Mon 24 Dec 00:35:26 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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 00:35:31 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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 513 and 0 Target number of residues in the AU: 513 Target solvent content: 0.6220 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 62.41 9184 reflections ( 99.99 % complete ) and 0 restraints for refining 7475 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3768 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3691 (Rfree = 0.000) for 7475 atoms. Found 39 (47 requested) and removed 243 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.94 Search for helices and strands: 0 residues in 0 chains, 7377 seeds are put forward NCS extension: 0 residues added, 7377 seeds are put forward Round 1: 199 peptides, 46 chains. Longest chain 7 peptides. Score 0.208 Round 2: 253 peptides, 51 chains. Longest chain 9 peptides. Score 0.294 Round 3: 270 peptides, 54 chains. Longest chain 9 peptides. Score 0.305 Round 4: 282 peptides, 52 chains. Longest chain 13 peptides. Score 0.353 Round 5: 290 peptides, 56 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 4 Chains 53, Residues 230, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15310 restraints for refining 6149 atoms. 14379 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2755 (Rfree = 0.000) for 6149 atoms. Found 21 (39 requested) and removed 115 (19 requested) atoms. Cycle 2: After refmac, R = 0.2539 (Rfree = 0.000) for 5977 atoms. Found 18 (38 requested) and removed 67 (19 requested) atoms. Cycle 3: After refmac, R = 0.2537 (Rfree = 0.000) for 5886 atoms. Found 24 (38 requested) and removed 69 (19 requested) atoms. Cycle 4: After refmac, R = 0.2419 (Rfree = 0.000) for 5817 atoms. Found 19 (37 requested) and removed 51 (18 requested) atoms. Cycle 5: After refmac, R = 0.2434 (Rfree = 0.000) for 5770 atoms. Found 32 (37 requested) and removed 41 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 5942 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5957 seeds are put forward Round 1: 249 peptides, 54 chains. Longest chain 7 peptides. Score 0.253 Round 2: 295 peptides, 55 chains. Longest chain 13 peptides. Score 0.353 Round 3: 287 peptides, 51 chains. Longest chain 13 peptides. Score 0.374 Round 4: 294 peptides, 52 chains. Longest chain 12 peptides. Score 0.380 Round 5: 312 peptides, 54 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 5 Chains 54, Residues 258, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14082 restraints for refining 5930 atoms. 13038 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2640 (Rfree = 0.000) for 5930 atoms. Found 31 (38 requested) and removed 141 (19 requested) atoms. Cycle 7: After refmac, R = 0.2345 (Rfree = 0.000) for 5784 atoms. Found 16 (37 requested) and removed 54 (18 requested) atoms. Cycle 8: After refmac, R = 0.2277 (Rfree = 0.000) for 5719 atoms. Found 30 (36 requested) and removed 34 (18 requested) atoms. Cycle 9: After refmac, R = 0.2219 (Rfree = 0.000) for 5701 atoms. Found 36 (36 requested) and removed 38 (18 requested) atoms. Cycle 10: After refmac, R = 0.2071 (Rfree = 0.000) for 5691 atoms. Found 32 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 5842 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5862 seeds are put forward Round 1: 258 peptides, 56 chains. Longest chain 9 peptides. Score 0.255 Round 2: 288 peptides, 54 chains. Longest chain 12 peptides. Score 0.347 Round 3: 316 peptides, 59 chains. Longest chain 11 peptides. Score 0.362 Round 4: 320 peptides, 52 chains. Longest chain 12 peptides. Score 0.436 Round 5: 307 peptides, 54 chains. Longest chain 11 peptides. Score 0.390 Taking the results from Round 4 Chains 53, Residues 268, Estimated correctness of the model 0.0 % 6 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 13983 restraints for refining 5930 atoms. 