Sun 23 Dec 22:23:08 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.2-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 22:23:17 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-3.2-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 527 and 0 Target number of residues in the AU: 527 Target solvent content: 0.6117 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 57.34 12968 reflections ( 99.99 % complete ) and 0 restraints for refining 7494 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3785 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3435 (Rfree = 0.000) for 7494 atoms. Found 37 (67 requested) and removed 163 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.67 Search for helices and strands: 0 residues in 0 chains, 7458 seeds are put forward NCS extension: 0 residues added, 7458 seeds are put forward Round 1: 186 peptides, 42 chains. Longest chain 7 peptides. Score 0.218 Round 2: 250 peptides, 54 chains. Longest chain 7 peptides. Score 0.255 Round 3: 254 peptides, 51 chains. Longest chain 13 peptides. Score 0.296 Round 4: 277 peptides, 56 chains. Longest chain 9 peptides. Score 0.301 Round 5: 292 peptides, 53 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 5 Chains 53, Residues 239, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 15033 restraints for refining 6191 atoms. 14130 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2800 (Rfree = 0.000) for 6191 atoms. Found 27 (55 requested) and removed 151 (27 requested) atoms. Cycle 2: After refmac, R = 0.2617 (Rfree = 0.000) for 6009 atoms. Found 20 (54 requested) and removed 55 (27 requested) atoms. Cycle 3: After refmac, R = 0.2569 (Rfree = 0.000) for 5953 atoms. Found 14 (53 requested) and removed 51 (26 requested) atoms. Cycle 4: After refmac, R = 0.2262 (Rfree = 0.000) for 5905 atoms. Found 11 (53 requested) and removed 34 (26 requested) atoms. Cycle 5: After refmac, R = 0.2270 (Rfree = 0.000) for 5870 atoms. Found 5 (52 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 6005 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 6027 seeds are put forward Round 1: 238 peptides, 50 chains. Longest chain 8 peptides. Score 0.267 Round 2: 325 peptides, 62 chains. Longest chain 10 peptides. Score 0.354 Round 3: 322 peptides, 58 chains. Longest chain 13 peptides. Score 0.385 Round 4: 342 peptides, 59 chains. Longest chain 17 peptides. Score 0.419 Round 5: 336 peptides, 59 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 4 Chains 59, Residues 283, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 13663 restraints for refining 5914 atoms. 12540 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2532 (Rfree = 0.000) for 5914 atoms. Found 25 (53 requested) and removed 73 (26 requested) atoms. Cycle 7: After refmac, R = 0.2430 (Rfree = 0.000) for 5847 atoms. Found 12 (52 requested) and removed 34 (26 requested) atoms. Cycle 8: After refmac, R = 0.2384 (Rfree = 0.000) for 5809 atoms. Found 24 (52 requested) and removed 32 (26 requested) atoms. Cycle 9: After refmac, R = 0.2292 (Rfree = 0.000) for 5790 atoms. Found 15 (52 requested) and removed 39 (26 requested) atoms. Cycle 10: After refmac, R = 0.2161 (Rfree = 0.000) for 5756 atoms. Found 13 (51 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 5897 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 5930 seeds are put forward Round 1: 300 peptides, 64 chains. Longest chain 12 peptides. Score 0.277 Round 2: 326 peptides, 64 chains. Longest chain 13 peptides. Score 0.337 Round 3: 335 peptides, 65 chains. Longest chain 9 peptides. Score 0.348 Round 4: 344 peptides, 64 chains. Longest chain 11 peptides. Score 0.377 Round 5: 322 peptides, 61 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 4 Chains 64, Residues 280, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14104 restraints for refining 6003 atoms. 13037 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2387 (Rfree = 0.000) for 6003 atoms. Found 26 (53 requested) and removed 52 (26 requested) atoms. Cycle 12: After refmac, R = 0.2298 (Rfree = 0.000) for 5958 atoms. Found 21 (53 requested) and removed 49 (26 requested) atoms. Cycle 13: After refmac, R = 0.2234 (Rfree = 0.000) for 5922 atoms. Found 12 (53 requested) and removed 38 (26 requested) atoms. Cycle 14: After refmac, R = 0.2117 (Rfree = 0.000) for 5892 atoms. Found 7 (52 requested) and removed 34 (26 requested) atoms. Cycle 15: After refmac, R = 0.2155 (Rfree = 0.000) for 5859 atoms. Found 11 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.64 Search for helices and strands: 0 residues in 0 chains, 6000 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6013 seeds are put forward Round 1: 288 peptides, 63 chains. Longest chain 9 peptides. Score 0.258 Round 2: 319 peptides, 62 chains. Longest chain 16 peptides. Score 0.340 Round 3: 295 peptides, 55 chains. Longest chain 11 peptides. Score 0.353 Round 4: 311 peptides, 60 chains. Longest chain 10 peptides. Score 0.341 Round 5: 312 peptides, 54 chains. Longest chain 15 peptides. Score 0.401 Taking the results from Round 5 Chains 54, Residues 258, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14146 restraints for refining 6114 atoms. 