Mon 24 Dec 01:08:19 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.4-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 01:08:24 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.4-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 308 and 0 Target number of residues in the AU: 308 Target solvent content: 0.6169 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 59.63 6289 reflections ( 99.16 % complete ) and 0 restraints for refining 2286 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3446 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3531 (Rfree = 0.000) for 2286 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.51 Search for helices and strands: 0 residues in 0 chains, 2330 seeds are put forward NCS extension: 0 residues added, 2330 seeds are put forward Round 1: 144 peptides, 27 chains. Longest chain 10 peptides. Score 0.326 Round 2: 192 peptides, 23 chains. Longest chain 20 peptides. Score 0.558 Round 3: 206 peptides, 27 chains. Longest chain 16 peptides. Score 0.546 Round 4: 195 peptides, 23 chains. Longest chain 31 peptides. Score 0.567 Round 5: 198 peptides, 25 chains. Longest chain 17 peptides. Score 0.549 Taking the results from Round 4 Chains 23, Residues 172, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3873 restraints for refining 1877 atoms. 3208 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3082 (Rfree = 0.000) for 1877 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. Cycle 2: After refmac, R = 0.3001 (Rfree = 0.000) for 1855 atoms. Found 8 (14 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.3074 (Rfree = 0.000) for 1839 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.2982 (Rfree = 0.000) for 1835 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.2802 (Rfree = 0.000) for 1826 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 2.60 Search for helices and strands: 0 residues in 0 chains, 1911 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 1945 seeds are put forward Round 1: 175 peptides, 26 chains. Longest chain 21 peptides. Score 0.459 Round 2: 194 peptides, 25 chains. Longest chain 21 peptides. Score 0.536 Round 3: 191 peptides, 22 chains. Longest chain 17 peptides. Score 0.569 Round 4: 200 peptides, 25 chains. Longest chain 18 peptides. Score 0.555 Round 5: 195 peptides, 24 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 3 Chains 23, Residues 169, Estimated correctness of the model 18.2 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3729 restraints for refining 1877 atoms. 3009 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3366 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 7: After refmac, R = 0.3352 (Rfree = 0.000) for 1861 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 8: After refmac, R = 0.3321 (Rfree = 0.000) for 1852 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.3289 (Rfree = 0.000) for 1840 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.2849 (Rfree = 0.000) for 1829 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.49 Search for helices and strands: 0 residues in 0 chains, 1908 seeds are put forward NCS extension: 0 residues added, 1908 seeds are put forward Round 1: 197 peptides, 31 chains. Longest chain 14 peptides. Score 0.459 Round 2: 194 peptides, 23 chains. Longest chain 18 peptides. Score 0.564 Round 3: 198 peptides, 24 chains. Longest chain 21 peptides. Score 0.563 Round 4: 182 peptides, 23 chains. Longest chain 23 peptides. Score 0.527 Round 5: 194 peptides, 21 chains. Longest chain 25 peptides. Score 0.591 Taking the results from Round 5 Chains 24, Residues 173, Estimated correctness of the model 25.7 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3579 restraints for refining 1877 atoms. 2807 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3338 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 12: After refmac, R = 0.3148 (Rfree = 0.000) for 1838 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.3055 (Rfree = 0.000) for 1825 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.3007 (Rfree = 0.000) for 1820 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.3082 (Rfree = 0.000) for 1805 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 2.51 Search for helices and strands: 0 residues in 0 chains, 1880 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 1916 seeds are put forward Round 1: 182 peptides, 26 chains. Longest chain 21 peptides. Score 0.483 Round 2: 203 peptides, 27 chains. Longest chain 21 peptides. Score 0.536 Round 3: 199 peptides, 23 chains. Longest chain 29 peptides. Score 0.579 Round 4: 193 peptides, 22 chains. Longest chain 26 peptides. Score 0.575 Round 5: 195 peptides, 24 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 3 Chains 25, Residues 176, Estimated correctness of the model 21.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3849 restraints for refining 1877 atoms. 3139 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3217 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 46 (7 requested) atoms. Cycle 17: After refmac, R = 0.3136 (Rfree = 0.000) for 1824 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.3027 (Rfree = 0.000) for 1820 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.2950 (Rfree = 0.000) for 1812 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2869 (Rfree = 0.000) for 1811 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 1912 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 1932 seeds are put forward Round 1: 177 peptides, 27 chains. Longest chain 21 peptides. Score 0.450 Round 2: 180 peptides, 24 chains. Longest chain 27 peptides. Score 0.506 Round 3: 186 peptides, 22 chains. Longest chain 36 peptides. Score 0.554 Round 4: 183 peptides, 22 chains. Longest chain 26 peptides. Score 0.545 Round 5: 197 peptides, 25 chains. Longest chain 26 peptides. Score 0.546 Taking the results from Round 3 Chains 22, Residues 164, Estimated correctness of the model 13.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3960 restraints for refining 1877 atoms. 