null Mon 24 Dec 07:30:42 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.4-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 07:30:47 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.4-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 279 and 0 Target number of residues in the AU: 279 Target solvent content: 0.6391 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 70.81 5885 reflections ( 99.85 % complete ) and 0 restraints for refining 3512 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3200 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3022 (Rfree = 0.000) for 3512 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 0 residues added, 3627 seeds are put forward Round 1: 151 peptides, 34 chains. Longest chain 7 peptides. Score 0.235 Round 2: 197 peptides, 38 chains. Longest chain 10 peptides. Score 0.356 Round 3: 213 peptides, 34 chains. Longest chain 11 peptides. Score 0.478 Round 4: 209 peptides, 33 chains. Longest chain 13 peptides. Score 0.479 Round 5: 218 peptides, 33 chains. Longest chain 15 peptides. Score 0.509 Taking the results from Round 5 Chains 33, Residues 185, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6320 restraints for refining 2849 atoms. 5557 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2340 (Rfree = 0.000) for 2849 atoms. Found 14 (21 requested) and removed 20 (10 requested) atoms. Cycle 2: After refmac, R = 0.2216 (Rfree = 0.000) for 2807 atoms. Found 10 (21 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.2101 (Rfree = 0.000) for 2783 atoms. Found 4 (21 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.1836 (Rfree = 0.000) for 2757 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.1833 (Rfree = 0.000) for 2743 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 2925 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2950 seeds are put forward Round 1: 185 peptides, 34 chains. Longest chain 13 peptides. Score 0.375 Round 2: 219 peptides, 36 chains. Longest chain 17 peptides. Score 0.469 Round 3: 216 peptides, 33 chains. Longest chain 16 peptides. Score 0.503 Round 4: 220 peptides, 29 chains. Longest chain 16 peptides. Score 0.571 Round 5: 212 peptides, 30 chains. Longest chain 16 peptides. Score 0.533 Taking the results from Round 4 Chains 32, Residues 191, Estimated correctness of the model 18.9 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6213 restraints for refining 2827 atoms. 5395 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2174 (Rfree = 0.000) for 2827 atoms. Found 11 (21 requested) and removed 26 (10 requested) atoms. Cycle 7: After refmac, R = 0.2040 (Rfree = 0.000) for 2804 atoms. Found 6 (21 requested) and removed 14 (10 requested) atoms. Cycle 8: After refmac, R = 0.1981 (Rfree = 0.000) for 2787 atoms. Found 7 (21 requested) and removed 16 (10 requested) atoms. Cycle 9: After refmac, R = 0.1815 (Rfree = 0.000) for 2770 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. Cycle 10: After refmac, R = 0.1738 (Rfree = 0.000) for 2755 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2898 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2922 seeds are put forward Round 1: 171 peptides, 32 chains. Longest chain 11 peptides. Score 0.354 Round 2: 193 peptides, 30 chains. Longest chain 10 peptides. Score 0.469 Round 3: 214 peptides, 32 chains. Longest chain 20 peptides. Score 0.511 Round 4: 232 peptides, 31 chains. Longest chain 22 peptides. Score 0.581 Round 5: 218 peptides, 29 chains. Longest chain 17 peptides. Score 0.565 Taking the results from Round 4 Chains 31, Residues 201, Estimated correctness of the model 22.4 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6260 restraints for refining 2843 atoms. 5463 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2000 (Rfree = 0.000) for 2843 atoms. Found 13 (21 requested) and removed 24 (10 requested) atoms. Cycle 12: After refmac, R = 0.1850 (Rfree = 0.000) for 2826 atoms. Found 6 (21 requested) and removed 17 (10 requested) atoms. Cycle 13: After refmac, R = 0.1768 (Rfree = 0.000) for 2811 atoms. Found 1 (21 requested) and removed 16 (10 requested) atoms. Cycle 14: After refmac, R = 0.1741 (Rfree = 0.000) for 2794 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.1705 (Rfree = 0.000) for 2786 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2936 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2964 seeds are put forward Round 1: 185 peptides, 35 chains. Longest chain 9 peptides. Score 0.359 Round 2: 207 peptides, 32 chains. Longest chain 10 peptides. Score 0.487 Round 3: 216 peptides, 33 chains. Longest chain 16 peptides. Score 0.503 Round 4: 218 peptides, 32 chains. Longest chain 11 peptides. Score 0.524 Round 5: 205 peptides, 33 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 4 Chains 32, Residues 186, Estimated correctness of the model 1.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6586 restraints for refining 2850 atoms. 5874 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2070 (Rfree = 0.000) for 2850 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. Cycle 17: After refmac, R = 0.1927 (Rfree = 0.000) for 2837 atoms. Found 9 (21 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.1842 (Rfree = 0.000) for 2824 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.1955 (Rfree = 0.000) for 2809 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 20: After refmac, R = 0.2190 (Rfree = 0.000) for 2799 atoms. Found 13 (21 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 2936 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2947 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 12 peptides. Score 0.340 Round 2: 199 peptides, 32 chains. Longest chain 11 peptides. Score 0.459 Round 3: 198 peptides, 32 chains. Longest chain 17 peptides. Score 0.456 Round 4: 188 peptides, 32 chains. Longest chain 12 peptides. Score 0.419 Round 5: 196 peptides, 29 chains. Longest chain 14 peptides. Score 0.494 Taking the results from Round 5 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6455 restraints for refining 2852 atoms. 