null Mon 24 Dec 00:54:50 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 2i5i-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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/2i5i-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 00:54:55 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/2i5i-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 371 and 0 Target number of residues in the AU: 371 Target solvent content: 0.6430 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4208 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: 29.446 3.401 Wilson plot Bfac: 73.53 7444 reflections ( 99.32 % complete ) and 0 restraints for refining 4665 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3366 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3204 (Rfree = 0.000) for 4665 atoms. Found 35 (35 requested) and removed 82 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 4668 seeds are put forward NCS extension: 0 residues added, 4668 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 10 peptides. Score 0.246 Round 2: 179 peptides, 33 chains. Longest chain 10 peptides. Score 0.329 Round 3: 204 peptides, 38 chains. Longest chain 10 peptides. Score 0.340 Round 4: 216 peptides, 37 chains. Longest chain 10 peptides. Score 0.389 Round 5: 224 peptides, 38 chains. Longest chain 13 peptides. Score 0.399 Taking the results from Round 5 Chains 40, Residues 186, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8697 restraints for refining 3826 atoms. 7928 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2531 (Rfree = 0.000) for 3826 atoms. Found 21 (28 requested) and removed 37 (14 requested) atoms. Cycle 2: After refmac, R = 0.2311 (Rfree = 0.000) for 3764 atoms. Found 21 (28 requested) and removed 25 (14 requested) atoms. Cycle 3: After refmac, R = 0.2177 (Rfree = 0.000) for 3735 atoms. Found 14 (28 requested) and removed 19 (14 requested) atoms. Cycle 4: After refmac, R = 0.2056 (Rfree = 0.000) for 3715 atoms. Found 13 (28 requested) and removed 25 (14 requested) atoms. Cycle 5: After refmac, R = 0.1792 (Rfree = 0.000) for 3691 atoms. Found 8 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3798 seeds are put forward Round 1: 221 peptides, 47 chains. Longest chain 9 peptides. Score 0.275 Round 2: 232 peptides, 44 chains. Longest chain 9 peptides. Score 0.347 Round 3: 258 peptides, 46 chains. Longest chain 10 peptides. Score 0.398 Round 4: 257 peptides, 45 chains. Longest chain 17 peptides. Score 0.407 Round 5: 258 peptides, 45 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 5 Chains 45, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8726 restraints for refining 3815 atoms. 7919 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2123 (Rfree = 0.000) for 3815 atoms. Found 20 (28 requested) and removed 29 (14 requested) atoms. Cycle 7: After refmac, R = 0.2000 (Rfree = 0.000) for 3784 atoms. Found 19 (28 requested) and removed 23 (14 requested) atoms. Cycle 8: After refmac, R = 0.1903 (Rfree = 0.000) for 3772 atoms. Found 10 (28 requested) and removed 28 (14 requested) atoms. Cycle 9: After refmac, R = 0.1867 (Rfree = 0.000) for 3747 atoms. Found 18 (28 requested) and removed 17 (14 requested) atoms. Cycle 10: After refmac, R = 0.1810 (Rfree = 0.000) for 3738 atoms. Found 10 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 3826 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3844 seeds are put forward Round 1: 206 peptides, 42 chains. Longest chain 8 peptides. Score 0.294 Round 2: 242 peptides, 43 chains. Longest chain 11 peptides. Score 0.389 Round 3: 253 peptides, 46 chains. Longest chain 11 peptides. Score 0.384 Round 4: 260 peptides, 45 chains. Longest chain 13 peptides. Score 0.416 Round 5: 262 peptides, 45 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 5 Chains 45, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8626 restraints for refining 3825 atoms. 