Mon 24 Dec 08:07:36 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 2a9v-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-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/2a9v-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-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 08:07:41 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/2a9v-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-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 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-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.2-parrot-noncs.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 7506 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3776 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3218 (Rfree = 0.000) for 7506 atoms. Found 15 (67 requested) and removed 170 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.65 Search for helices and strands: 0 residues in 0 chains, 7473 seeds are put forward NCS extension: 0 residues added, 7473 seeds are put forward Round 1: 193 peptides, 43 chains. Longest chain 8 peptides. Score 0.226 Round 2: 238 peptides, 48 chains. Longest chain 13 peptides. Score 0.288 Round 3: 253 peptides, 51 chains. Longest chain 8 peptides. Score 0.294 Round 4: 278 peptides, 55 chains. Longest chain 10 peptides. Score 0.314 Round 5: 278 peptides, 49 chains. Longest chain 12 peptides. Score 0.373 Taking the results from Round 5 Chains 49, Residues 229, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 15180 restraints for refining 6193 atoms. 14265 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2938 (Rfree = 0.000) for 6193 atoms. Found 22 (55 requested) and removed 85 (27 requested) atoms. Cycle 2: After refmac, R = 0.2901 (Rfree = 0.000) for 6095 atoms. Found 32 (55 requested) and removed 64 (27 requested) atoms. Cycle 3: After refmac, R = 0.2821 (Rfree = 0.000) for 6041 atoms. Found 29 (54 requested) and removed 56 (27 requested) atoms. Cycle 4: After refmac, R = 0.2799 (Rfree = 0.000) for 6006 atoms. Found 29 (53 requested) and removed 63 (26 requested) atoms. Cycle 5: After refmac, R = 0.2487 (Rfree = 0.000) for 5961 atoms. Found 11 (53 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.01 3.54 Search for helices and strands: 0 residues in 0 chains, 6126 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6140 seeds are put forward Round 1: 270 peptides, 58 chains. Longest chain 9 peptides. Score 0.264 Round 2: 307 peptides, 59 chains. Longest chain 12 peptides. Score 0.342 Round 3: 335 peptides, 60 chains. Longest chain 15 peptides. Score 0.395 Round 4: 326 peptides, 59 chains. Longest chain 15 peptides. Score 0.384 Round 5: 322 peptides, 55 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 5 Chains 55, Residues 267, Estimated correctness of the model 0.0 % 8 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14422 restraints for refining 6066 atoms. 13326 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2642 (Rfree = 0.000) for 6066 atoms. Found 18 (54 requested) and removed 98 (27 requested) atoms. Cycle 7: After refmac, R = 0.2609 (Rfree = 0.000) for 5962 atoms. Found 24 (53 requested) and removed 56 (26 requested) atoms. Cycle 8: After refmac, R = 0.2556 (Rfree = 0.000) for 5918 atoms. Found 20 (53 requested) and removed 48 (26 requested) atoms. Cycle 9: After refmac, R = 0.2456 (Rfree = 0.000) for 5880 atoms. Found 18 (52 requested) and removed 35 (26 requested) atoms. Cycle 10: After refmac, R = 0.2215 (Rfree = 0.000) for 5849 atoms. Found 10 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 3.52 Search for helices and strands: 0 residues in 0 chains, 5983 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6004 seeds are put forward Round 1: 272 peptides, 60 chains. Longest chain 9 peptides. Score 0.249 Round 2: 295 peptides, 57 chains. Longest chain 10 peptides. Score 0.334 Round 3: 302 peptides, 57 chains. Longest chain 10 peptides. Score 0.350 Round 4: 309 peptides, 57 chains. Longest chain 11 peptides. Score 0.366 Round 5: 330 peptides, 61 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 5 Chains 61, Residues 269, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14266 restraints for refining 6070 atoms. 