Mon 24 Dec 07:30:55 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 2owp-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2owp-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2owp-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-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/2owp-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-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 07:30:59 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/2owp-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-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 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-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.4-parrot-noncs.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 2299 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3724 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3676 (Rfree = 0.000) for 2299 atoms. Found 11 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 2.89 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward NCS extension: 0 residues added, 2336 seeds are put forward Round 1: 107 peptides, 21 chains. Longest chain 9 peptides. Score 0.278 Round 2: 157 peptides, 25 chains. Longest chain 12 peptides. Score 0.410 Round 3: 171 peptides, 25 chains. Longest chain 18 peptides. Score 0.460 Round 4: 161 peptides, 25 chains. Longest chain 12 peptides. Score 0.425 Round 5: 182 peptides, 26 chains. Longest chain 18 peptides. Score 0.483 Taking the results from Round 5 Chains 28, Residues 156, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3855 restraints for refining 1875 atoms. 3194 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3676 (Rfree = 0.000) for 1875 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.3623 (Rfree = 0.000) for 1852 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.3638 (Rfree = 0.000) for 1831 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 4: After refmac, R = 0.3287 (Rfree = 0.000) for 1813 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.3182 (Rfree = 0.000) for 1806 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 1879 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1891 seeds are put forward Round 1: 165 peptides, 27 chains. Longest chain 14 peptides. Score 0.407 Round 2: 181 peptides, 27 chains. Longest chain 23 peptides. Score 0.464 Round 3: 188 peptides, 29 chains. Longest chain 17 peptides. Score 0.458 Round 4: 171 peptides, 25 chains. Longest chain 16 peptides. Score 0.460 Round 5: 172 peptides, 25 chains. Longest chain 20 peptides. Score 0.464 Taking the results from Round 5 Chains 25, Residues 147, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3984 restraints for refining 1877 atoms. 3367 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3550 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 7: After refmac, R = 0.3619 (Rfree = 0.000) for 1850 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.3500 (Rfree = 0.000) for 1838 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 9: After refmac, R = 0.3542 (Rfree = 0.000) for 1829 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 10: After refmac, R = 0.3415 (Rfree = 0.000) for 1814 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.47 Search for helices and strands: 0 residues in 0 chains, 1901 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1927 seeds are put forward Round 1: 172 peptides, 29 chains. Longest chain 17 peptides. Score 0.401 Round 2: 179 peptides, 28 chains. Longest chain 20 peptides. Score 0.442 Round 3: 173 peptides, 28 chains. Longest chain 14 peptides. Score 0.420 Round 4: 180 peptides, 28 chains. Longest chain 12 peptides. Score 0.445 Round 5: 183 peptides, 27 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 5 Chains 27, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3922 restraints for refining 1877 atoms. 3325 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3678 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 12: After refmac, R = 0.3519 (Rfree = 0.000) for 1842 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 13: After refmac, R = 0.3206 (Rfree = 0.000) for 1826 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.3434 (Rfree = 0.000) for 1819 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.3355 (Rfree = 0.000) for 1818 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.60 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 1923 seeds are put forward Round 1: 149 peptides, 27 chains. Longest chain 11 peptides. Score 0.346 Round 2: 175 peptides, 26 chains. Longest chain 16 peptides. Score 0.459 Round 3: 170 peptides, 24 chains. Longest chain 16 peptides. Score 0.473 Round 4: 172 peptides, 25 chains. Longest chain 17 peptides. Score 0.464 Round 5: 169 peptides, 24 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 3 Chains 25, Residues 146, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3814 restraints for refining 1877 atoms. 3207 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3642 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 17: After refmac, R = 0.3338 (Rfree = 0.000) for 1839 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.3225 (Rfree = 0.000) for 1829 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.3123 (Rfree = 0.000) for 1818 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.3107 (Rfree = 0.000) for 1813 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 1869 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1886 seeds are put forward Round 1: 154 peptides, 29 chains. Longest chain 10 peptides. Score 0.331 Round 2: 169 peptides, 22 chains. Longest chain 23 peptides. Score 0.500 Round 3: 170 peptides, 21 chains. Longest chain 15 peptides. Score 0.518 Round 4: 168 peptides, 23 chains. Longest chain 14 peptides. Score 0.481 Round 5: 158 peptides, 21 chains. Longest chain 17 peptides. Score 0.478 Taking the results from Round 3 Chains 21, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 4019 restraints for refining 1877 atoms. 