Sun 23 Dec 23:51:11 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 2a9v-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-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/2a9v-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-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 ============================================================ Sun 23 Dec 23:51:16 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/2a9v-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.8-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 502 and 0 Target number of residues in the AU: 502 Target solvent content: 0.6301 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-3.8-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.50 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: 137.806 3.800 Wilson plot Bfac: 66.39 7872 reflections ( 99.99 % complete ) and 0 restraints for refining 7473 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3772 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3541 (Rfree = 0.000) for 7473 atoms. Found 41 (41 requested) and removed 213 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 7398 seeds are put forward NCS extension: 0 residues added, 7398 seeds are put forward Round 1: 161 peptides, 37 chains. Longest chain 7 peptides. Score 0.205 Round 2: 213 peptides, 43 chains. Longest chain 11 peptides. Score 0.278 Round 3: 230 peptides, 45 chains. Longest chain 11 peptides. Score 0.300 Round 4: 240 peptides, 44 chains. Longest chain 12 peptides. Score 0.335 Round 5: 249 peptides, 44 chains. Longest chain 13 peptides. Score 0.356 Taking the results from Round 5 Chains 44, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 15736 restraints for refining 6135 atoms. 14960 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2896 (Rfree = 0.000) for 6135 atoms. Found 33 (33 requested) and removed 77 (16 requested) atoms. Cycle 2: After refmac, R = 0.2781 (Rfree = 0.000) for 5996 atoms. Found 33 (33 requested) and removed 64 (16 requested) atoms. Cycle 3: After refmac, R = 0.2635 (Rfree = 0.000) for 5915 atoms. Found 32 (32 requested) and removed 66 (16 requested) atoms. Cycle 4: After refmac, R = 0.2102 (Rfree = 0.000) for 5838 atoms. Found 12 (32 requested) and removed 42 (16 requested) atoms. Cycle 5: After refmac, R = 0.1867 (Rfree = 0.000) for 5774 atoms. Found 6 (31 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 5925 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5944 seeds are put forward Round 1: 231 peptides, 53 chains. Longest chain 6 peptides. Score 0.217 Round 2: 272 peptides, 54 chains. Longest chain 10 peptides. Score 0.309 Round 3: 269 peptides, 51 chains. Longest chain 12 peptides. Score 0.332 Round 4: 283 peptides, 55 chains. Longest chain 12 peptides. Score 0.325 Round 5: 279 peptides, 53 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 5 Chains 53, Residues 226, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14125 restraints for refining 5744 atoms. 13260 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2374 (Rfree = 0.000) for 5744 atoms. Found 31 (31 requested) and removed 81 (15 requested) atoms. Cycle 7: After refmac, R = 0.2215 (Rfree = 0.000) for 5659 atoms. Found 30 (31 requested) and removed 69 (15 requested) atoms. Cycle 8: After refmac, R = 0.2031 (Rfree = 0.000) for 5594 atoms. Found 19 (30 requested) and removed 42 (15 requested) atoms. Cycle 9: After refmac, R = 0.2072 (Rfree = 0.000) for 5556 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 10: After refmac, R = 0.1997 (Rfree = 0.000) for 5542 atoms. Found 30 (30 requested) and removed 40 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 5674 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5691 seeds are put forward Round 1: 249 peptides, 53 chains. Longest chain 10 peptides. Score 0.263 Round 2: 274 peptides, 50 chains. Longest chain 13 peptides. Score 0.354 Round 3: 295 peptides, 51 chains. Longest chain 17 peptides. Score 0.392 Round 4: 298 peptides, 55 chains. Longest chain 13 peptides. Score 0.360 Round 5: 271 peptides, 47 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 3 Chains 51, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13566 restraints for refining 5695 atoms. 