null Mon 24 Dec 07:27:24 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 2i5i-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-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/2i5i-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-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 07:27:28 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/2i5i-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-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 382 and 0 Target number of residues in the AU: 382 Target solvent content: 0.6324 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-3.2-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.75 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 3.200 Wilson plot Bfac: 67.70 8937 reflections ( 99.43 % complete ) and 0 restraints for refining 4671 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3501 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2539 (Rfree = 0.000) for 4671 atoms. Found 23 (41 requested) and removed 48 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.24 Search for helices and strands: 0 residues in 0 chains, 4681 seeds are put forward NCS extension: 0 residues added, 4681 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 10 peptides. Score 0.268 Round 2: 205 peptides, 40 chains. Longest chain 10 peptides. Score 0.317 Round 3: 238 peptides, 44 chains. Longest chain 10 peptides. Score 0.365 Round 4: 239 peptides, 45 chains. Longest chain 13 peptides. Score 0.356 Round 5: 251 peptides, 46 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 5 Chains 46, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8754 restraints for refining 3842 atoms. 7980 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2550 (Rfree = 0.000) for 3842 atoms. Found 15 (34 requested) and removed 21 (17 requested) atoms. Cycle 2: After refmac, R = 0.2450 (Rfree = 0.000) for 3815 atoms. Found 16 (34 requested) and removed 19 (17 requested) atoms. Cycle 3: After refmac, R = 0.2381 (Rfree = 0.000) for 3803 atoms. Found 7 (34 requested) and removed 21 (17 requested) atoms. Cycle 4: After refmac, R = 0.2344 (Rfree = 0.000) for 3780 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2311 (Rfree = 0.000) for 3766 atoms. Found 3 (33 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.24 Search for helices and strands: 0 residues in 0 chains, 3822 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3841 seeds are put forward Round 1: 222 peptides, 46 chains. Longest chain 8 peptides. Score 0.291 Round 2: 243 peptides, 44 chains. Longest chain 10 peptides. Score 0.380 Round 3: 255 peptides, 44 chains. Longest chain 11 peptides. Score 0.414 Round 4: 260 peptides, 46 chains. Longest chain 13 peptides. Score 0.404 Round 5: 265 peptides, 47 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 3 Chains 44, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8868 restraints for refining 3842 atoms. 8068 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2392 (Rfree = 0.000) for 3842 atoms. Found 13 (34 requested) and removed 18 (17 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 3821 atoms. Found 7 (34 requested) and removed 19 (17 requested) atoms. Cycle 8: After refmac, R = 0.2532 (Rfree = 0.000) for 3803 atoms. Found 15 (34 requested) and removed 21 (17 requested) atoms. Cycle 9: After refmac, R = 0.2054 (Rfree = 0.000) for 3783 atoms. Found 12 (34 requested) and removed 19 (17 requested) atoms. Cycle 10: After refmac, R = 0.2496 (Rfree = 0.000) for 3767 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 3850 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3864 seeds are put forward Round 1: 209 peptides, 43 chains. Longest chain 11 peptides. Score 0.290 Round 2: 252 peptides, 46 chains. Longest chain 12 peptides. Score 0.381 Round 3: 253 peptides, 46 chains. Longest chain 10 peptides. Score 0.384 Round 4: 250 peptides, 41 chains. Longest chain 15 peptides. Score 0.436 Round 5: 255 peptides, 41 chains. Longest chain 18 peptides. Score 0.449 Taking the results from Round 5 Chains 41, Residues 214, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8609 restraints for refining 3842 atoms. 