3326 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3593 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.3367 (Rfree = 0.000) for 1858 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.3363 (Rfree = 0.000) for 1845 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 24: After refmac, R = 0.3256 (Rfree = 0.000) for 1841 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.3239 (Rfree = 0.000) for 1834 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.44 Search for helices and strands: 0 residues in 0 chains, 1918 seeds are put forward NCS extension: 50 residues added (1 deleted due to clashes), 1968 seeds are put forward Round 1: 153 peptides, 23 chains. Longest chain 17 peptides. Score 0.428 Round 2: 162 peptides, 19 chains. Longest chain 15 peptides. Score 0.522 Round 3: 173 peptides, 23 chains. Longest chain 22 peptides. Score 0.498 Round 4: 169 peptides, 22 chains. Longest chain 18 peptides. Score 0.500 Round 5: 180 peptides, 24 chains. Longest chain 27 peptides. Score 0.506 Taking the results from Round 2 Chains 21, Residues 143, Estimated correctness of the model 1.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 4007 restraints for refining 1877 atoms. 3425 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3616 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.3590 (Rfree = 0.000) for 1865 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.3495 (Rfree = 0.000) for 1854 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.3498 (Rfree = 0.000) for 1846 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 30: After refmac, R = 0.3111 (Rfree = 0.000) for 1840 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.47 Search for helices and strands: 0 residues in 0 chains, 1893 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1909 seeds are put forward Round 1: 157 peptides, 27 chains. Longest chain 15 peptides. Score 0.377 Round 2: 186 peptides, 24 chains. Longest chain 24 peptides. Score 0.525 Round 3: 171 peptides, 27 chains. Longest chain 17 peptides. Score 0.429 Round 4: 185 peptides, 24 chains. Longest chain 28 peptides. Score 0.522 Round 5: 185 peptides, 25 chains. Longest chain 27 peptides. Score 0.508 Taking the results from Round 2 Chains 24, Residues 162, Estimated correctness of the model 2.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3883 restraints for refining 1877 atoms. 3259 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3529 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.3342 (Rfree = 0.000) for 1868 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 33: After refmac, R = 0.3272 (Rfree = 0.000) for 1851 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.3159 (Rfree = 0.000) for 1843 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.2857 (Rfree = 0.000) for 1840 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 2.54 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 1951 seeds are put forward Round 1: 155 peptides, 27 chains. Longest chain 17 peptides. Score 0.369 Round 2: 174 peptides, 26 chains. Longest chain 17 peptides. Score 0.455 Round 3: 169 peptides, 26 chains. Longest chain 22 peptides. Score 0.438 Round 4: 182 peptides, 24 chains. Longest chain 18 peptides. Score 0.513 Round 5: 169 peptides, 23 chains. Longest chain 23 peptides. Score 0.485 Taking the results from Round 4 Chains 24, Residues 158, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3761 restraints for refining 1877 atoms. 3076 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3394 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.3363 (Rfree = 0.000) for 1857 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.3321 (Rfree = 0.000) for 1856 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.3035 (Rfree = 0.000) for 1851 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.2997 (Rfree = 0.000) for 1847 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 1922 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 1947 seeds are put forward Round 1: 150 peptides, 27 chains. Longest chain 18 peptides. Score 0.350 Round 2: 166 peptides, 26 chains. Longest chain 19 peptides. Score 0.427 Round 3: 171 peptides, 25 chains. Longest chain 19 peptides. Score 0.460 Round 4: 162 peptides, 25 chains. Longest chain 19 peptides. Score 0.428 Round 5: 172 peptides, 25 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 5 Chains 25, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 4057 restraints for refining 1876 atoms. 3494 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3595 (Rfree = 0.000) for 1876 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 42: After refmac, R = 0.3503 (Rfree = 0.000) for 1864 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.3407 (Rfree = 0.000) for 1853 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.3086 (Rfree = 0.000) for 1846 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.3248 (Rfree = 0.000) for 1842 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 2.66 Search for helices and strands: 0 residues in 0 chains, 1925 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1951 seeds are put forward Round 1: 144 peptides, 29 chains. Longest chain 8 peptides. Score 0.291 Round 2: 163 peptides, 25 chains. Longest chain 17 peptides. Score 0.432 Round 3: 172 peptides, 25 chains. Longest chain 27 peptides. Score 0.464 Round 4: 171 peptides, 22 chains. Longest chain 18 peptides. Score 0.507 Round 5: 173 peptides, 21 chains. Longest chain 27 peptides. Score 0.528 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 152, Estimated correctness of the model 3.4 % 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. 6289 reflections ( 99.16 % complete ) and 3956 restraints for refining 1877 atoms. 3369 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3414 (Rfree = 0.000) for 1877 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.3381 (Rfree = 0.000) for 1857 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.3060 (Rfree = 0.000) for 1844 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3288 (Rfree = 0.000) for 1832 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 35.27