13094 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2412 (Rfree = 0.000) for 6114 atoms. Found 33 (54 requested) and removed 63 (27 requested) atoms. Cycle 17: After refmac, R = 0.2313 (Rfree = 0.000) for 6064 atoms. Found 19 (54 requested) and removed 46 (27 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2165 (Rfree = 0.000) for 6029 atoms. Found 8 (54 requested) and removed 35 (27 requested) atoms. Cycle 19: After refmac, R = 0.2164 (Rfree = 0.000) for 5997 atoms. Found 14 (53 requested) and removed 32 (26 requested) atoms. Cycle 20: After refmac, R = 0.2135 (Rfree = 0.000) for 5974 atoms. Found 8 (53 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.61 Search for helices and strands: 0 residues in 0 chains, 6103 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 6131 seeds are put forward Round 1: 278 peptides, 56 chains. Longest chain 10 peptides. Score 0.304 Round 2: 306 peptides, 59 chains. Longest chain 11 peptides. Score 0.340 Round 3: 323 peptides, 60 chains. Longest chain 13 peptides. Score 0.368 Round 4: 317 peptides, 55 chains. Longest chain 13 peptides. Score 0.402 Round 5: 319 peptides, 55 chains. Longest chain 10 peptides. Score 0.406 Taking the results from Round 5 Chains 55, Residues 264, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14494 restraints for refining 6172 atoms. 13478 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2353 (Rfree = 0.000) for 6172 atoms. Found 26 (55 requested) and removed 60 (27 requested) atoms. Cycle 22: After refmac, R = 0.2198 (Rfree = 0.000) for 6132 atoms. Found 29 (55 requested) and removed 35 (27 requested) atoms. Cycle 23: After refmac, R = 0.2126 (Rfree = 0.000) for 6115 atoms. Found 21 (54 requested) and removed 34 (27 requested) atoms. Cycle 24: After refmac, R = 0.2053 (Rfree = 0.000) for 6096 atoms. Found 21 (54 requested) and removed 33 (27 requested) atoms. Cycle 25: After refmac, R = 0.1986 (Rfree = 0.000) for 6077 atoms. Found 9 (54 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 3.60 Search for helices and strands: 0 residues in 0 chains, 6175 seeds are put forward NCS extension: 0 residues added, 6175 seeds are put forward Round 1: 269 peptides, 56 chains. Longest chain 10 peptides. Score 0.282 Round 2: 298 peptides, 53 chains. Longest chain 15 peptides. Score 0.379 Round 3: 301 peptides, 54 chains. Longest chain 11 peptides. Score 0.376 Round 4: 318 peptides, 58 chains. Longest chain 11 peptides. Score 0.376 Round 5: 314 peptides, 59 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 2 Chains 54, Residues 245, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14295 restraints for refining 6178 atoms. 13288 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2135 (Rfree = 0.000) for 6178 atoms. Found 27 (55 requested) and removed 53 (27 requested) atoms. Cycle 27: After refmac, R = 0.2075 (Rfree = 0.000) for 6142 atoms. Found 14 (55 requested) and removed 39 (27 requested) atoms. Cycle 28: After refmac, R = 0.2102 (Rfree = 0.000) for 6112 atoms. Found 12 (54 requested) and removed 33 (27 requested) atoms. Cycle 29: After refmac, R = 0.2088 (Rfree = 0.000) for 6081 atoms. Found 5 (54 requested) and removed 29 (27 requested) atoms. Cycle 30: After refmac, R = 0.1955 (Rfree = 0.000) for 6056 atoms. Found 7 (54 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 3.55 Search for helices and strands: 0 residues in 0 chains, 6180 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6195 seeds are put forward Round 1: 272 peptides, 57 chains. Longest chain 10 peptides. Score 0.279 Round 2: 288 peptides, 50 chains. Longest chain 12 peptides. Score 0.386 Round 3: 290 peptides, 50 chains. Longest chain 16 peptides. Score 0.390 Round 4: 271 peptides, 46 chains. Longest chain 16 peptides. Score 0.386 Round 5: 249 peptides, 43 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 3 Chains 50, Residues 240, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14363 restraints for refining 6156 atoms. 