7750 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2205 (Rfree = 0.000) for 3842 atoms. Found 22 (34 requested) and removed 23 (17 requested) atoms. Cycle 12: After refmac, R = 0.2079 (Rfree = 0.000) for 3832 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 13: After refmac, R = 0.2031 (Rfree = 0.000) for 3820 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 14: After refmac, R = 0.1903 (Rfree = 0.000) for 3809 atoms. Found 5 (34 requested) and removed 19 (17 requested) atoms. Cycle 15: After refmac, R = 0.1940 (Rfree = 0.000) for 3786 atoms. Found 10 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 3851 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3872 seeds are put forward Round 1: 228 peptides, 46 chains. Longest chain 11 peptides. Score 0.310 Round 2: 243 peptides, 45 chains. Longest chain 12 peptides. Score 0.367 Round 3: 251 peptides, 46 chains. Longest chain 13 peptides. Score 0.378 Round 4: 269 peptides, 45 chains. Longest chain 13 peptides. Score 0.440 Round 5: 275 peptides, 48 chains. Longest chain 10 peptides. Score 0.422 Taking the results from Round 4 Chains 45, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8670 restraints for refining 3842 atoms. 7819 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2092 (Rfree = 0.000) for 3842 atoms. Found 27 (34 requested) and removed 24 (17 requested) atoms. Cycle 17: After refmac, R = 0.2088 (Rfree = 0.000) for 3833 atoms. Found 12 (34 requested) and removed 19 (17 requested) atoms. Cycle 18: After refmac, R = 0.1897 (Rfree = 0.000) for 3823 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.2264 (Rfree = 0.000) for 3810 atoms. Found 29 (34 requested) and removed 20 (17 requested) atoms. Cycle 20: After refmac, R = 0.1844 (Rfree = 0.000) for 3813 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3911 seeds are put forward Round 1: 237 peptides, 49 chains. Longest chain 9 peptides. Score 0.299 Round 2: 232 peptides, 42 chains. Longest chain 18 peptides. Score 0.373 Round 3: 247 peptides, 44 chains. Longest chain 14 peptides. Score 0.391 Round 4: 235 peptides, 40 chains. Longest chain 14 peptides. Score 0.406 Round 5: 247 peptides, 42 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 5 Chains 42, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8771 restraints for refining 3842 atoms. 7993 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2010 (Rfree = 0.000) for 3842 atoms. Found 23 (34 requested) and removed 18 (17 requested) atoms. Cycle 22: After refmac, R = 0.1916 (Rfree = 0.000) for 3842 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. Cycle 23: After refmac, R = 0.1894 (Rfree = 0.000) for 3829 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.2078 (Rfree = 0.000) for 3813 atoms. Found 20 (34 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.1812 (Rfree = 0.000) for 3809 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 3871 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3885 seeds are put forward Round 1: 213 peptides, 45 chains. Longest chain 10 peptides. Score 0.276 Round 2: 233 peptides, 43 chains. Longest chain 11 peptides. Score 0.363 Round 3: 242 peptides, 41 chains. Longest chain 14 peptides. Score 0.414 Round 4: 243 peptides, 44 chains. Longest chain 14 peptides. Score 0.380 Round 5: 245 peptides, 43 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 3 Chains 41, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8715 restraints for refining 3842 atoms. 7952 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1921 (Rfree = 0.000) for 3842 atoms. Found 16 (34 requested) and removed 20 (17 requested) atoms. Cycle 27: After refmac, R = 0.2139 (Rfree = 0.000) for 3830 atoms. Found 34 (34 requested) and removed 19 (17 requested) atoms. Cycle 28: After refmac, R = 0.1828 (Rfree = 0.000) for 3832 atoms. Found 15 (34 requested) and removed 17 (17 requested) atoms. Cycle 29: After refmac, R = 0.2206 (Rfree = 0.000) for 3823 atoms. Found 34 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.1801 (Rfree = 0.000) for 3825 atoms. Found 16 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3908 seeds are put forward Round 1: 187 peptides, 41 chains. Longest chain 8 peptides. Score 0.246 Round 2: 211 peptides, 42 chains. Longest chain 12 peptides. Score 0.309 Round 3: 221 peptides, 38 chains. Longest chain 13 peptides. Score 0.391 Round 4: 227 peptides, 40 chains. Longest chain 12 peptides. Score 0.383 Round 5: 208 peptides, 35 chains. Longest chain 18 peptides. Score 0.391 Taking the results from Round 5 Chains 35, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8786 restraints for refining 3841 atoms. 