Mon 24 Dec 00:22:43 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-4.0-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 00:22:47 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-4.0-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 382 and 0 Target number of residues in the AU: 382 Target solvent content: 0.6581 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-4.0-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-4.0-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 4.000 Wilson plot Bfac: 83.29 5507 reflections ( 99.30 % complete ) and 0 restraints for refining 5139 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3647 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3418 (Rfree = 0.000) for 5139 atoms. Found 24 (24 requested) and removed 57 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5216 seeds are put forward NCS extension: 0 residues added, 5216 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 10 peptides. Score 0.241 Round 2: 208 peptides, 39 chains. Longest chain 9 peptides. Score 0.330 Round 3: 213 peptides, 38 chains. Longest chain 10 peptides. Score 0.357 Round 4: 218 peptides, 35 chains. Longest chain 12 peptides. Score 0.407 Round 5: 217 peptides, 36 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 4 Chains 35, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10443 restraints for refining 4181 atoms. 9746 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2648 (Rfree = 0.000) for 4181 atoms. Found 15 (19 requested) and removed 31 (9 requested) atoms. Cycle 2: After refmac, R = 0.2723 (Rfree = 0.000) for 4121 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 3: After refmac, R = 0.2521 (Rfree = 0.000) for 4082 atoms. Found 15 (19 requested) and removed 27 (9 requested) atoms. Cycle 4: After refmac, R = 0.2083 (Rfree = 0.000) for 4033 atoms. Found 6 (19 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1967 (Rfree = 0.000) for 4009 atoms. Found 3 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 4146 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4162 seeds are put forward Round 1: 197 peptides, 41 chains. Longest chain 8 peptides. Score 0.273 Round 2: 233 peptides, 38 chains. Longest chain 14 peptides. Score 0.412 Round 3: 225 peptides, 36 chains. Longest chain 18 peptides. Score 0.414 Round 4: 235 peptides, 42 chains. Longest chain 12 peptides. Score 0.370 Round 5: 238 peptides, 40 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 3 Chains 36, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9748 restraints for refining 4021 atoms. 9028 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2362 (Rfree = 0.000) for 4021 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 4000 atoms. Found 14 (19 requested) and removed 23 (9 requested) atoms. Cycle 8: After refmac, R = 0.1915 (Rfree = 0.000) for 3973 atoms. Found 10 (18 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.1834 (Rfree = 0.000) for 3955 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.1860 (Rfree = 0.000) for 3944 atoms. Found 1 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 4042 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 4078 seeds are put forward Round 1: 205 peptides, 39 chains. Longest chain 8 peptides. Score 0.322 Round 2: 226 peptides, 37 chains. Longest chain 14 peptides. Score 0.405 Round 3: 217 peptides, 35 chains. Longest chain 15 peptides. Score 0.404 Round 4: 218 peptides, 35 chains. Longest chain 14 peptides. Score 0.407 Round 5: 238 peptides, 35 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 5 Chains 35, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9910 restraints for refining 4183 atoms. 9133 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2243 (Rfree = 0.000) for 4183 atoms. Found 15 (19 requested) and removed 40 (9 requested) atoms. Cycle 12: After refmac, R = 0.2026 (Rfree = 0.000) for 4129 atoms. Found 5 (19 requested) and removed 26 (9 requested) atoms. Cycle 13: After refmac, R = 0.2165 (Rfree = 0.000) for 4095 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 14: After refmac, R = 0.2049 (Rfree = 0.000) for 4070 atoms. Found 10 (19 requested) and removed 23 (9 requested) atoms. Cycle 15: After refmac, R = 0.2009 (Rfree = 0.000) for 4046 atoms. Found 5 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 4143 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 4174 seeds are put forward Round 1: 208 peptides, 42 chains. Longest chain 9 peptides. Score 0.293 Round 2: 228 peptides, 39 chains. Longest chain 12 peptides. Score 0.387 Round 3: 236 peptides, 39 chains. Longest chain 11 peptides. Score 0.408 Round 4: 232 peptides, 36 chains. Longest chain 13 peptides. Score 0.432 Round 5: 233 peptides, 38 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 4 Chains 36, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9967 restraints for refining 4182 atoms. 9219 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2141 (Rfree = 0.000) for 4182 atoms. Found 17 (19 requested) and removed 25 (9 requested) atoms. Cycle 17: After refmac, R = 0.2243 (Rfree = 0.000) for 4154 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 18: After refmac, R = 0.1939 (Rfree = 0.000) for 4135 atoms. Found 17 (19 requested) and removed 27 (9 requested) atoms. Cycle 19: After refmac, R = 0.1948 (Rfree = 0.000) for 4113 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 20: After refmac, R = 0.1976 (Rfree = 0.000) for 4096 atoms. Found 18 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 4217 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4231 seeds are put forward Round 1: 207 peptides, 45 chains. Longest chain 7 peptides. Score 0.252 Round 2: 234 peptides, 41 chains. Longest chain 16 peptides. Score 0.379 Round 3: 251 peptides, 37 chains. Longest chain 18 peptides. Score 0.469 Round 4: 242 peptides, 42 chains. Longest chain 14 peptides. Score 0.389 Round 5: 247 peptides, 39 chains. Longest chain 15 peptides. Score 0.437 Taking the results from Round 3 Chains 37, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9636 restraints for refining 4183 atoms. 