13229 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2471 (Rfree = 0.000) for 6070 atoms. Found 25 (54 requested) and removed 58 (27 requested) atoms. Cycle 12: After refmac, R = 0.2509 (Rfree = 0.000) for 6024 atoms. Found 25 (54 requested) and removed 48 (27 requested) atoms. Cycle 13: After refmac, R = 0.2172 (Rfree = 0.000) for 5989 atoms. Found 9 (53 requested) and removed 41 (26 requested) atoms. Cycle 14: After refmac, R = 0.2166 (Rfree = 0.000) for 5949 atoms. Found 15 (53 requested) and removed 42 (26 requested) atoms. Cycle 15: After refmac, R = 0.2252 (Rfree = 0.000) for 5916 atoms. Found 28 (53 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 3.54 Search for helices and strands: 0 residues in 0 chains, 6069 seeds are put forward NCS extension: 0 residues added, 6069 seeds are put forward Round 1: 296 peptides, 66 chains. Longest chain 12 peptides. Score 0.247 Round 2: 320 peptides, 63 chains. Longest chain 15 peptides. Score 0.333 Round 3: 300 peptides, 57 chains. Longest chain 14 peptides. Score 0.345 Round 4: 282 peptides, 53 chains. Longest chain 12 peptides. Score 0.343 Round 5: 284 peptides, 53 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 5 Chains 53, Residues 231, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12968 reflections ( 99.99 % complete ) and 14637 restraints for refining 6134 atoms. 13747 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2263 (Rfree = 0.000) for 6134 atoms. Found 29 (55 requested) and removed 50 (27 requested) atoms. Cycle 17: After refmac, R = 0.2144 (Rfree = 0.000) for 6108 atoms. Found 24 (54 requested) and removed 33 (27 requested) atoms. Cycle 18: After refmac, R = 0.2052 (Rfree = 0.000) for 6086 atoms. Found 6 (54 requested) and removed 39 (27 requested) atoms. Cycle 19: After refmac, R = 0.2040 (Rfree = 0.000) for 6044 atoms. Found 27 (54 requested) and removed 32 (27 requested) atoms. Cycle 20: After refmac, R = 0.1915 (Rfree = 0.000) for 6033 atoms. Found 14 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 3.52 Search for helices and strands: 0 residues in 0 chains, 6127 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6138 seeds are put forward Round 1: 239 peptides, 50 chains. Longest chain 7 peptides. Score 0.270 Round 2: 279 peptides, 55 chains. Longest chain 10 peptides. Score 0.316 Round 3: 293 peptides, 54 chains. Longest chain 12 peptides. Score 0.358 Round 4: 311 peptides, 56 chains. Longest chain 10 peptides. Score 0.380 Round 5: 282 peptides, 50 chains. Longest chain 14 peptides. Score 0.372 Taking the results from Round 4 Chains 56, Residues 255, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14228 restraints for refining 6163 atoms. 13235 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2142 (Rfree = 0.000) for 6163 atoms. Found 22 (55 requested) and removed 57 (27 requested) atoms. Cycle 22: After refmac, R = 0.2590 (Rfree = 0.000) for 6120 atoms. Found 45 (54 requested) and removed 56 (27 requested) atoms. Cycle 23: After refmac, R = 0.1951 (Rfree = 0.000) for 6100 atoms. Found 12 (54 requested) and removed 36 (27 requested) atoms. Cycle 24: After refmac, R = 0.2543 (Rfree = 0.000) for 6067 atoms. Found 52 (54 requested) and removed 52 (27 requested) atoms. Cycle 25: After refmac, R = 0.1972 (Rfree = 0.000) for 6064 atoms. Found 16 (54 requested) and removed 42 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.97 3.50 Search for helices and strands: 0 residues in 0 chains, 6161 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 6171 seeds are put forward Round 1: 270 peptides, 57 chains. Longest chain 10 peptides. Score 0.274 Round 2: 278 peptides, 50 chains. Longest chain 12 peptides. Score 0.363 Round 3: 279 peptides, 50 chains. Longest chain 13 peptides. Score 0.365 Round 4: 267 peptides, 48 chains. Longest chain 13 peptides. Score 0.358 Round 5: 278 peptides, 44 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 5 Chains 44, Residues 234, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14454 restraints for refining 6193 atoms. 13551 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1985 (Rfree = 0.000) for 6193 atoms. Found 25 (55 requested) and removed 36 (27 requested) atoms. Cycle 27: After refmac, R = 0.2377 (Rfree = 0.000) for 6169 atoms. Found 51 (55 requested) and removed 50 (27 requested) atoms. Cycle 28: After refmac, R = 0.1967 (Rfree = 0.000) for 6162 atoms. Found 21 (55 requested) and removed 35 (27 requested) atoms. Cycle 29: After refmac, R = 0.1937 (Rfree = 0.000) for 6145 atoms. Found 13 (55 requested) and removed 31 (27 requested) atoms. Cycle 30: After refmac, R = 0.1940 (Rfree = 0.000) for 6122 atoms. Found 9 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 6214 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6227 seeds are put forward Round 1: 232 peptides, 47 chains. Longest chain 11 peptides. Score 0.284 Round 2: 263 peptides, 50 chains. Longest chain 11 peptides. Score 0.328 Round 3: 265 peptides, 45 chains. Longest chain 12 peptides. Score 0.383 Round 4: 255 peptides, 43 chains. Longest chain 12 peptides. Score 0.380 Round 5: 261 peptides, 43 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 5 Chains 43, Residues 218, Estimated correctness of the model 0.0 % 4 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14425 restraints for refining 6192 atoms. 