12909 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2219 (Rfree = 0.000) for 5930 atoms. Found 15 (38 requested) and removed 84 (19 requested) atoms. Cycle 12: After refmac, R = 0.2143 (Rfree = 0.000) for 5830 atoms. Found 16 (37 requested) and removed 51 (18 requested) atoms. Cycle 13: After refmac, R = 0.2081 (Rfree = 0.000) for 5776 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 14: After refmac, R = 0.1962 (Rfree = 0.000) for 5767 atoms. Found 33 (37 requested) and removed 31 (18 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 5762 atoms. Found 33 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.81 Search for helices and strands: 0 residues in 0 chains, 5942 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5958 seeds are put forward Round 1: 239 peptides, 49 chains. Longest chain 9 peptides. Score 0.280 Round 2: 297 peptides, 53 chains. Longest chain 13 peptides. Score 0.377 Round 3: 274 peptides, 45 chains. Longest chain 10 peptides. Score 0.403 Round 4: 275 peptides, 44 chains. Longest chain 15 peptides. Score 0.415 Round 5: 301 peptides, 47 chains. Longest chain 18 peptides. Score 0.442 Taking the results from Round 5 Chains 47, Residues 254, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14648 restraints for refining 6082 atoms. 13627 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2176 (Rfree = 0.000) for 6082 atoms. Found 26 (39 requested) and removed 95 (19 requested) atoms. Cycle 17: After refmac, R = 0.2022 (Rfree = 0.000) for 5993 atoms. Found 38 (38 requested) and removed 57 (19 requested) atoms. Cycle 18: After refmac, R = 0.2115 (Rfree = 0.000) for 5965 atoms. Found 35 (38 requested) and removed 63 (19 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 5931 atoms. Found 19 (38 requested) and removed 38 (19 requested) atoms. Cycle 20: After refmac, R = 0.2125 (Rfree = 0.000) for 5906 atoms. Found 37 (37 requested) and removed 43 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 6085 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6110 seeds are put forward Round 1: 234 peptides, 53 chains. Longest chain 7 peptides. Score 0.225 Round 2: 256 peptides, 45 chains. Longest chain 10 peptides. Score 0.362 Round 3: 256 peptides, 47 chains. Longest chain 11 peptides. Score 0.342 Round 4: 281 peptides, 49 chains. Longest chain 11 peptides. Score 0.380 Round 5: 273 peptides, 46 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 46, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14968 restraints for refining 6114 atoms. 14106 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2211 (Rfree = 0.000) for 6114 atoms. Found 34 (39 requested) and removed 54 (19 requested) atoms. Cycle 22: After refmac, R = 0.2146 (Rfree = 0.000) for 6076 atoms. Found 32 (39 requested) and removed 55 (19 requested) atoms. Cycle 23: After refmac, R = 0.2154 (Rfree = 0.000) for 6038 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. Cycle 24: After refmac, R = 0.2021 (Rfree = 0.000) for 6020 atoms. Found 35 (38 requested) and removed 55 (19 requested) atoms. Cycle 25: After refmac, R = 0.1977 (Rfree = 0.000) for 5993 atoms. Found 31 (38 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 6131 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6146 seeds are put forward Round 1: 227 peptides, 50 chains. Longest chain 8 peptides. Score 0.239 Round 2: 273 peptides, 53 chains. Longest chain 10 peptides. Score 0.322 Round 3: 251 peptides, 46 chains. Longest chain 11 peptides. Score 0.340 Round 4: 270 peptides, 49 chains. Longest chain 17 peptides. Score 0.355 Round 5: 269 peptides, 48 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 5 Chains 48, Residues 221, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14743 restraints for refining 6133 atoms. 13877 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2075 (Rfree = 0.000) for 6133 atoms. Found 31 (39 requested) and removed 68 (19 requested) atoms. Cycle 27: After refmac, R = 0.2079 (Rfree = 0.000) for 6083 atoms. Found 39 (39 requested) and removed 43 (19 requested) atoms. Cycle 28: After refmac, R = 0.2069 (Rfree = 0.000) for 6063 atoms. Found 39 (39 requested) and removed 34 (19 requested) atoms. Cycle 29: After refmac, R = 0.2164 (Rfree = 0.000) for 6061 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 30: After refmac, R = 0.2058 (Rfree = 0.000) for 6054 atoms. Found 37 (38 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 6244 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6257 seeds are put forward Round 1: 213 peptides, 45 chains. Longest chain 8 peptides. Score 0.257 Round 2: 261 peptides, 51 chains. Longest chain 8 peptides. Score 0.313 Round 3: 259 peptides, 49 chains. Longest chain 11 peptides. Score 0.329 Round 4: 263 peptides, 48 chains. Longest chain 9 peptides. Score 0.348 Round 5: 264 peptides, 44 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 5 Chains 44, Residues 220, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14830 restraints for refining 6150 atoms. 