Mon 24 Dec 00:31:05 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 2gfg-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-3.8-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/2gfg-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-3.8-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 00:31:09 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/2gfg-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-3.8-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 391 and 0 Target number of residues in the AU: 391 Target solvent content: 0.6500 Checking the provided sequence file Detected sequence length: 193 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 579 Adjusted target solvent content: 0.48 Input MTZ file: 2gfg-3.8-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: 19 Cell parameters: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4632 target number of atoms Had to go as low as 0.70 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: 94.065 3.800 Wilson plot Bfac: 77.83 6403 reflections ( 99.39 % complete ) and 0 restraints for refining 5109 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3580 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3335 (Rfree = 0.000) for 5109 atoms. Found 28 (28 requested) and removed 46 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 5166 seeds are put forward NCS extension: 0 residues added, 5166 seeds are put forward Round 1: 168 peptides, 35 chains. Longest chain 12 peptides. Score 0.261 Round 2: 216 peptides, 41 chains. Longest chain 9 peptides. Score 0.329 Round 3: 231 peptides, 43 chains. Longest chain 11 peptides. Score 0.347 Round 4: 249 peptides, 46 chains. Longest chain 12 peptides. Score 0.362 Round 5: 251 peptides, 43 chains. Longest chain 18 peptides. Score 0.402 Taking the results from Round 5 Chains 43, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 10259 restraints for refining 4187 atoms. 9470 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2617 (Rfree = 0.000) for 4187 atoms. Found 11 (23 requested) and removed 38 (11 requested) atoms. Cycle 2: After refmac, R = 0.2397 (Rfree = 0.000) for 4106 atoms. Found 15 (22 requested) and removed 31 (11 requested) atoms. Cycle 3: After refmac, R = 0.2411 (Rfree = 0.000) for 4067 atoms. Found 16 (22 requested) and removed 20 (11 requested) atoms. Cycle 4: After refmac, R = 0.2321 (Rfree = 0.000) for 4055 atoms. Found 12 (22 requested) and removed 19 (11 requested) atoms. Cycle 5: After refmac, R = 0.2103 (Rfree = 0.000) for 4037 atoms. Found 10 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 4158 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4187 seeds are put forward Round 1: 204 peptides, 41 chains. Longest chain 15 peptides. Score 0.294 Round 2: 251 peptides, 45 chains. Longest chain 13 peptides. Score 0.379 Round 3: 275 peptides, 43 chains. Longest chain 17 peptides. Score 0.463 Round 4: 265 peptides, 42 chains. Longest chain 17 peptides. Score 0.449 Round 5: 265 peptides, 40 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 5 Chains 40, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9682 restraints for refining 4161 atoms. 8822 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2345 (Rfree = 0.000) for 4161 atoms. Found 12 (22 requested) and removed 35 (11 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 4098 atoms. Found 12 (22 requested) and removed 30 (11 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 4068 atoms. Found 14 (22 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.2053 (Rfree = 0.000) for 4042 atoms. Found 19 (22 requested) and removed 22 (11 requested) atoms. Cycle 10: After refmac, R = 0.1992 (Rfree = 0.000) for 4031 atoms. Found 15 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 4185 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4199 seeds are put forward Round 1: 235 peptides, 46 chains. Longest chain 14 peptides. Score 0.323 Round 2: 269 peptides, 49 chains. Longest chain 15 peptides. Score 0.381 Round 3: 262 peptides, 43 chains. Longest chain 11 peptides. Score 0.430 Round 4: 278 peptides, 45 chains. Longest chain 18 peptides. Score 0.449 Round 5: 263 peptides, 44 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 45, Residues 233, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9404 restraints for refining 4190 atoms. 8491 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2049 (Rfree = 0.000) for 4190 atoms. Found 19 (23 requested) and removed 33 (11 requested) atoms. Cycle 12: After refmac, R = 0.1917 (Rfree = 0.000) for 4165 atoms. Found 16 (22 requested) and removed 22 (11 requested) atoms. Cycle 13: After refmac, R = 0.1887 (Rfree = 0.000) for 4150 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 14: After refmac, R = 0.1849 (Rfree = 0.000) for 4139 atoms. Found 13 (22 requested) and removed 19 (11 requested) atoms. Cycle 15: After refmac, R = 0.1697 (Rfree = 0.000) for 4127 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 4269 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 4298 seeds are put forward Round 1: 220 peptides, 45 chains. Longest chain 10 peptides. Score 0.291 Round 2: 277 peptides, 46 chains. Longest chain 20 peptides. Score 0.436 Round 3: 274 peptides, 46 chains. Longest chain 10 peptides. Score 0.428 Round 4: 255 peptides, 42 chains. Longest chain 14 peptides. Score 0.424 Round 5: 277 peptides, 47 chains. Longest chain 16 peptides. Score 0.425 Taking the results from Round 2 Chains 46, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9597 restraints for refining 4189 atoms. 8719 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1915 (Rfree = 0.000) for 4189 atoms. Found 12 (23 requested) and removed 20 (11 requested) atoms. Cycle 17: After refmac, R = 0.1867 (Rfree = 0.000) for 4164 atoms. Found 12 (22 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.1842 (Rfree = 0.000) for 4153 atoms. Found 13 (22 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.1650 (Rfree = 0.000) for 4142 atoms. Found 13 (22 requested) and removed 18 (11 requested) atoms. Cycle 20: After refmac, R = 0.1744 (Rfree = 0.000) for 4131 atoms. Found 20 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 4265 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4286 seeds are put forward Round 1: 201 peptides, 42 chains. Longest chain 7 peptides. Score 0.272 Round 2: 233 peptides, 41 chains. Longest chain 13 peptides. Score 0.377 Round 3: 229 peptides, 37 chains. Longest chain 14 peptides. Score 0.413 Round 4: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.396 Round 5: 231 peptides, 35 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 5 Chains 35, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9884 restraints for refining 4190 atoms. 