13400 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2123 (Rfree = 0.000) for 6156 atoms. Found 32 (55 requested) and removed 47 (27 requested) atoms. Cycle 32: After refmac, R = 0.2016 (Rfree = 0.000) for 6136 atoms. Found 8 (55 requested) and removed 29 (27 requested) atoms. Cycle 33: After refmac, R = 0.1997 (Rfree = 0.000) for 6110 atoms. Found 18 (54 requested) and removed 29 (27 requested) atoms. Cycle 34: After refmac, R = 0.1919 (Rfree = 0.000) for 6091 atoms. Found 8 (54 requested) and removed 27 (27 requested) atoms. Cycle 35: After refmac, R = 0.2136 (Rfree = 0.000) for 6070 atoms. Found 33 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 3.55 Search for helices and strands: 0 residues in 0 chains, 6172 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6192 seeds are put forward Round 1: 247 peptides, 52 chains. Longest chain 10 peptides. Score 0.269 Round 2: 235 peptides, 44 chains. Longest chain 12 peptides. Score 0.323 Round 3: 241 peptides, 41 chains. Longest chain 21 peptides. Score 0.368 Round 4: 252 peptides, 46 chains. Longest chain 12 peptides. Score 0.343 Round 5: 243 peptides, 42 chains. Longest chain 15 peptides. Score 0.362 Taking the results from Round 3 Chains 41, Residues 200, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14786 restraints for refining 6193 atoms. 13989 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2149 (Rfree = 0.000) for 6193 atoms. Found 26 (55 requested) and removed 36 (27 requested) atoms. Cycle 37: After refmac, R = 0.1982 (Rfree = 0.000) for 6176 atoms. Found 19 (55 requested) and removed 28 (27 requested) atoms. Cycle 38: After refmac, R = 0.1893 (Rfree = 0.000) for 6163 atoms. Found 12 (55 requested) and removed 28 (27 requested) atoms. Cycle 39: After refmac, R = 0.1869 (Rfree = 0.000) for 6145 atoms. Found 12 (55 requested) and removed 27 (27 requested) atoms. Cycle 40: After refmac, R = 0.1872 (Rfree = 0.000) for 6126 atoms. Found 26 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 3.58 Search for helices and strands: 0 residues in 0 chains, 6244 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6271 seeds are put forward Round 1: 235 peptides, 49 chains. Longest chain 10 peptides. Score 0.270 Round 2: 257 peptides, 48 chains. Longest chain 9 peptides. Score 0.334 Round 3: 266 peptides, 48 chains. Longest chain 12 peptides. Score 0.355 Round 4: 271 peptides, 49 chains. Longest chain 11 peptides. Score 0.357 Round 5: 264 peptides, 43 chains. Longest chain 16 peptides. Score 0.400 Taking the results from Round 5 Chains 44, Residues 221, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14459 restraints for refining 6192 atoms. 13541 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2099 (Rfree = 0.000) for 6192 atoms. Found 25 (55 requested) and removed 34 (27 requested) atoms. Cycle 42: After refmac, R = 0.2110 (Rfree = 0.000) for 6176 atoms. Found 26 (55 requested) and removed 30 (27 requested) atoms. Cycle 43: After refmac, R = 0.2323 (Rfree = 0.000) for 6165 atoms. Found 44 (55 requested) and removed 34 (27 requested) atoms. Cycle 44: After refmac, R = 0.1958 (Rfree = 0.000) for 6169 atoms. Found 15 (55 requested) and removed 28 (27 requested) atoms. Cycle 45: After refmac, R = 0.2009 (Rfree = 0.000) for 6152 atoms. Found 19 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.57 Search for helices and strands: 0 residues in 0 chains, 6274 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6293 seeds are put forward Round 1: 254 peptides, 55 chains. Longest chain 13 peptides. Score 0.255 Round 2: 258 peptides, 52 chains. Longest chain 11 peptides. Score 0.296 Round 3: 267 peptides, 51 chains. Longest chain 12 peptides. Score 0.328 Round 4: 258 peptides, 46 chains. Longest chain 17 peptides. Score 0.357 Round 5: 254 peptides, 43 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 211, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (211 residues) following loop building 4 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12968 reflections ( 99.99 % complete ) and 14365 restraints for refining 6193 atoms. 13502 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1964 (Rfree = 0.000) for 6193 atoms. Found 0 (55 requested) and removed 24 (27 requested) atoms. Cycle 47: After refmac, R = 0.1925 (Rfree = 0.000) for 6165 atoms. Found 0 (55 requested) and removed 16 (27 requested) atoms. Cycle 48: After refmac, R = 0.2197 (Rfree = 0.000) for 6145 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2131 (Rfree = 0.000) for 6114 atoms. TimeTaking 79.48