12641 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2220 (Rfree = 0.000) for 5695 atoms. Found 31 (31 requested) and removed 74 (15 requested) atoms. Cycle 12: After refmac, R = 0.2115 (Rfree = 0.000) for 5624 atoms. Found 31 (31 requested) and removed 53 (15 requested) atoms. Cycle 13: After refmac, R = 0.1930 (Rfree = 0.000) for 5587 atoms. Found 22 (30 requested) and removed 38 (15 requested) atoms. Cycle 14: After refmac, R = 0.1548 (Rfree = 0.000) for 5560 atoms. Found 13 (30 requested) and removed 29 (15 requested) atoms. Cycle 15: After refmac, R = 0.1436 (Rfree = 0.000) for 5534 atoms. Found 5 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 5682 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5702 seeds are put forward Round 1: 272 peptides, 58 chains. Longest chain 9 peptides. Score 0.269 Round 2: 307 peptides, 57 chains. Longest chain 18 peptides. Score 0.361 Round 3: 321 peptides, 60 chains. Longest chain 15 peptides. Score 0.364 Round 4: 318 peptides, 57 chains. Longest chain 17 peptides. Score 0.386 Round 5: 326 peptides, 56 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 56, Residues 270, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13921 restraints for refining 5930 atoms. 12876 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2099 (Rfree = 0.000) for 5930 atoms. Found 29 (32 requested) and removed 75 (16 requested) atoms. Cycle 17: After refmac, R = 0.2047 (Rfree = 0.000) for 5846 atoms. Found 32 (32 requested) and removed 55 (16 requested) atoms. Cycle 18: After refmac, R = 0.2011 (Rfree = 0.000) for 5810 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 19: After refmac, R = 0.1486 (Rfree = 0.000) for 5778 atoms. Found 12 (31 requested) and removed 25 (15 requested) atoms. Cycle 20: After refmac, R = 0.1355 (Rfree = 0.000) for 5757 atoms. Found 8 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 5902 seeds are put forward NCS extension: 0 residues added, 5902 seeds are put forward Round 1: 243 peptides, 51 chains. Longest chain 9 peptides. Score 0.269 Round 2: 278 peptides, 54 chains. Longest chain 10 peptides. Score 0.324 Round 3: 286 peptides, 49 chains. Longest chain 16 peptides. Score 0.391 Round 4: 273 peptides, 54 chains. Longest chain 13 peptides. Score 0.312 Round 5: 283 peptides, 50 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 3 Chains 49, Residues 237, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14004 restraints for refining 5920 atoms. 13091 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1971 (Rfree = 0.000) for 5920 atoms. Found 32 (32 requested) and removed 102 (16 requested) atoms. Cycle 22: After refmac, R = 0.2089 (Rfree = 0.000) for 5834 atoms. Found 32 (32 requested) and removed 70 (16 requested) atoms. Cycle 23: After refmac, R = 0.2038 (Rfree = 0.000) for 5779 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. Cycle 24: After refmac, R = 0.1693 (Rfree = 0.000) for 5761 atoms. Found 23 (31 requested) and removed 32 (15 requested) atoms. Cycle 25: After refmac, R = 0.1691 (Rfree = 0.000) for 5744 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 5902 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5927 seeds are put forward Round 1: 241 peptides, 51 chains. Longest chain 8 peptides. Score 0.264 Round 2: 271 peptides, 50 chains. Longest chain 12 peptides. Score 0.347 Round 3: 278 peptides, 50 chains. Longest chain 12 peptides. Score 0.363 Round 4: 273 peptides, 49 chains. Longest chain 11 peptides. Score 0.361 Round 5: 260 peptides, 46 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 3 Chains 50, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 13841 restraints for refining 5882 atoms. 12979 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1915 (Rfree = 0.000) for 5882 atoms. Found 24 (32 requested) and removed 58 (16 requested) atoms. Cycle 27: After refmac, R = 0.1962 (Rfree = 0.000) for 5830 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 28: After refmac, R = 0.1870 (Rfree = 0.000) for 5809 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 29: After refmac, R = 0.1388 (Rfree = 0.000) for 5800 atoms. Found 6 (31 requested) and removed 25 (15 requested) atoms. Cycle 30: After refmac, R = 0.1289 (Rfree = 0.000) for 5776 atoms. Found 9 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 4.05 Search for helices and strands: 0 residues in 0 chains, 5908 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5925 seeds are put forward Round 1: 249 peptides, 55 chains. Longest chain 7 peptides. Score 0.243 Round 2: 266 peptides, 51 chains. Longest chain 10 peptides. Score 0.325 Round 3: 254 peptides, 49 chains. Longest chain 12 peptides. Score 0.317 Round 4: 256 peptides, 47 chains. Longest chain 13 peptides. Score 0.342 Round 5: 273 peptides, 50 chains. Longest chain 12 peptides. Score 0.352 Taking the results from Round 5 Chains 50, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14210 restraints for refining 5958 atoms. 