Mon 24 Dec 01:05:32 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-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/2a9v-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-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 01:05:37 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-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 518 and 0 Target number of residues in the AU: 518 Target solvent content: 0.6183 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-3.4-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.4-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 3.400 Wilson plot Bfac: 60.53 10860 reflections ( 99.99 % complete ) and 0 restraints for refining 7501 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3714 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3450 (Rfree = 0.000) for 7501 atoms. Found 48 (56 requested) and removed 206 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 7461 seeds are put forward NCS extension: 0 residues added, 7461 seeds are put forward Round 1: 220 peptides, 48 chains. Longest chain 8 peptides. Score 0.242 Round 2: 253 peptides, 51 chains. Longest chain 9 peptides. Score 0.294 Round 3: 310 peptides, 61 chains. Longest chain 11 peptides. Score 0.329 Round 4: 300 peptides, 57 chains. Longest chain 10 peptides. Score 0.345 Round 5: 315 peptides, 57 chains. Longest chain 11 peptides. Score 0.379 Taking the results from Round 5 Chains 58, Residues 258, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 15050 restraints for refining 6167 atoms. 14037 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2853 (Rfree = 0.000) for 6167 atoms. Found 18 (46 requested) and removed 85 (23 requested) atoms. Cycle 2: After refmac, R = 0.2793 (Rfree = 0.000) for 6014 atoms. Found 40 (46 requested) and removed 55 (23 requested) atoms. Cycle 3: After refmac, R = 0.2592 (Rfree = 0.000) for 5949 atoms. Found 33 (45 requested) and removed 54 (22 requested) atoms. Cycle 4: After refmac, R = 0.2628 (Rfree = 0.000) for 5897 atoms. Found 35 (44 requested) and removed 53 (22 requested) atoms. Cycle 5: After refmac, R = 0.2728 (Rfree = 0.000) for 5845 atoms. Found 36 (44 requested) and removed 50 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 6022 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6033 seeds are put forward Round 1: 261 peptides, 57 chains. Longest chain 8 peptides. Score 0.252 Round 2: 293 peptides, 57 chains. Longest chain 10 peptides. Score 0.329 Round 3: 287 peptides, 51 chains. Longest chain 13 peptides. Score 0.374 Round 4: 285 peptides, 51 chains. Longest chain 15 peptides. Score 0.369 Round 5: 281 peptides, 50 chains. Longest chain 14 peptides. Score 0.370 Taking the results from Round 3 Chains 52, Residues 236, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13557 restraints for refining 5801 atoms. 12565 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2517 (Rfree = 0.000) for 5801 atoms. Found 42 (43 requested) and removed 69 (21 requested) atoms. Cycle 7: After refmac, R = 0.2300 (Rfree = 0.000) for 5755 atoms. Found 18 (43 requested) and removed 42 (21 requested) atoms. Cycle 8: After refmac, R = 0.2173 (Rfree = 0.000) for 5719 atoms. Found 18 (43 requested) and removed 41 (21 requested) atoms. Cycle 9: After refmac, R = 0.2099 (Rfree = 0.000) for 5685 atoms. Found 17 (43 requested) and removed 36 (21 requested) atoms. Cycle 10: After refmac, R = 0.2058 (Rfree = 0.000) for 5653 atoms. Found 18 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 5791 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5805 seeds are put forward Round 1: 277 peptides, 60 chains. Longest chain 7 peptides. Score 0.261 Round 2: 307 peptides, 59 chains. Longest chain 9 peptides. Score 0.342 Round 3: 322 peptides, 58 chains. Longest chain 12 peptides. Score 0.385 Round 4: 320 peptides, 57 chains. Longest chain 12 peptides. Score 0.390 Round 5: 319 peptides, 56 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 5 Chains 56, Residues 263, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13813 restraints for refining 5870 atoms. 