null Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i5i-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.4-parrot-hancs/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-hancs.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-hancs.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 4652 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3385 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3058 (Rfree = 0.000) for 4652 atoms. Found 32 (35 requested) and removed 47 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 4704 seeds are put forward NCS extension: 0 residues added, 4704 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 8 peptides. Score 0.248 Round 2: 195 peptides, 39 chains. Longest chain 8 peptides. Score 0.299 Round 3: 206 peptides, 38 chains. Longest chain 9 peptides. Score 0.346 Round 4: 222 peptides, 41 chains. Longest chain 12 peptides. Score 0.356 Round 5: 229 peptides, 41 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 5 Chains 41, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8931 restraints for refining 3826 atoms. 8220 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2520 (Rfree = 0.000) for 3826 atoms. Found 15 (28 requested) and removed 43 (14 requested) atoms. Cycle 2: After refmac, R = 0.2431 (Rfree = 0.000) for 3753 atoms. Found 23 (28 requested) and removed 26 (14 requested) atoms. Cycle 3: After refmac, R = 0.1910 (Rfree = 0.000) for 3727 atoms. Found 11 (28 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.2085 (Rfree = 0.000) for 3710 atoms. Found 11 (28 requested) and removed 15 (14 requested) atoms. Cycle 5: After refmac, R = 0.1818 (Rfree = 0.000) for 3699 atoms. Found 8 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 3798 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3809 seeds are put forward Round 1: 217 peptides, 40 chains. Longest chain 10 peptides. Score 0.353 Round 2: 242 peptides, 39 chains. Longest chain 13 peptides. Score 0.438 Round 3: 260 peptides, 41 chains. Longest chain 15 peptides. Score 0.463 Round 4: 260 peptides, 42 chains. Longest chain 15 peptides. Score 0.451 Round 5: 239 peptides, 38 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 3 Chains 41, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8561 restraints for refining 3807 atoms. 7726 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2222 (Rfree = 0.000) for 3807 atoms. Found 24 (28 requested) and removed 37 (14 requested) atoms. Cycle 7: After refmac, R = 0.2164 (Rfree = 0.000) for 3769 atoms. Found 27 (28 requested) and removed 26 (14 requested) atoms. Cycle 8: After refmac, R = 0.2044 (Rfree = 0.000) for 3765 atoms. Found 16 (28 requested) and removed 20 (14 requested) atoms. Cycle 9: After refmac, R = 0.2020 (Rfree = 0.000) for 3753 atoms. Found 16 (28 requested) and removed 20 (14 requested) atoms. Cycle 10: After refmac, R = 0.1951 (Rfree = 0.000) for 3744 atoms. Found 19 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 3849 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3864 seeds are put forward Round 1: 201 peptides, 37 chains. Longest chain 14 peptides. Score 0.344 Round 2: 249 peptides, 42 chains. Longest chain 13 peptides. Score 0.421 Round 3: 242 peptides, 40 chains. Longest chain 13 peptides. Score 0.426 Round 4: 249 peptides, 43 chains. Longest chain 13 peptides. Score 0.409 Round 5: 274 peptides, 47 chains. Longest chain 13 peptides. Score 0.431 Taking the results from Round 5 Chains 47, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8604 restraints for refining 3824 atoms. 