7803 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2040 (Rfree = 0.000) for 3825 atoms. Found 11 (28 requested) and removed 21 (14 requested) atoms. Cycle 12: After refmac, R = 0.1893 (Rfree = 0.000) for 3795 atoms. Found 13 (28 requested) and removed 23 (14 requested) atoms. Cycle 13: After refmac, R = 0.1847 (Rfree = 0.000) for 3777 atoms. Found 9 (28 requested) and removed 20 (14 requested) atoms. Cycle 14: After refmac, R = 0.1731 (Rfree = 0.000) for 3759 atoms. Found 6 (28 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.1734 (Rfree = 0.000) for 3738 atoms. Found 13 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 3837 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3859 seeds are put forward Round 1: 212 peptides, 44 chains. Longest chain 10 peptides. Score 0.286 Round 2: 239 peptides, 43 chains. Longest chain 10 peptides. Score 0.381 Round 3: 239 peptides, 43 chains. Longest chain 12 peptides. Score 0.381 Round 4: 234 peptides, 40 chains. Longest chain 10 peptides. Score 0.403 Round 5: 247 peptides, 40 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 5 Chains 40, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8745 restraints for refining 3825 atoms. 7957 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2096 (Rfree = 0.000) for 3825 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 17: After refmac, R = 0.1981 (Rfree = 0.000) for 3811 atoms. Found 17 (28 requested) and removed 18 (14 requested) atoms. Cycle 18: After refmac, R = 0.1873 (Rfree = 0.000) for 3804 atoms. Found 14 (28 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.1799 (Rfree = 0.000) for 3787 atoms. Found 12 (28 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.1539 (Rfree = 0.000) for 3774 atoms. Found 6 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 3842 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3858 seeds are put forward Round 1: 224 peptides, 48 chains. Longest chain 8 peptides. Score 0.272 Round 2: 264 peptides, 46 chains. Longest chain 13 peptides. Score 0.415 Round 3: 270 peptides, 48 chains. Longest chain 15 peptides. Score 0.408 Round 4: 279 peptides, 49 chains. Longest chain 11 peptides. Score 0.421 Round 5: 271 peptides, 46 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 5 Chains 46, Residues 225, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8430 restraints for refining 3824 atoms. 7544 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2150 (Rfree = 0.000) for 3824 atoms. Found 24 (28 requested) and removed 27 (14 requested) atoms. Cycle 22: After refmac, R = 0.2000 (Rfree = 0.000) for 3803 atoms. Found 28 (28 requested) and removed 17 (14 requested) atoms. Cycle 23: After refmac, R = 0.1893 (Rfree = 0.000) for 3803 atoms. Found 16 (28 requested) and removed 22 (14 requested) atoms. Cycle 24: After refmac, R = 0.1809 (Rfree = 0.000) for 3792 atoms. Found 27 (28 requested) and removed 19 (14 requested) atoms. Cycle 25: After refmac, R = 0.1743 (Rfree = 0.000) for 3794 atoms. Found 18 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3876 seeds are put forward Round 1: 209 peptides, 46 chains. Longest chain 8 peptides. Score 0.250 Round 2: 231 peptides, 44 chains. Longest chain 9 peptides. Score 0.345 Round 3: 237 peptides, 42 chains. Longest chain 10 peptides. Score 0.387 Round 4: 249 peptides, 40 chains. Longest chain 17 peptides. Score 0.445 Round 5: 228 peptides, 39 chains. Longest chain 10 peptides. Score 0.398 Taking the results from Round 4 Chains 40, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8552 restraints for refining 3825 atoms. 7756 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1904 (Rfree = 0.000) for 3825 atoms. Found 26 (28 requested) and removed 20 (14 requested) atoms. Cycle 27: After refmac, R = 0.1794 (Rfree = 0.000) for 3820 atoms. Found 23 (28 requested) and removed 18 (14 requested) atoms. Cycle 28: After refmac, R = 0.1755 (Rfree = 0.000) for 3820 atoms. Found 16 (28 requested) and removed 18 (14 requested) atoms. Cycle 29: After refmac, R = 0.1716 (Rfree = 0.000) for 3813 atoms. Found 19 (28 requested) and removed 22 (14 requested) atoms. Cycle 30: After refmac, R = 0.1625 (Rfree = 0.000) for 3803 atoms. Found 17 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3891 seeds are put forward Round 1: 198 peptides, 44 chains. Longest chain 6 peptides. Score 0.241 Round 2: 229 peptides, 43 chains. Longest chain 11 peptides. Score 0.351 Round 3: 244 peptides, 43 chains. Longest chain 9 peptides. Score 0.395 Round 4: 237 peptides, 42 chains. Longest chain 10 peptides. Score 0.387 Round 5: 250 peptides, 45 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 3 Chains 43, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8682 restraints for refining 3824 atoms. 