13368 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1872 (Rfree = 0.000) for 5958 atoms. Found 25 (32 requested) and removed 74 (16 requested) atoms. Cycle 32: After refmac, R = 0.1883 (Rfree = 0.000) for 5890 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 33: After refmac, R = 0.1911 (Rfree = 0.000) for 5853 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 34: After refmac, R = 0.1851 (Rfree = 0.000) for 5842 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 35: After refmac, R = 0.1769 (Rfree = 0.000) for 5835 atoms. Found 28 (32 requested) and removed 34 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 5991 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6004 seeds are put forward Round 1: 189 peptides, 43 chains. Longest chain 8 peptides. Score 0.215 Round 2: 250 peptides, 52 chains. Longest chain 8 peptides. Score 0.276 Round 3: 251 peptides, 47 chains. Longest chain 15 peptides. Score 0.330 Round 4: 235 peptides, 43 chains. Longest chain 12 peptides. Score 0.333 Round 5: 231 peptides, 45 chains. Longest chain 8 peptides. Score 0.302 Taking the results from Round 4 Chains 43, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14560 restraints for refining 6079 atoms. 13835 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2022 (Rfree = 0.000) for 6079 atoms. Found 33 (33 requested) and removed 72 (16 requested) atoms. Cycle 37: After refmac, R = 0.1949 (Rfree = 0.000) for 6015 atoms. Found 33 (33 requested) and removed 34 (16 requested) atoms. Cycle 38: After refmac, R = 0.1889 (Rfree = 0.000) for 5996 atoms. Found 33 (33 requested) and removed 38 (16 requested) atoms. Cycle 39: After refmac, R = 0.1871 (Rfree = 0.000) for 5976 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 40: After refmac, R = 0.1358 (Rfree = 0.000) for 5967 atoms. Found 15 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 6114 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6130 seeds are put forward Round 1: 196 peptides, 44 chains. Longest chain 9 peptides. Score 0.223 Round 2: 197 peptides, 39 chains. Longest chain 9 peptides. Score 0.281 Round 3: 235 peptides, 46 chains. Longest chain 10 peptides. Score 0.302 Round 4: 218 peptides, 44 chains. Longest chain 9 peptides. Score 0.280 Round 5: 200 peptides, 38 chains. Longest chain 10 peptides. Score 0.300 Taking the results from Round 3 Chains 46, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7872 reflections ( 99.99 % complete ) and 14276 restraints for refining 6000 atoms. 13566 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1796 (Rfree = 0.000) for 6000 atoms. Found 32 (33 requested) and removed 53 (16 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 5954 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 43: After refmac, R = 0.1847 (Rfree = 0.000) for 5933 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 44: After refmac, R = 0.1754 (Rfree = 0.000) for 5919 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 45: After refmac, R = 0.1273 (Rfree = 0.000) for 5910 atoms. Found 7 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 6038 seeds are put forward NCS extension: 0 residues added, 6038 seeds are put forward Round 1: 178 peptides, 40 chains. Longest chain 8 peptides. Score 0.219 Round 2: 202 peptides, 41 chains. Longest chain 8 peptides. Score 0.272 Round 3: 194 peptides, 38 chains. Longest chain 9 peptides. Score 0.284 Round 4: 203 peptides, 37 chains. Longest chain 9 peptides. Score 0.318 Round 5: 203 peptides, 39 chains. Longest chain 9 peptides. Score 0.296 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 166, 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 2a9v-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7872 reflections ( 99.99 % complete ) and 14268 restraints for refining 5954 atoms. 13641 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1978 (Rfree = 0.000) for 5954 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1896 (Rfree = 0.000) for 5928 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1937 (Rfree = 0.000) for 5903 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1830 (Rfree = 0.000) for 5876 atoms. TimeTaking 74.1