7743 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2310 (Rfree = 0.000) for 3824 atoms. Found 23 (28 requested) and removed 32 (14 requested) atoms. Cycle 12: After refmac, R = 0.2057 (Rfree = 0.000) for 3792 atoms. Found 15 (28 requested) and removed 24 (14 requested) atoms. Cycle 13: After refmac, R = 0.1938 (Rfree = 0.000) for 3773 atoms. Found 6 (28 requested) and removed 20 (14 requested) atoms. Cycle 14: After refmac, R = 0.2001 (Rfree = 0.000) for 3752 atoms. Found 19 (28 requested) and removed 22 (14 requested) atoms. Cycle 15: After refmac, R = 0.1884 (Rfree = 0.000) for 3737 atoms. Found 8 (28 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 3820 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3837 seeds are put forward Round 1: 231 peptides, 46 chains. Longest chain 11 peptides. Score 0.319 Round 2: 242 peptides, 43 chains. Longest chain 14 peptides. Score 0.389 Round 3: 267 peptides, 44 chains. Longest chain 16 peptides. Score 0.447 Round 4: 260 peptides, 41 chains. Longest chain 18 peptides. Score 0.463 Round 5: 246 peptides, 39 chains. Longest chain 11 peptides. Score 0.448 Taking the results from Round 4 Chains 41, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8589 restraints for refining 3826 atoms. 7754 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2015 (Rfree = 0.000) for 3826 atoms. Found 17 (28 requested) and removed 28 (14 requested) atoms. Cycle 17: After refmac, R = 0.1868 (Rfree = 0.000) for 3795 atoms. Found 12 (28 requested) and removed 22 (14 requested) atoms. Cycle 18: After refmac, R = 0.1847 (Rfree = 0.000) for 3781 atoms. Found 17 (28 requested) and removed 23 (14 requested) atoms. Cycle 19: After refmac, R = 0.1796 (Rfree = 0.000) for 3771 atoms. Found 11 (28 requested) and removed 18 (14 requested) atoms. Cycle 20: After refmac, R = 0.1768 (Rfree = 0.000) for 3761 atoms. Found 16 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3885 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 8 peptides. Score 0.264 Round 2: 226 peptides, 39 chains. Longest chain 20 peptides. Score 0.393 Round 3: 239 peptides, 43 chains. Longest chain 11 peptides. Score 0.381 Round 4: 234 peptides, 40 chains. Longest chain 15 peptides. Score 0.403 Round 5: 240 peptides, 38 chains. Longest chain 12 peptides. Score 0.444 Taking the results from Round 5 Chains 39, Residues 202, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8602 restraints for refining 3825 atoms. 7807 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2134 (Rfree = 0.000) for 3825 atoms. Found 18 (28 requested) and removed 24 (14 requested) atoms. Cycle 22: After refmac, R = 0.1978 (Rfree = 0.000) for 3804 atoms. Found 19 (28 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.1920 (Rfree = 0.000) for 3788 atoms. Found 7 (28 requested) and removed 19 (14 requested) atoms. Cycle 24: After refmac, R = 0.1677 (Rfree = 0.000) for 3774 atoms. Found 8 (28 requested) and removed 17 (14 requested) atoms. Cycle 25: After refmac, R = 0.1799 (Rfree = 0.000) for 3757 atoms. Found 5 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 3816 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3829 seeds are put forward Round 1: 195 peptides, 40 chains. Longest chain 8 peptides. Score 0.285 Round 2: 221 peptides, 36 chains. Longest chain 17 peptides. Score 0.416 Round 3: 233 peptides, 38 chains. Longest chain 14 peptides. Score 0.425 Round 4: 240 peptides, 36 chains. Longest chain 18 peptides. Score 0.468 Round 5: 225 peptides, 38 chains. Longest chain 17 peptides. Score 0.402 Taking the results from Round 4 Chains 36, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8590 restraints for refining 3826 atoms. 7810 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1986 (Rfree = 0.000) for 3826 atoms. Found 12 (28 requested) and removed 15 (14 requested) atoms. Cycle 27: After refmac, R = 0.1881 (Rfree = 0.000) for 3818 atoms. Found 20 (28 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.1907 (Rfree = 0.000) for 3812 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. Cycle 29: After refmac, R = 0.1920 (Rfree = 0.000) for 3805 atoms. Found 23 (28 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.1584 (Rfree = 0.000) for 3804 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3881 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3903 seeds are put forward Round 1: 173 peptides, 36 chains. Longest chain 9 peptides. Score 0.268 Round 2: 204 peptides, 36 chains. Longest chain 15 peptides. Score 0.366 Round 3: 190 peptides, 33 chains. Longest chain 15 peptides. Score 0.363 Round 4: 202 peptides, 35 chains. Longest chain 15 peptides. Score 0.373 Round 5: 203 peptides, 31 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 5 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8778 restraints for refining 3825 atoms. 