5787 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2031 (Rfree = 0.000) for 2852 atoms. Found 12 (21 requested) and removed 20 (10 requested) atoms. Cycle 22: After refmac, R = 0.1833 (Rfree = 0.000) for 2834 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 23: After refmac, R = 0.1851 (Rfree = 0.000) for 2829 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.1828 (Rfree = 0.000) for 2823 atoms. Found 6 (21 requested) and removed 14 (10 requested) atoms. Cycle 25: After refmac, R = 0.1653 (Rfree = 0.000) for 2812 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2981 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 10 peptides. Score 0.261 Round 2: 172 peptides, 29 chains. Longest chain 13 peptides. Score 0.408 Round 3: 173 peptides, 29 chains. Longest chain 11 peptides. Score 0.411 Round 4: 186 peptides, 32 chains. Longest chain 13 peptides. Score 0.412 Round 5: 197 peptides, 31 chains. Longest chain 11 peptides. Score 0.467 Taking the results from Round 5 Chains 31, Residues 166, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6257 restraints for refining 2850 atoms. 5553 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1973 (Rfree = 0.000) for 2850 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.1865 (Rfree = 0.000) for 2845 atoms. Found 14 (21 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.1898 (Rfree = 0.000) for 2838 atoms. Found 13 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1782 (Rfree = 0.000) for 2839 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1755 (Rfree = 0.000) for 2836 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 2977 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2989 seeds are put forward Round 1: 155 peptides, 34 chains. Longest chain 7 peptides. Score 0.252 Round 2: 166 peptides, 30 chains. Longest chain 11 peptides. Score 0.368 Round 3: 178 peptides, 31 chains. Longest chain 10 peptides. Score 0.398 Round 4: 175 peptides, 29 chains. Longest chain 11 peptides. Score 0.419 Round 5: 182 peptides, 31 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 4 Chains 29, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6645 restraints for refining 2852 atoms. 6090 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1843 (Rfree = 0.000) for 2852 atoms. Found 13 (21 requested) and removed 10 (10 requested) atoms. Cycle 32: After refmac, R = 0.1730 (Rfree = 0.000) for 2847 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1709 (Rfree = 0.000) for 2840 atoms. Found 9 (21 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.1615 (Rfree = 0.000) for 2837 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1543 (Rfree = 0.000) for 2827 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.35 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2984 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 8 peptides. Score 0.283 Round 2: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.366 Round 3: 159 peptides, 30 chains. Longest chain 9 peptides. Score 0.339 Round 4: 169 peptides, 29 chains. Longest chain 14 peptides. Score 0.396 Round 5: 157 peptides, 26 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 5 Chains 26, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6619 restraints for refining 2852 atoms. 6121 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1778 (Rfree = 0.000) for 2852 atoms. Found 14 (21 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.1606 (Rfree = 0.000) for 2851 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.1567 (Rfree = 0.000) for 2845 atoms. Found 10 (21 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1352 (Rfree = 0.000) for 2844 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1437 (Rfree = 0.000) for 2833 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2968 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2984 seeds are put forward Round 1: 143 peptides, 28 chains. Longest chain 12 peptides. Score 0.308 Round 2: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.387 Round 3: 165 peptides, 29 chains. Longest chain 11 peptides. Score 0.381 Round 4: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.387 Round 5: 150 peptides, 28 chains. Longest chain 11 peptides. Score 0.337 Taking the results from Round 4 Chains 27, Residues 131, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6331 restraints for refining 2850 atoms. 5766 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1742 (Rfree = 0.000) for 2850 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. Cycle 42: After refmac, R = 0.1660 (Rfree = 0.000) for 2843 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.1646 (Rfree = 0.000) for 2830 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1551 (Rfree = 0.000) for 2822 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1515 (Rfree = 0.000) for 2813 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2952 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 7 peptides. Score 0.251 Round 2: 157 peptides, 27 chains. Longest chain 12 peptides. Score 0.383 Round 3: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.363 Round 4: 162 peptides, 26 chains. Longest chain 11 peptides. Score 0.419 Round 5: 154 peptides, 27 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 136, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5885 reflections ( 99.85 % complete ) and 6463 restraints for refining 2852 atoms. 5926 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1770 (Rfree = 0.000) for 2852 atoms. Found 0 (21 requested) and removed 3 (10 requested) atoms. Cycle 47: After refmac, R = 0.1654 (Rfree = 0.000) for 2843 atoms. Found 0 (21 requested) and removed 3 (10 requested) atoms. Cycle 48: After refmac, R = 0.1688 (Rfree = 0.000) for 2835 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. Cycle 49: After refmac, R = 0.1668 (Rfree = 0.000) for 2834 atoms. Found 0 (21 requested) and removed 3 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:14:26 GMT 2018 Job finished. TimeTaking 43.73 Used memory is bytes: 7201968