13970 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2210 (Rfree = 0.000) for 6150 atoms. Found 39 (39 requested) and removed 64 (19 requested) atoms. Cycle 32: After refmac, R = 0.2025 (Rfree = 0.000) for 6105 atoms. Found 36 (39 requested) and removed 44 (19 requested) atoms. Cycle 33: After refmac, R = 0.2074 (Rfree = 0.000) for 6089 atoms. Found 39 (39 requested) and removed 35 (19 requested) atoms. Cycle 34: After refmac, R = 0.2023 (Rfree = 0.000) for 6085 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. Cycle 35: After refmac, R = 0.2021 (Rfree = 0.000) for 6089 atoms. Found 34 (39 requested) and removed 39 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.86 Search for helices and strands: 0 residues in 0 chains, 6230 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6243 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 7 peptides. Score 0.246 Round 2: 207 peptides, 40 chains. Longest chain 9 peptides. Score 0.296 Round 3: 218 peptides, 40 chains. Longest chain 11 peptides. Score 0.323 Round 4: 216 peptides, 39 chains. Longest chain 9 peptides. Score 0.329 Round 5: 227 peptides, 44 chains. Longest chain 8 peptides. Score 0.303 Taking the results from Round 4 Chains 39, Residues 177, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15216 restraints for refining 6150 atoms. 14534 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2061 (Rfree = 0.000) for 6150 atoms. Found 25 (39 requested) and removed 50 (19 requested) atoms. Cycle 37: After refmac, R = 0.2067 (Rfree = 0.000) for 6113 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. Cycle 38: After refmac, R = 0.1985 (Rfree = 0.000) for 6098 atoms. Found 36 (39 requested) and removed 27 (19 requested) atoms. Cycle 39: After refmac, R = 0.2028 (Rfree = 0.000) for 6095 atoms. Found 38 (39 requested) and removed 33 (19 requested) atoms. Cycle 40: After refmac, R = 0.1957 (Rfree = 0.000) for 6095 atoms. Found 39 (39 requested) and removed 31 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 6261 seeds are put forward NCS extension: 0 residues added, 6261 seeds are put forward Round 1: 178 peptides, 38 chains. Longest chain 7 peptides. Score 0.242 Round 2: 221 peptides, 42 chains. Longest chain 16 peptides. Score 0.309 Round 3: 220 peptides, 42 chains. Longest chain 12 peptides. Score 0.307 Round 4: 225 peptides, 42 chains. Longest chain 15 peptides. Score 0.319 Round 5: 218 peptides, 41 chains. Longest chain 16 peptides. Score 0.312 Taking the results from Round 4 Chains 42, Residues 183, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15103 restraints for refining 6150 atoms. 14400 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1975 (Rfree = 0.000) for 6150 atoms. Found 36 (39 requested) and removed 37 (19 requested) atoms. Cycle 42: After refmac, R = 0.1946 (Rfree = 0.000) for 6136 atoms. Found 38 (39 requested) and removed 36 (19 requested) atoms. Cycle 43: After refmac, R = 0.1873 (Rfree = 0.000) for 6130 atoms. Found 38 (39 requested) and removed 36 (19 requested) atoms. Cycle 44: After refmac, R = 0.1906 (Rfree = 0.000) for 6125 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. Cycle 45: After refmac, R = 0.1876 (Rfree = 0.000) for 6135 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 6302 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6327 seeds are put forward Round 1: 173 peptides, 38 chains. Longest chain 8 peptides. Score 0.228 Round 2: 202 peptides, 41 chains. Longest chain 8 peptides. Score 0.272 Round 3: 184 peptides, 34 chains. Longest chain 9 peptides. Score 0.303 Round 4: 190 peptides, 34 chains. Longest chain 16 peptides. Score 0.319 Round 5: 172 peptides, 34 chains. Longest chain 8 peptides. Score 0.272 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 156, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2a9v-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9184 reflections ( 99.99 % complete ) and 15321 restraints for refining 6150 atoms. 14714 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1973 (Rfree = 0.000) for 6150 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1975 (Rfree = 0.000) for 6123 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2043 (Rfree = 0.000) for 6100 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1924 (Rfree = 0.000) for 6072 atoms. TimeTaking 65.68