7921 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1818 (Rfree = 0.000) for 3824 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 32: After refmac, R = 0.1671 (Rfree = 0.000) for 3820 atoms. Found 17 (28 requested) and removed 16 (14 requested) atoms. Cycle 33: After refmac, R = 0.1670 (Rfree = 0.000) for 3816 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 34: After refmac, R = 0.1608 (Rfree = 0.000) for 3819 atoms. Found 14 (28 requested) and removed 20 (14 requested) atoms. Cycle 35: After refmac, R = 0.1596 (Rfree = 0.000) for 3809 atoms. Found 20 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 0 residues added, 3892 seeds are put forward Round 1: 159 peptides, 33 chains. Longest chain 9 peptides. Score 0.264 Round 2: 193 peptides, 35 chains. Longest chain 13 peptides. Score 0.346 Round 3: 188 peptides, 37 chains. Longest chain 9 peptides. Score 0.303 Round 4: 181 peptides, 33 chains. Longest chain 10 peptides. Score 0.335 Round 5: 198 peptides, 36 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 5 Chains 36, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8865 restraints for refining 3826 atoms. 8253 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1750 (Rfree = 0.000) for 3826 atoms. Found 27 (28 requested) and removed 18 (14 requested) atoms. Cycle 37: After refmac, R = 0.1651 (Rfree = 0.000) for 3828 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 38: After refmac, R = 0.1649 (Rfree = 0.000) for 3835 atoms. Found 21 (28 requested) and removed 20 (14 requested) atoms. Cycle 39: After refmac, R = 0.1613 (Rfree = 0.000) for 3831 atoms. Found 25 (28 requested) and removed 16 (14 requested) atoms. Cycle 40: After refmac, R = 0.1611 (Rfree = 0.000) for 3835 atoms. Found 18 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 3919 seeds are put forward NCS extension: 0 residues added, 3919 seeds are put forward Round 1: 160 peptides, 36 chains. Longest chain 9 peptides. Score 0.224 Round 2: 187 peptides, 38 chains. Longest chain 9 peptides. Score 0.287 Round 3: 195 peptides, 38 chains. Longest chain 9 peptides. Score 0.312 Round 4: 188 peptides, 36 chains. Longest chain 9 peptides. Score 0.317 Round 5: 194 peptides, 38 chains. Longest chain 9 peptides. Score 0.309 Taking the results from Round 4 Chains 36, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8857 restraints for refining 3825 atoms. 8285 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1793 (Rfree = 0.000) for 3825 atoms. Found 28 (28 requested) and removed 17 (14 requested) atoms. Cycle 42: After refmac, R = 0.1614 (Rfree = 0.000) for 3828 atoms. Found 19 (28 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.1487 (Rfree = 0.000) for 3826 atoms. Found 14 (28 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.1582 (Rfree = 0.000) for 3819 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 45: After refmac, R = 0.1454 (Rfree = 0.000) for 3826 atoms. Found 15 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 3896 seeds are put forward NCS extension: 0 residues added, 3896 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 10 peptides. Score 0.288 Round 2: 183 peptides, 32 chains. Longest chain 12 peptides. Score 0.355 Round 3: 170 peptides, 31 chains. Longest chain 11 peptides. Score 0.328 Round 4: 185 peptides, 31 chains. Longest chain 10 peptides. Score 0.374 Round 5: 178 peptides, 30 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 154, 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 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7444 reflections ( 99.32 % complete ) and 8847 restraints for refining 3826 atoms. 8262 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1637 (Rfree = 0.000) for 3826 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1607 (Rfree = 0.000) for 3807 atoms. Found 0 (28 requested) and removed 12 (14 requested) atoms. Cycle 48: After refmac, R = 0.1521 (Rfree = 0.000) for 3793 atoms. Found 0 (28 requested) and removed 9 (14 requested) atoms. Cycle 49: After refmac, R = 0.1509 (Rfree = 0.000) for 3783 atoms. Found 0 (28 requested) and removed 9 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:46:43 GMT 2018 Job finished. TimeTaking 51.89 Used memory is bytes: 11079432