9135 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2052 (Rfree = 0.000) for 4190 atoms. Found 10 (23 requested) and removed 23 (11 requested) atoms. Cycle 22: After refmac, R = 0.1937 (Rfree = 0.000) for 4161 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.1877 (Rfree = 0.000) for 4160 atoms. Found 17 (22 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1735 (Rfree = 0.000) for 4157 atoms. Found 14 (22 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1893 (Rfree = 0.000) for 4154 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 4274 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4291 seeds are put forward Round 1: 181 peptides, 39 chains. Longest chain 8 peptides. Score 0.249 Round 2: 219 peptides, 40 chains. Longest chain 11 peptides. Score 0.349 Round 3: 235 peptides, 43 chains. Longest chain 12 peptides. Score 0.358 Round 4: 232 peptides, 42 chains. Longest chain 11 peptides. Score 0.362 Round 5: 241 peptides, 41 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 5 Chains 41, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9923 restraints for refining 4190 atoms. 9164 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2079 (Rfree = 0.000) for 4190 atoms. Found 16 (23 requested) and removed 16 (11 requested) atoms. Cycle 27: After refmac, R = 0.2100 (Rfree = 0.000) for 4165 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 28: After refmac, R = 0.1953 (Rfree = 0.000) for 4155 atoms. Found 17 (22 requested) and removed 18 (11 requested) atoms. Cycle 29: After refmac, R = 0.1545 (Rfree = 0.000) for 4148 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1456 (Rfree = 0.000) for 4139 atoms. Found 2 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 4260 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4277 seeds are put forward Round 1: 172 peptides, 37 chains. Longest chain 9 peptides. Score 0.247 Round 2: 222 peptides, 40 chains. Longest chain 11 peptides. Score 0.358 Round 3: 224 peptides, 39 chains. Longest chain 18 peptides. Score 0.376 Round 4: 206 peptides, 35 chains. Longest chain 12 peptides. Score 0.374 Round 5: 207 peptides, 37 chains. Longest chain 10 peptides. Score 0.352 Taking the results from Round 3 Chains 39, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9910 restraints for refining 4190 atoms. 9209 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1900 (Rfree = 0.000) for 4190 atoms. Found 11 (23 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.1922 (Rfree = 0.000) for 4166 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.1865 (Rfree = 0.000) for 4163 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1497 (Rfree = 0.000) for 4157 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.1463 (Rfree = 0.000) for 4145 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 4255 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 4287 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 9 peptides. Score 0.259 Round 2: 206 peptides, 39 chains. Longest chain 12 peptides. Score 0.325 Round 3: 219 peptides, 40 chains. Longest chain 12 peptides. Score 0.349 Round 4: 225 peptides, 40 chains. Longest chain 12 peptides. Score 0.366 Round 5: 223 peptides, 41 chains. Longest chain 12 peptides. Score 0.349 Taking the results from Round 4 Chains 40, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9940 restraints for refining 4190 atoms. 9240 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1846 (Rfree = 0.000) for 4190 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. Cycle 37: After refmac, R = 0.1762 (Rfree = 0.000) for 4173 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1720 (Rfree = 0.000) for 4166 atoms. Found 11 (22 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1574 (Rfree = 0.000) for 4164 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1423 (Rfree = 0.000) for 4148 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 4266 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4280 seeds are put forward Round 1: 200 peptides, 45 chains. Longest chain 7 peptides. Score 0.231 Round 2: 206 peptides, 40 chains. Longest chain 12 peptides. Score 0.312 Round 3: 210 peptides, 38 chains. Longest chain 11 peptides. Score 0.348 Round 4: 195 peptides, 38 chains. Longest chain 8 peptides. Score 0.305 Round 5: 207 peptides, 38 chains. Longest chain 11 peptides. Score 0.340 Taking the results from Round 3 Chains 38, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6403 reflections ( 99.39 % complete ) and 9996 restraints for refining 4190 atoms. 9346 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1757 (Rfree = 0.000) for 4190 atoms. Found 12 (23 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.1788 (Rfree = 0.000) for 4179 atoms. Found 16 (23 requested) and removed 12 (11 requested) atoms. Cycle 43: After refmac, R = 0.1810 (Rfree = 0.000) for 4180 atoms. Found 21 (23 requested) and removed 15 (11 requested) atoms. Cycle 44: After refmac, R = 0.1827 (Rfree = 0.000) for 4184 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 45: After refmac, R = 0.1420 (Rfree = 0.000) for 4189 atoms. Found 7 (23 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 4288 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 4292 seeds are put forward Round 1: 148 peptides, 33 chains. Longest chain 7 peptides. Score 0.223 Round 2: 182 peptides, 33 chains. Longest chain 11 peptides. Score 0.330 Round 3: 173 peptides, 30 chains. Longest chain 11 peptides. Score 0.342 Round 4: 177 peptides, 32 chains. Longest chain 12 peptides. Score 0.328 Round 5: 168 peptides, 29 chains. Longest chain 16 peptides. Score 0.340 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gfg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6403 reflections ( 99.39 % complete ) and 10204 restraints for refining 4190 atoms. 9662 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1782 (Rfree = 0.000) for 4190 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1592 (Rfree = 0.000) for 4168 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1668 (Rfree = 0.000) for 4154 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1416 (Rfree = 0.000) for 4138 atoms. TimeTaking 51.17