rfree = 0.000) for 2816 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1682 (Rfree = 0.000) for 2806 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1294 (Rfree = 0.000) for 2796 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:24:31 GMT 2018 Job finished. TimeTaking 36.52 Used memory is bytes: 19207352