12736 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2451 (Rfree = 0.000) for 5870 atoms. Found 25 (44 requested) and removed 71 (22 requested) atoms. Cycle 12: After refmac, R = 0.2347 (Rfree = 0.000) for 5806 atoms. Found 18 (43 requested) and removed 46 (21 requested) atoms. Cycle 13: After refmac, R = 0.2256 (Rfree = 0.000) for 5762 atoms. Found 17 (43 requested) and removed 32 (21 requested) atoms. Cycle 14: After refmac, R = 0.2156 (Rfree = 0.000) for 5741 atoms. Found 15 (43 requested) and removed 33 (21 requested) atoms. Cycle 15: After refmac, R = 0.2094 (Rfree = 0.000) for 5718 atoms. Found 15 (43 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.71 Search for helices and strands: 0 residues in 0 chains, 5852 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5869 seeds are put forward Round 1: 264 peptides, 56 chains. Longest chain 9 peptides. Score 0.270 Round 2: 316 peptides, 57 chains. Longest chain 12 peptides. Score 0.381 Round 3: 305 peptides, 50 chains. Longest chain 13 peptides. Score 0.423 Round 4: 314 peptides, 53 chains. Longest chain 14 peptides. Score 0.414 Round 5: 301 peptides, 52 chains. Longest chain 24 peptides. Score 0.395 Taking the results from Round 3 Chains 50, Residues 255, Estimated correctness of the model 0.0 % 6 chains (21 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13875 restraints for refining 5958 atoms. 12866 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2185 (Rfree = 0.000) for 5958 atoms. Found 28 (44 requested) and removed 42 (22 requested) atoms. Cycle 17: After refmac, R = 0.2026 (Rfree = 0.000) for 5929 atoms. Found 30 (44 requested) and removed 36 (22 requested) atoms. Cycle 18: After refmac, R = 0.2062 (Rfree = 0.000) for 5916 atoms. Found 35 (44 requested) and removed 36 (22 requested) atoms. Cycle 19: After refmac, R = 0.2031 (Rfree = 0.000) for 5910 atoms. Found 29 (44 requested) and removed 34 (22 requested) atoms. Cycle 20: After refmac, R = 0.2021 (Rfree = 0.000) for 5900 atoms. Found 35 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.73 Search for helices and strands: 0 residues in 0 chains, 6093 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 6104 seeds are put forward Round 1: 280 peptides, 62 chains. Longest chain 7 peptides. Score 0.248 Round 2: 297 peptides, 52 chains. Longest chain 15 peptides. Score 0.387 Round 3: 295 peptides, 49 chains. Longest chain 11 peptides. Score 0.411 Round 4: 292 peptides, 51 chains. Longest chain 15 peptides. Score 0.385 Round 5: 296 peptides, 50 chains. Longest chain 15 peptides. Score 0.403 Taking the results from Round 3 Chains 49, Residues 246, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14198 restraints for refining 6072 atoms. 13263 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2073 (Rfree = 0.000) for 6072 atoms. Found 21 (45 requested) and removed 56 (22 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1960 (Rfree = 0.000) for 6023 atoms. Found 17 (45 requested) and removed 36 (22 requested) atoms. Cycle 23: After refmac, R = 0.1899 (Rfree = 0.000) for 5993 atoms. Found 17 (45 requested) and removed 37 (22 requested) atoms. Cycle 24: After refmac, R = 0.1862 (Rfree = 0.000) for 5971 atoms. Found 17 (45 requested) and removed 27 (22 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1847 (Rfree = 0.000) for 5953 atoms. Found 20 (45 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 6103 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 6106 seeds are put forward Round 1: 244 peptides, 51 chains. Longest chain 9 peptides. Score 0.272 Round 2: 309 peptides, 57 chains. Longest chain 13 peptides. Score 0.366 Round 3: 292 peptides, 54 chains. Longest chain 11 peptides. Score 0.356 Round 4: 292 peptides, 52 chains. Longest chain 15 peptides. Score 0.375 Round 5: 298 peptides, 51 chains. Longest chain 16 peptides. Score 0.398 Taking the results from Round 5 Chains 51, Residues 247, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14078 restraints for refining 6040 atoms. 13122 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2006 (Rfree = 0.000) for 6040 atoms. Found 18 (45 requested) and removed 47 (22 requested) atoms. Cycle 27: After refmac, R = 0.1877 (Rfree = 0.000) for 5990 atoms. Found 21 (45 requested) and removed 38 (22 requested) atoms. Cycle 28: After refmac, R = 0.1786 (Rfree = 0.000) for 5967 atoms. Found 8 (45 requested) and removed 28 (22 requested) atoms. Cycle 29: After refmac, R = 0.1771 (Rfree = 0.000) for 5941 atoms. Found 5 (44 requested) and removed 30 (22 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 5908 atoms. Found 8 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.71 Search for helices and strands: 0 residues in 0 chains, 6061 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6085 seeds are put forward Round 1: 260 peptides, 53 chains. Longest chain 9 peptides. Score 0.291 Round 2: 291 peptides, 54 chains. Longest chain 13 peptides. Score 0.354 Round 3: 307 peptides, 55 chains. Longest chain 13 peptides. Score 0.380 Round 4: 307 peptides, 53 chains. Longest chain 11 peptides. Score 0.399 Round 5: 292 peptides, 49 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Chains 49, Residues 243, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14321 restraints for refining 6135 atoms. 