Sun 23 Dec 22:22:41 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 2a9v-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-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/2a9v-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-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 22:22:50 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/2a9v-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-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 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-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.4-parrot-hancs.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 7505 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3795 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3631 (Rfree = 0.000) for 7505 atoms. Found 51 (56 requested) and removed 219 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.81 Search for helices and strands: 0 residues in 0 chains, 7435 seeds are put forward NCS extension: 0 residues added, 7435 seeds are put forward Round 1: 173 peptides, 38 chains. Longest chain 7 peptides. Score 0.228 Round 2: 230 peptides, 47 chains. Longest chain 13 peptides. Score 0.279 Round 3: 246 peptides, 50 chains. Longest chain 9 peptides. Score 0.287 Round 4: 273 peptides, 51 chains. Longest chain 12 peptides. Score 0.342 Round 5: 262 peptides, 51 chains. Longest chain 10 peptides. Score 0.316 Taking the results from Round 4 Chains 51, Residues 222, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 15185 restraints for refining 6166 atoms. 14280 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2977 (Rfree = 0.000) for 6166 atoms. Found 29 (46 requested) and removed 88 (23 requested) atoms. Cycle 2: After refmac, R = 0.2907 (Rfree = 0.000) for 6025 atoms. Found 33 (46 requested) and removed 59 (23 requested) atoms. Cycle 3: After refmac, R = 0.2815 (Rfree = 0.000) for 5944 atoms. Found 30 (45 requested) and removed 47 (22 requested) atoms. Cycle 4: After refmac, R = 0.2857 (Rfree = 0.000) for 5890 atoms. Found 44 (44 requested) and removed 43 (22 requested) atoms. Cycle 5: After refmac, R = 0.2758 (Rfree = 0.000) for 5861 atoms. Found 31 (44 requested) and removed 40 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 5993 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6010 seeds are put forward Round 1: 236 peptides, 53 chains. Longest chain 7 peptides. Score 0.230 Round 2: 297 peptides, 60 chains. Longest chain 11 peptides. Score 0.309 Round 3: 328 peptides, 62 chains. Longest chain 13 peptides. Score 0.361 Round 4: 304 peptides, 55 chains. Longest chain 15 peptides. Score 0.373 Round 5: 313 peptides, 57 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 5 Chains 57, Residues 256, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13847 restraints for refining 5745 atoms. 12846 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2703 (Rfree = 0.000) for 5745 atoms. Found 23 (43 requested) and removed 80 (21 requested) atoms. Cycle 7: After refmac, R = 0.2518 (Rfree = 0.000) for 5659 atoms. Found 28 (42 requested) and removed 59 (21 requested) atoms. Cycle 8: After refmac, R = 0.2406 (Rfree = 0.000) for 5615 atoms. Found 31 (42 requested) and removed 32 (21 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2065 (Rfree = 0.000) for 5599 atoms. Found 12 (42 requested) and removed 27 (21 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 5581 atoms. Found 14 (42 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 5768 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5780 seeds are put forward Round 1: 301 peptides, 64 chains. Longest chain 9 peptides. Score 0.279 Round 2: 310 peptides, 57 chains. Longest chain 13 peptides. Score 0.368 Round 3: 324 peptides, 59 chains. Longest chain 9 peptides. Score 0.380 Round 4: 331 peptides, 60 chains. Longest chain 12 peptides. Score 0.386 Round 5: 334 peptides, 64 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 4 Chains 60, Residues 271, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13758 restraints for refining 5774 atoms. 