Mon 24 Dec 01:07:31 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 2owp-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.6-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/2owp-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.6-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 ============================================================ Mon 24 Dec 01:07:36 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/2owp-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.6-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 299 and 0 Target number of residues in the AU: 299 Target solvent content: 0.6281 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-3.6-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.15 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: 29.899 3.600 Wilson plot Bfac: 64.92 5332 reflections ( 99.20 % complete ) and 0 restraints for refining 2298 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3531 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3286 (Rfree = 0.000) for 2298 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.49 Search for helices and strands: 0 residues in 0 chains, 2329 seeds are put forward NCS extension: 0 residues added, 2329 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 9 peptides. Score 0.301 Round 2: 177 peptides, 28 chains. Longest chain 14 peptides. Score 0.435 Round 3: 180 peptides, 26 chains. Longest chain 18 peptides. Score 0.476 Round 4: 190 peptides, 25 chains. Longest chain 20 peptides. Score 0.524 Round 5: 177 peptides, 21 chains. Longest chain 17 peptides. Score 0.541 Taking the results from Round 5 Chains 21, Residues 156, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3797 restraints for refining 1870 atoms. 3121 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3230 (Rfree = 0.000) for 1870 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.3103 (Rfree = 0.000) for 1852 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.3100 (Rfree = 0.000) for 1831 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.3097 (Rfree = 0.000) for 1812 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.3041 (Rfree = 0.000) for 1799 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 2.54 Search for helices and strands: 0 residues in 0 chains, 1863 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1887 seeds are put forward Round 1: 170 peptides, 25 chains. Longest chain 24 peptides. Score 0.457 Round 2: 188 peptides, 25 chains. Longest chain 19 peptides. Score 0.517 Round 3: 175 peptides, 23 chains. Longest chain 36 peptides. Score 0.505 Round 4: 181 peptides, 20 chains. Longest chain 30 peptides. Score 0.567 Round 5: 178 peptides, 20 chains. Longest chain 28 peptides. Score 0.558 Taking the results from Round 4 Chains 22, Residues 161, Estimated correctness of the model 1.3 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3587 restraints for refining 1870 atoms. 2785 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3369 (Rfree = 0.000) for 1870 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 7: After refmac, R = 0.3323 (Rfree = 0.000) for 1844 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.3293 (Rfree = 0.000) for 1829 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.3272 (Rfree = 0.000) for 1824 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.3212 (Rfree = 0.000) for 1811 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.37 Search for helices and strands: 0 residues in 0 chains, 1883 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 1897 seeds are put forward Round 1: 163 peptides, 26 chains. Longest chain 18 peptides. Score 0.416 Round 2: 179 peptides, 26 chains. Longest chain 15 peptides. Score 0.473 Round 3: 193 peptides, 26 chains. Longest chain 29 peptides. Score 0.519 Round 4: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.411 Round 5: 182 peptides, 25 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 3 Chains 26, Residues 167, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3859 restraints for refining 1871 atoms. 3187 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3508 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.3385 (Rfree = 0.000) for 1836 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.3328 (Rfree = 0.000) for 1818 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 14: After refmac, R = 0.3295 (Rfree = 0.000) for 1800 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.3253 (Rfree = 0.000) for 1790 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1846 seeds are put forward NCS extension: 51 residues added (1 deleted due to clashes), 1897 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 11 peptides. Score 0.342 Round 2: 174 peptides, 26 chains. Longest chain 17 peptides. Score 0.455 Round 3: 172 peptides, 24 chains. Longest chain 21 peptides. Score 0.479 Round 4: 179 peptides, 24 chains. Longest chain 30 peptides. Score 0.503 Round 5: 184 peptides, 27 chains. Longest chain 19 peptides. Score 0.475 Taking the results from Round 4 Chains 26, Residues 155, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3756 restraints for refining 1870 atoms. 3092 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3573 (Rfree = 0.000) for 1870 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 17: After refmac, R = 0.3384 (Rfree = 0.000) for 1839 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.3272 (Rfree = 0.000) for 1825 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.3184 (Rfree = 0.000) for 1822 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.3090 (Rfree = 0.000) for 1819 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1868 seeds are put forward NCS extension: 47 residues added (0 deleted due to clashes), 1915 seeds are put forward Round 1: 153 peptides, 28 chains. Longest chain 10 peptides. Score 0.344 Round 2: 181 peptides, 31 chains. Longest chain 20 peptides. Score 0.402 Round 3: 167 peptides, 25 chains. Longest chain 16 peptides. Score 0.446 Round 4: 185 peptides, 25 chains. Longest chain 23 peptides. Score 0.508 Round 5: 181 peptides, 24 chains. Longest chain 19 peptides. Score 0.509 Taking the results from Round 5 Chains 24, Residues 157, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3905 restraints for refining 1871 atoms. 