13360 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1978 (Rfree = 0.000) for 6135 atoms. Found 19 (46 requested) and removed 49 (23 requested) atoms. Cycle 32: After refmac, R = 0.1857 (Rfree = 0.000) for 6088 atoms. Found 11 (46 requested) and removed 36 (23 requested) atoms. Cycle 33: After refmac, R = 0.1841 (Rfree = 0.000) for 6057 atoms. Found 20 (45 requested) and removed 30 (22 requested) atoms. Cycle 34: After refmac, R = 0.1771 (Rfree = 0.000) for 6041 atoms. Found 14 (45 requested) and removed 25 (22 requested) atoms. Cycle 35: After refmac, R = 0.1752 (Rfree = 0.000) for 6027 atoms. Found 13 (45 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 6169 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6186 seeds are put forward Round 1: 223 peptides, 45 chains. Longest chain 11 peptides. Score 0.282 Round 2: 274 peptides, 50 chains. Longest chain 12 peptides. Score 0.354 Round 3: 279 peptides, 50 chains. Longest chain 12 peptides. Score 0.365 Round 4: 284 peptides, 48 chains. Longest chain 15 peptides. Score 0.396 Round 5: 286 peptides, 50 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 48, Residues 236, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14436 restraints for refining 6168 atoms. 13500 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1921 (Rfree = 0.000) for 6168 atoms. Found 12 (46 requested) and removed 48 (23 requested) atoms. Cycle 37: After refmac, R = 0.1819 (Rfree = 0.000) for 6121 atoms. Found 18 (46 requested) and removed 35 (23 requested) atoms. Cycle 38: After refmac, R = 0.1798 (Rfree = 0.000) for 6097 atoms. Found 16 (46 requested) and removed 28 (23 requested) atoms. Cycle 39: After refmac, R = 0.1743 (Rfree = 0.000) for 6082 atoms. Found 13 (45 requested) and removed 24 (22 requested) atoms. Cycle 40: After refmac, R = 0.1698 (Rfree = 0.000) for 6068 atoms. Found 14 (45 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.70 Search for helices and strands: 0 residues in 0 chains, 6197 seeds are put forward NCS extension: 0 residues added, 6197 seeds are put forward Round 1: 229 peptides, 50 chains. Longest chain 7 peptides. Score 0.244 Round 2: 265 peptides, 50 chains. Longest chain 9 peptides. Score 0.333 Round 3: 257 peptides, 49 chains. Longest chain 10 peptides. Score 0.324 Round 4: 258 peptides, 47 chains. Longest chain 11 peptides. Score 0.347 Round 5: 259 peptides, 50 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 4 Chains 47, Residues 211, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14579 restraints for refining 6168 atoms. 13714 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1906 (Rfree = 0.000) for 6168 atoms. Found 26 (46 requested) and removed 32 (23 requested) atoms. Cycle 42: After refmac, R = 0.1801 (Rfree = 0.000) for 6154 atoms. Found 13 (46 requested) and removed 26 (23 requested) atoms. Cycle 43: After refmac, R = 0.1725 (Rfree = 0.000) for 6136 atoms. Found 9 (46 requested) and removed 30 (23 requested) atoms. Cycle 44: After refmac, R = 0.1736 (Rfree = 0.000) for 6110 atoms. Found 12 (46 requested) and removed 32 (23 requested) atoms. Cycle 45: After refmac, R = 0.1726 (Rfree = 0.000) for 6087 atoms. Found 11 (45 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.70 Search for helices and strands: 0 residues in 0 chains, 6214 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6228 seeds are put forward Round 1: 212 peptides, 48 chains. Longest chain 7 peptides. Score 0.221 Round 2: 221 peptides, 45 chains. Longest chain 9 peptides. Score 0.277 Round 3: 219 peptides, 41 chains. Longest chain 9 peptides. Score 0.315 Round 4: 228 peptides, 43 chains. Longest chain 11 peptides. Score 0.316 Round 5: 219 peptides, 43 chains. Longest chain 9 peptides. Score 0.294 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 185, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (185 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10860 reflections ( 99.99 % complete ) and 14810 restraints for refining 6166 atoms. 14086 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1905 (Rfree = 0.000) for 6166 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.1921 (Rfree = 0.000) for 6132 atoms. Found 0 (46 requested) and removed 22 (23 requested) atoms. Cycle 48: After refmac, R = 0.1872 (Rfree = 0.000) for 6106 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1859 (Rfree = 0.000) for 6080 atoms. TimeTaking 72.42