8121 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1890 (Rfree = 0.000) for 3825 atoms. Found 16 (28 requested) and removed 15 (14 requested) atoms. Cycle 32: After refmac, R = 0.1821 (Rfree = 0.000) for 3824 atoms. Found 14 (28 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.1916 (Rfree = 0.000) for 3821 atoms. Found 26 (28 requested) and removed 20 (14 requested) atoms. Cycle 34: After refmac, R = 0.1660 (Rfree = 0.000) for 3826 atoms. Found 7 (28 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.2254 (Rfree = 0.000) for 3814 atoms. Found 28 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3905 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3921 seeds are put forward Round 1: 182 peptides, 39 chains. Longest chain 7 peptides. Score 0.257 Round 2: 193 peptides, 35 chains. Longest chain 10 peptides. Score 0.346 Round 3: 208 peptides, 37 chains. Longest chain 9 peptides. Score 0.365 Round 4: 196 peptides, 34 chains. Longest chain 14 peptides. Score 0.368 Round 5: 211 peptides, 36 chains. Longest chain 10 peptides. Score 0.387 Taking the results from Round 5 Chains 36, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8844 restraints for refining 3826 atoms. 8180 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2025 (Rfree = 0.000) for 3826 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 37: After refmac, R = 0.1826 (Rfree = 0.000) for 3827 atoms. Found 19 (28 requested) and removed 22 (14 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 3817 atoms. Found 21 (28 requested) and removed 15 (14 requested) atoms. Cycle 39: After refmac, R = 0.1546 (Rfree = 0.000) for 3817 atoms. Found 10 (28 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1483 (Rfree = 0.000) for 3812 atoms. Found 4 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 3858 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3870 seeds are put forward Round 1: 176 peptides, 39 chains. Longest chain 7 peptides. Score 0.236 Round 2: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.345 Round 3: 188 peptides, 34 chains. Longest chain 14 peptides. Score 0.344 Round 4: 195 peptides, 34 chains. Longest chain 14 peptides. Score 0.365 Round 5: 202 peptides, 36 chains. Longest chain 11 peptides. Score 0.360 Taking the results from Round 4 Chains 34, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7444 reflections ( 99.32 % complete ) and 8728 restraints for refining 3826 atoms. 8118 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1784 (Rfree = 0.000) for 3826 atoms. Found 14 (28 requested) and removed 15 (14 requested) atoms. Cycle 42: After refmac, R = 0.1811 (Rfree = 0.000) for 3810 atoms. Found 17 (28 requested) and removed 17 (14 requested) atoms. Cycle 43: After refmac, R = 0.1859 (Rfree = 0.000) for 3809 atoms. Found 28 (28 requested) and removed 16 (14 requested) atoms. Cycle 44: After refmac, R = 0.1796 (Rfree = 0.000) for 3815 atoms. Found 25 (28 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1505 (Rfree = 0.000) for 3824 atoms. Found 8 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 3871 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3891 seeds are put forward Round 1: 192 peptides, 43 chains. Longest chain 11 peptides. Score 0.235 Round 2: 192 peptides, 36 chains. Longest chain 12 peptides. Score 0.329 Round 3: 191 peptides, 34 chains. Longest chain 11 peptides. Score 0.353 Round 4: 179 peptides, 32 chains. Longest chain 10 peptides. Score 0.343 Round 5: 174 peptides, 30 chains. Longest chain 16 peptides. Score 0.354 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 144, 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 8863 restraints for refining 3826 atoms. 8317 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1795 (Rfree = 0.000) for 3826 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1831 (Rfree = 0.000) for 3804 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1716 (Rfree = 0.000) for 3787 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1477 (Rfree = 0.000) for 3768 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:25:11 GMT 2018 Job finished. TimeTaking 62.42 Used memory is bytes: 6676048