12727 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2498 (Rfree = 0.000) for 5774 atoms. Found 31 (43 requested) and removed 48 (21 requested) atoms. Cycle 12: After refmac, R = 0.2483 (Rfree = 0.000) for 5734 atoms. Found 35 (43 requested) and removed 44 (21 requested) atoms. Cycle 13: After refmac, R = 0.2026 (Rfree = 0.000) for 5710 atoms. Found 7 (43 requested) and removed 26 (21 requested) atoms. Cycle 14: After refmac, R = 0.2117 (Rfree = 0.000) for 5679 atoms. Found 22 (42 requested) and removed 30 (21 requested) atoms. Cycle 15: After refmac, R = 0.1940 (Rfree = 0.000) for 5667 atoms. Found 6 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 5811 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5824 seeds are put forward Round 1: 282 peptides, 59 chains. Longest chain 9 peptides. Score 0.283 Round 2: 311 peptides, 58 chains. Longest chain 10 peptides. Score 0.361 Round 3: 327 peptides, 57 chains. Longest chain 15 peptides. Score 0.405 Round 4: 339 peptides, 59 chains. Longest chain 16 peptides. Score 0.413 Round 5: 325 peptides, 58 chains. Longest chain 13 peptides. Score 0.392 Taking the results from Round 4 Chains 59, Residues 280, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 13954 restraints for refining 5868 atoms. 12878 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2399 (Rfree = 0.000) for 5868 atoms. Found 34 (44 requested) and removed 65 (22 requested) atoms. Cycle 17: After refmac, R = 0.2292 (Rfree = 0.000) for 5814 atoms. Found 37 (44 requested) and removed 35 (22 requested) atoms. Cycle 18: After refmac, R = 0.2272 (Rfree = 0.000) for 5806 atoms. Found 23 (43 requested) and removed 36 (21 requested) atoms. Cycle 19: After refmac, R = 0.2201 (Rfree = 0.000) for 5784 atoms. Found 28 (43 requested) and removed 26 (21 requested) atoms. Cycle 20: After refmac, R = 0.2183 (Rfree = 0.000) for 5774 atoms. Found 26 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 5935 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5954 seeds are put forward Round 1: 274 peptides, 58 chains. Longest chain 11 peptides. Score 0.274 Round 2: 322 peptides, 61 chains. Longest chain 11 peptides. Score 0.357 Round 3: 318 peptides, 59 chains. Longest chain 11 peptides. Score 0.367 Round 4: 326 peptides, 57 chains. Longest chain 11 peptides. Score 0.403 Round 5: 317 peptides, 55 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 4 Chains 57, Residues 269, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14173 restraints for refining 5961 atoms. 13126 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2377 (Rfree = 0.000) for 5961 atoms. Found 25 (45 requested) and removed 70 (22 requested) atoms. Cycle 22: After refmac, R = 0.2338 (Rfree = 0.000) for 5906 atoms. Found 30 (44 requested) and removed 49 (22 requested) atoms. Cycle 23: After refmac, R = 0.2196 (Rfree = 0.000) for 5883 atoms. Found 30 (44 requested) and removed 33 (22 requested) atoms. Cycle 24: After refmac, R = 0.2170 (Rfree = 0.000) for 5870 atoms. Found 30 (44 requested) and removed 39 (22 requested) atoms. Cycle 25: After refmac, R = 0.2112 (Rfree = 0.000) for 5853 atoms. Found 36 (44 requested) and removed 46 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.75 Search for helices and strands: 0 residues in 0 chains, 5989 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6002 seeds are put forward Round 1: 256 peptides, 53 chains. Longest chain 11 peptides. Score 0.281 Round 2: 283 peptides, 56 chains. Longest chain 12 peptides. Score 0.315 Round 3: 298 peptides, 57 chains. Longest chain 12 peptides. Score 0.341 Round 4: 302 peptides, 56 chains. Longest chain 14 peptides. Score 0.359 Round 5: 307 peptides, 54 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 5 Chains 55, Residues 253, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14342 restraints for refining 6091 atoms. 13283 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2188 (Rfree = 0.000) for 6091 atoms. Found 37 (46 requested) and removed 62 (23 requested) atoms. Cycle 27: After refmac, R = 0.2061 (Rfree = 0.000) for 6054 atoms. Found 33 (45 requested) and removed 41 (22 requested) atoms. Cycle 28: After refmac, R = 0.2131 (Rfree = 0.000) for 6026 atoms. Found 43 (45 requested) and removed 46 (22 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 6013 atoms. Found 39 (45 requested) and removed 35 (22 requested) atoms. Cycle 30: After refmac, R = 0.2056 (Rfree = 0.000) for 6009 atoms. Found 39 (45 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 6178 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6191 seeds are put forward Round 1: 216 peptides, 46 chains. Longest chain 10 peptides. Score 0.254 Round 2: 272 peptides, 52 chains. Longest chain 11 peptides. Score 0.329 Round 3: 272 peptides, 51 chains. Longest chain 9 peptides. Score 0.339 Round 4: 292 peptides, 50 chains. Longest chain 13 peptides. Score 0.395 Round 5: 293 peptides, 50 chains. Longest chain 15 peptides. Score 0.397 Taking the results from Round 5 Chains 50, Residues 243, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14574 restraints for refining 6168 atoms. 