3444 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3440 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.3439 (Rfree = 0.000) for 1866 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.3522 (Rfree = 0.000) for 1853 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 24: After refmac, R = 0.3382 (Rfree = 0.000) for 1839 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.3456 (Rfree = 0.000) for 1835 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 1912 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1926 seeds are put forward Round 1: 158 peptides, 31 chains. Longest chain 11 peptides. Score 0.313 Round 2: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.418 Round 3: 165 peptides, 24 chains. Longest chain 15 peptides. Score 0.455 Round 4: 162 peptides, 22 chains. Longest chain 15 peptides. Score 0.476 Round 5: 168 peptides, 25 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 4 Chains 24, Residues 140, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3961 restraints for refining 1877 atoms. 3388 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3699 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 27: After refmac, R = 0.3580 (Rfree = 0.000) for 1851 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 28: After refmac, R = 0.3482 (Rfree = 0.000) for 1840 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 29: After refmac, R = 0.3114 (Rfree = 0.000) for 1827 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.3051 (Rfree = 0.000) for 1826 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.45 Search for helices and strands: 0 residues in 0 chains, 1886 seeds are put forward NCS extension: 0 residues added, 1886 seeds are put forward Round 1: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.324 Round 2: 140 peptides, 23 chains. Longest chain 16 peptides. Score 0.379 Round 3: 158 peptides, 24 chains. Longest chain 15 peptides. Score 0.430 Round 4: 174 peptides, 28 chains. Longest chain 17 peptides. Score 0.424 Round 5: 170 peptides, 24 chains. Longest chain 26 peptides. Score 0.473 Taking the results from Round 5 Chains 24, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 4038 restraints for refining 1877 atoms. 3478 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3573 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.3412 (Rfree = 0.000) for 1860 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.3459 (Rfree = 0.000) for 1854 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 34: After refmac, R = 0.3202 (Rfree = 0.000) for 1845 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.3418 (Rfree = 0.000) for 1839 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 2.72 Search for helices and strands: 0 residues in 0 chains, 1909 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1930 seeds are put forward Round 1: 151 peptides, 28 chains. Longest chain 11 peptides. Score 0.337 Round 2: 144 peptides, 25 chains. Longest chain 11 peptides. Score 0.360 Round 3: 146 peptides, 22 chains. Longest chain 12 peptides. Score 0.419 Round 4: 161 peptides, 24 chains. Longest chain 19 peptides. Score 0.441 Round 5: 152 peptides, 23 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 4 Chains 24, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 4028 restraints for refining 1877 atoms. 3504 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3717 (Rfree = 0.000) for 1877 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.3665 (Rfree = 0.000) for 1852 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 38: After refmac, R = 0.3682 (Rfree = 0.000) for 1841 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.3625 (Rfree = 0.000) for 1831 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.3655 (Rfree = 0.000) for 1822 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 1891 seeds are put forward NCS extension: 0 residues added, 1891 seeds are put forward Round 1: 141 peptides, 27 chains. Longest chain 9 peptides. Score 0.313 Round 2: 153 peptides, 27 chains. Longest chain 9 peptides. Score 0.361 Round 3: 165 peptides, 27 chains. Longest chain 12 peptides. Score 0.407 Round 4: 150 peptides, 26 chains. Longest chain 13 peptides. Score 0.367 Round 5: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 3 Chains 27, Residues 138, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6289 reflections ( 99.16 % complete ) and 3956 restraints for refining 1875 atoms. 3407 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3744 (Rfree = 0.000) for 1875 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 42: After refmac, R = 0.3426 (Rfree = 0.000) for 1847 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.3575 (Rfree = 0.000) for 1839 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 44: After refmac, R = 0.3292 (Rfree = 0.000) for 1831 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.3526 (Rfree = 0.000) for 1834 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.54 Search for helices and strands: 0 residues in 0 chains, 1883 seeds are put forward NCS extension: 0 residues added, 1883 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 10 peptides. Score 0.297 Round 2: 156 peptides, 26 chains. Longest chain 12 peptides. Score 0.390 Round 3: 160 peptides, 27 chains. Longest chain 9 peptides. Score 0.388 Round 4: 160 peptides, 26 chains. Longest chain 17 peptides. Score 0.405 Round 5: 152 peptides, 26 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 134, 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. 6289 reflections ( 99.16 % complete ) and 4063 restraints for refining 1877 atoms. 3553 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3746 (Rfree = 0.000) for 1877 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.3696 (Rfree = 0.000) for 1857 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.3302 (Rfree = 0.000) for 1840 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.3342 (Rfree = 0.000) for 1830 atoms. TimeTaking 30.67