3287 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3588 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.3492 (Rfree = 0.000) for 1845 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.3564 (Rfree = 0.000) for 1840 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 24: After refmac, R = 0.3429 (Rfree = 0.000) for 1825 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.3540 (Rfree = 0.000) for 1825 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.50 Search for helices and strands: 0 residues in 0 chains, 1884 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1902 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 15 peptides. Score 0.319 Round 2: 157 peptides, 26 chains. Longest chain 16 peptides. Score 0.394 Round 3: 165 peptides, 27 chains. Longest chain 14 peptides. Score 0.407 Round 4: 161 peptides, 22 chains. Longest chain 27 peptides. Score 0.473 Round 5: 160 peptides, 25 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 4 Chains 22, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 4182 restraints for refining 1871 atoms. 3648 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3766 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.3591 (Rfree = 0.000) for 1853 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.3549 (Rfree = 0.000) for 1838 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.3348 (Rfree = 0.000) for 1830 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.3318 (Rfree = 0.000) for 1822 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1887 seeds are put forward NCS extension: 46 residues added (2 deleted due to clashes), 1933 seeds are put forward Round 1: 125 peptides, 25 chains. Longest chain 8 peptides. Score 0.282 Round 2: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.367 Round 3: 148 peptides, 24 chains. Longest chain 12 peptides. Score 0.393 Round 4: 147 peptides, 25 chains. Longest chain 13 peptides. Score 0.372 Round 5: 169 peptides, 30 chains. Longest chain 11 peptides. Score 0.373 Taking the results from Round 3 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 4000 restraints for refining 1827 atoms. 3528 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3787 (Rfree = 0.000) for 1827 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 32: After refmac, R = 0.3861 (Rfree = 0.000) for 1805 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.3648 (Rfree = 0.000) for 1792 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.3354 (Rfree = 0.000) for 1780 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 35: After refmac, R = 0.3305 (Rfree = 0.000) for 1764 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.48 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 0 residues added, 1821 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.277 Round 2: 133 peptides, 22 chains. Longest chain 13 peptides. Score 0.369 Round 3: 133 peptides, 21 chains. Longest chain 14 peptides. Score 0.386 Round 4: 139 peptides, 22 chains. Longest chain 17 peptides. Score 0.392 Round 5: 143 peptides, 21 chains. Longest chain 19 peptides. Score 0.424 Taking the results from Round 5 Chains 23, Residues 122, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3817 restraints for refining 1871 atoms. 3297 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3968 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 37: After refmac, R = 0.3655 (Rfree = 0.000) for 1840 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 38: After refmac, R = 0.3640 (Rfree = 0.000) for 1820 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.3461 (Rfree = 0.000) for 1818 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.3305 (Rfree = 0.000) for 1813 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.51 Search for helices and strands: 0 residues in 0 chains, 1849 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 1891 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 8 peptides. Score 0.292 Round 2: 141 peptides, 24 chains. Longest chain 15 peptides. Score 0.366 Round 3: 148 peptides, 25 chains. Longest chain 19 peptides. Score 0.376 Round 4: 150 peptides, 27 chains. Longest chain 10 peptides. Score 0.350 Round 5: 144 peptides, 25 chains. Longest chain 13 peptides. Score 0.360 Taking the results from Round 3 Chains 25, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 4029 restraints for refining 1871 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3927 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 42: After refmac, R = 0.3840 (Rfree = 0.000) for 1842 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 43: After refmac, R = 0.3649 (Rfree = 0.000) for 1813 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.3791 (Rfree = 0.000) for 1808 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.3778 (Rfree = 0.000) for 1805 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 2.56 Search for helices and strands: 0 residues in 0 chains, 1852 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 1886 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.242 Round 2: 119 peptides, 23 chains. Longest chain 11 peptides. Score 0.293 Round 3: 127 peptides, 20 chains. Longest chain 14 peptides. Score 0.380 Round 4: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.346 Round 5: 132 peptides, 23 chains. Longest chain 14 peptides. Score 0.347 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 107, 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 2owp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5332 reflections ( 99.20 % complete ) and 3882 restraints for refining 1794 atoms. 3474 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.4039 (Rfree = 0.000) for 1794 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.4080 (Rfree = 0.000) for 1766 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3544 (Rfree = 0.000) for 1748 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3478 (Rfree = 0.000) for 1729 atoms. TimeTaking 31.42