13627 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2235 (Rfree = 0.000) for 6168 atoms. Found 38 (46 requested) and removed 64 (23 requested) atoms. Cycle 32: After refmac, R = 0.2148 (Rfree = 0.000) for 6128 atoms. Found 46 (46 requested) and removed 43 (23 requested) atoms. Cycle 33: After refmac, R = 0.2079 (Rfree = 0.000) for 6120 atoms. Found 37 (46 requested) and removed 35 (23 requested) atoms. Cycle 34: After refmac, R = 0.2094 (Rfree = 0.000) for 6111 atoms. Found 44 (46 requested) and removed 33 (23 requested) atoms. Cycle 35: After refmac, R = 0.2058 (Rfree = 0.000) for 6119 atoms. Found 35 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.72 Search for helices and strands: 0 residues in 0 chains, 6306 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6328 seeds are put forward Round 1: 233 peptides, 52 chains. Longest chain 7 peptides. Score 0.233 Round 2: 254 peptides, 49 chains. Longest chain 9 peptides. Score 0.317 Round 3: 276 peptides, 50 chains. Longest chain 15 peptides. Score 0.359 Round 4: 279 peptides, 50 chains. Longest chain 11 peptides. Score 0.365 Round 5: 278 peptides, 48 chains. Longest chain 15 peptides. Score 0.383 Taking the results from Round 5 Chains 48, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14857 restraints for refining 6167 atoms. 13985 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2011 (Rfree = 0.000) for 6167 atoms. Found 33 (46 requested) and removed 41 (23 requested) atoms. Cycle 37: After refmac, R = 0.1920 (Rfree = 0.000) for 6157 atoms. Found 34 (46 requested) and removed 31 (23 requested) atoms. Cycle 38: After refmac, R = 0.1846 (Rfree = 0.000) for 6156 atoms. Found 24 (46 requested) and removed 29 (23 requested) atoms. Cycle 39: After refmac, R = 0.1841 (Rfree = 0.000) for 6143 atoms. Found 35 (46 requested) and removed 27 (23 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 6147 atoms. Found 34 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.71 Search for helices and strands: 0 residues in 0 chains, 6273 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6291 seeds are put forward Round 1: 207 peptides, 47 chains. Longest chain 7 peptides. Score 0.219 Round 2: 234 peptides, 45 chains. Longest chain 10 peptides. Score 0.310 Round 3: 228 peptides, 46 chains. Longest chain 8 peptides. Score 0.284 Round 4: 247 peptides, 46 chains. Longest chain 9 peptides. Score 0.331 Round 5: 251 peptides, 49 chains. Longest chain 9 peptides. Score 0.310 Taking the results from Round 4 Chains 46, Residues 201, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10860 reflections ( 99.99 % complete ) and 14682 restraints for refining 6168 atoms. 13881 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1878 (Rfree = 0.000) for 6168 atoms. Found 37 (46 requested) and removed 36 (23 requested) atoms. Cycle 42: After refmac, R = 0.1790 (Rfree = 0.000) for 6158 atoms. Found 39 (46 requested) and removed 32 (23 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1754 (Rfree = 0.000) for 6161 atoms. Found 29 (46 requested) and removed 34 (23 requested) atoms. Cycle 44: After refmac, R = 0.1753 (Rfree = 0.000) for 6149 atoms. Found 42 (46 requested) and removed 29 (23 requested) atoms. Cycle 45: After refmac, R = 0.1737 (Rfree = 0.000) for 6155 atoms. Found 36 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 3.66 Search for helices and strands: 0 residues in 0 chains, 6280 seeds are put forward NCS extension: 0 residues added, 6280 seeds are put forward Round 1: 202 peptides, 47 chains. Longest chain 6 peptides. Score 0.206 Round 2: 225 peptides, 46 chains. Longest chain 8 peptides. Score 0.277 Round 3: 226 peptides, 45 chains. Longest chain 12 peptides. Score 0.290 Round 4: 235 peptides, 45 chains. Longest chain 9 peptides. Score 0.312 Round 5: 226 peptides, 44 chains. Longest chain 8 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 190, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (190 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10860 reflections ( 99.99 % complete ) and 14940 restraints for refining 6168 atoms. 14204 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1847 (Rfree = 0.000) for 6168 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.1835 (Rfree = 0.000) for 6130 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1741 (Rfree = 0.000) for 6100 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1723 (Rfree = 0.000) for 6072 atoms. TimeTaking 82.75