13572 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2046 (Rfree = 0.000) for 6192 atoms. Found 33 (55 requested) and removed 58 (27 requested) atoms. Cycle 32: After refmac, R = 0.2001 (Rfree = 0.000) for 6156 atoms. Found 29 (55 requested) and removed 31 (27 requested) atoms. Cycle 33: After refmac, R = 0.2072 (Rfree = 0.000) for 6148 atoms. Found 38 (55 requested) and removed 38 (27 requested) atoms. Cycle 34: After refmac, R = 0.1890 (Rfree = 0.000) for 6138 atoms. Found 23 (55 requested) and removed 33 (27 requested) atoms. Cycle 35: After refmac, R = 0.1892 (Rfree = 0.000) for 6127 atoms. Found 30 (54 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 6223 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6238 seeds are put forward Round 1: 219 peptides, 46 chains. Longest chain 10 peptides. Score 0.261 Round 2: 258 peptides, 48 chains. Longest chain 10 peptides. Score 0.337 Round 3: 246 peptides, 42 chains. Longest chain 14 peptides. Score 0.369 Round 4: 244 peptides, 44 chains. Longest chain 13 peptides. Score 0.344 Round 5: 244 peptides, 42 chains. Longest chain 16 peptides. Score 0.364 Taking the results from Round 3 Chains 42, Residues 204, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14330 restraints for refining 6193 atoms. 13530 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1968 (Rfree = 0.000) for 6193 atoms. Found 34 (55 requested) and removed 34 (27 requested) atoms. Cycle 37: After refmac, R = 0.1884 (Rfree = 0.000) for 6181 atoms. Found 23 (55 requested) and removed 33 (27 requested) atoms. Cycle 38: After refmac, R = 0.1823 (Rfree = 0.000) for 6168 atoms. Found 18 (55 requested) and removed 35 (27 requested) atoms. Cycle 39: After refmac, R = 0.1882 (Rfree = 0.000) for 6146 atoms. Found 20 (55 requested) and removed 32 (27 requested) atoms. Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 6134 atoms. Found 26 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 6235 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6257 seeds are put forward Round 1: 212 peptides, 46 chains. Longest chain 10 peptides. Score 0.243 Round 2: 250 peptides, 48 chains. Longest chain 15 peptides. Score 0.317 Round 3: 256 peptides, 49 chains. Longest chain 16 peptides. Score 0.322 Round 4: 266 peptides, 50 chains. Longest chain 15 peptides. Score 0.335 Round 5: 247 peptides, 47 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 4 Chains 50, Residues 216, Estimated correctness of the model 0.0 % 6 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12968 reflections ( 99.99 % complete ) and 14147 restraints for refining 6193 atoms. 13301 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1942 (Rfree = 0.000) for 6193 atoms. Found 45 (55 requested) and removed 31 (27 requested) atoms. Cycle 42: After refmac, R = 0.1904 (Rfree = 0.000) for 6197 atoms. Found 20 (55 requested) and removed 32 (27 requested) atoms. Cycle 43: After refmac, R = 0.1894 (Rfree = 0.000) for 6180 atoms. Found 30 (55 requested) and removed 32 (27 requested) atoms. Cycle 44: After refmac, R = 0.1857 (Rfree = 0.000) for 6173 atoms. Found 26 (55 requested) and removed 30 (27 requested) atoms. Cycle 45: After refmac, R = 0.1832 (Rfree = 0.000) for 6168 atoms. Found 18 (55 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.02 3.55 Search for helices and strands: 0 residues in 0 chains, 6263 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6282 seeds are put forward Round 1: 195 peptides, 41 chains. Longest chain 8 peptides. Score 0.254 Round 2: 221 peptides, 41 chains. Longest chain 14 peptides. Score 0.320 Round 3: 233 peptides, 45 chains. Longest chain 12 peptides. Score 0.307 Round 4: 239 peptides, 45 chains. Longest chain 18 peptides. Score 0.322 Round 5: 234 peptides, 39 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 195, Estimated correctness of the model 0.0 % 6 chains (24 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input Building loops using Loopy2018 39 chains (195 residues) following loop building 6 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12968 reflections ( 99.99 % complete ) and 14428 restraints for refining 6193 atoms. 13636 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2040 (Rfree = 0.000) for 6193 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1987 (Rfree = 0.000) for 6158 atoms. Found 0 (55 requested) and removed 11 (27 requested) atoms. Cycle 48: After refmac, R = 0.1931 (Rfree = 0.000) for 6145 atoms. Found 0 (55 requested) and removed 3 (27 requested) atoms. Cycle 49: After refmac, R = 0.1954 (Rfree = 0.000) for 6140 atoms. TimeTaking 67.58