8129 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1856 (Rfree = 0.000) for 3841 atoms. Found 21 (34 requested) and removed 18 (17 requested) atoms. Cycle 32: After refmac, R = 0.1766 (Rfree = 0.000) for 3837 atoms. Found 13 (34 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.1771 (Rfree = 0.000) for 3828 atoms. Found 16 (34 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.1765 (Rfree = 0.000) for 3824 atoms. Found 14 (34 requested) and removed 18 (17 requested) atoms. Cycle 35: After refmac, R = 0.1728 (Rfree = 0.000) for 3816 atoms. Found 11 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 3842 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 3872 seeds are put forward Round 1: 177 peptides, 39 chains. Longest chain 7 peptides. Score 0.240 Round 2: 213 peptides, 43 chains. Longest chain 10 peptides. Score 0.302 Round 3: 211 peptides, 39 chains. Longest chain 14 peptides. Score 0.348 Round 4: 218 peptides, 41 chains. Longest chain 10 peptides. Score 0.344 Round 5: 214 peptides, 36 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 5 Chains 37, Residues 178, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8644 restraints for refining 3842 atoms. 7939 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1867 (Rfree = 0.000) for 3842 atoms. Found 26 (34 requested) and removed 19 (17 requested) atoms. Cycle 37: After refmac, R = 0.1789 (Rfree = 0.000) for 3844 atoms. Found 15 (34 requested) and removed 19 (17 requested) atoms. Cycle 38: After refmac, R = 0.1753 (Rfree = 0.000) for 3834 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.1714 (Rfree = 0.000) for 3824 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.1560 (Rfree = 0.000) for 3813 atoms. Found 9 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 3850 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3862 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 8 peptides. Score 0.254 Round 2: 204 peptides, 40 chains. Longest chain 10 peptides. Score 0.314 Round 3: 219 peptides, 40 chains. Longest chain 18 peptides. Score 0.359 Round 4: 217 peptides, 39 chains. Longest chain 11 peptides. Score 0.366 Round 5: 232 peptides, 42 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 5 Chains 42, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8651 restraints for refining 3842 atoms. 7933 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1828 (Rfree = 0.000) for 3842 atoms. Found 22 (34 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.1707 (Rfree = 0.000) for 3837 atoms. Found 10 (34 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.1712 (Rfree = 0.000) for 3825 atoms. Found 10 (34 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1699 (Rfree = 0.000) for 3818 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1715 (Rfree = 0.000) for 3806 atoms. Found 9 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 3845 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3857 seeds are put forward Round 1: 153 peptides, 34 chains. Longest chain 7 peptides. Score 0.228 Round 2: 175 peptides, 34 chains. Longest chain 12 peptides. Score 0.302 Round 3: 184 peptides, 35 chains. Longest chain 9 peptides. Score 0.318 Round 4: 183 peptides, 35 chains. Longest chain 9 peptides. Score 0.315 Round 5: 175 peptides, 33 chains. Longest chain 10 peptides. Score 0.316 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 149, 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. 8937 reflections ( 99.43 % complete ) and 8925 restraints for refining 3842 atoms. 8364 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1734 (Rfree = 0.000) for 3842 atoms. Found 0 (34 requested) and removed 11 (17 requested) atoms. Cycle 47: After refmac, R = 0.1992 (Rfree = 0.000) for 3829 atoms. Found 0 (34 requested) and removed 6 (17 requested) atoms. Cycle 48: After refmac, R = 0.1647 (Rfree = 0.000) for 3818 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2050 (Rfree = 0.000) for 3796 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:12:23 GMT 2018 Job finished. TimeTaking 44.99 Used memory is bytes: 2887984