8817 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1941 (Rfree = 0.000) for 4183 atoms. Found 13 (19 requested) and removed 28 (9 requested) atoms. Cycle 22: After refmac, R = 0.1930 (Rfree = 0.000) for 4144 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 23: After refmac, R = 0.1771 (Rfree = 0.000) for 4128 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 24: After refmac, R = 0.1760 (Rfree = 0.000) for 4121 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 25: After refmac, R = 0.1744 (Rfree = 0.000) for 4124 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 4254 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 4281 seeds are put forward Round 1: 187 peptides, 38 chains. Longest chain 9 peptides. Score 0.280 Round 2: 214 peptides, 36 chains. Longest chain 13 peptides. Score 0.384 Round 3: 205 peptides, 35 chains. Longest chain 10 peptides. Score 0.371 Round 4: 201 peptides, 35 chains. Longest chain 14 peptides. Score 0.360 Round 5: 212 peptides, 36 chains. Longest chain 10 peptides. Score 0.378 Taking the results from Round 2 Chains 36, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9884 restraints for refining 4181 atoms. 9208 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1878 (Rfree = 0.000) for 4181 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 27: After refmac, R = 0.1954 (Rfree = 0.000) for 4164 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 28: After refmac, R = 0.2017 (Rfree = 0.000) for 4152 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1783 (Rfree = 0.000) for 4143 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 30: After refmac, R = 0.1943 (Rfree = 0.000) for 4132 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 4231 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4249 seeds are put forward Round 1: 196 peptides, 44 chains. Longest chain 8 peptides. Score 0.231 Round 2: 229 peptides, 44 chains. Longest chain 14 peptides. Score 0.330 Round 3: 239 peptides, 45 chains. Longest chain 13 peptides. Score 0.346 Round 4: 241 peptides, 40 chains. Longest chain 15 peptides. Score 0.410 Round 5: 225 peptides, 39 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 4 Chains 40, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9681 restraints for refining 4183 atoms. 8917 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1955 (Rfree = 0.000) for 4183 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 32: After refmac, R = 0.1832 (Rfree = 0.000) for 4154 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.1708 (Rfree = 0.000) for 4133 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 34: After refmac, R = 0.1852 (Rfree = 0.000) for 4118 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 35: After refmac, R = 0.1617 (Rfree = 0.000) for 4103 atoms. Found 17 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 4224 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4245 seeds are put forward Round 1: 174 peptides, 38 chains. Longest chain 9 peptides. Score 0.240 Round 2: 195 peptides, 36 chains. Longest chain 15 peptides. Score 0.330 Round 3: 200 peptides, 36 chains. Longest chain 13 peptides. Score 0.344 Round 4: 214 peptides, 36 chains. Longest chain 15 peptides. Score 0.384 Round 5: 207 peptides, 38 chains. Longest chain 10 peptides. Score 0.340 Taking the results from Round 4 Chains 36, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9823 restraints for refining 4183 atoms. 9147 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 4183 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 37: After refmac, R = 0.2018 (Rfree = 0.000) for 4161 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 38: After refmac, R = 0.1877 (Rfree = 0.000) for 4143 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 39: After refmac, R = 0.1779 (Rfree = 0.000) for 4126 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 40: After refmac, R = 0.1767 (Rfree = 0.000) for 4104 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 4246 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4263 seeds are put forward Round 1: 157 peptides, 34 chains. Longest chain 12 peptides. Score 0.239 Round 2: 188 peptides, 33 chains. Longest chain 10 peptides. Score 0.347 Round 3: 195 peptides, 34 chains. Longest chain 13 peptides. Score 0.355 Round 4: 190 peptides, 33 chains. Longest chain 13 peptides. Score 0.353 Round 5: 187 peptides, 34 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 3 Chains 34, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9820 restraints for refining 4179 atoms. 9210 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1916 (Rfree = 0.000) for 4179 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 42: After refmac, R = 0.1885 (Rfree = 0.000) for 4153 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 43: After refmac, R = 0.1763 (Rfree = 0.000) for 4139 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 44: After refmac, R = 0.1660 (Rfree = 0.000) for 4121 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 45: After refmac, R = 0.1135 (Rfree = 0.000) for 4112 atoms. Found 8 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 4242 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4259 seeds are put forward Round 1: 153 peptides, 35 chains. Longest chain 7 peptides. Score 0.212 Round 2: 183 peptides, 37 chains. Longest chain 10 peptides. Score 0.281 Round 3: 180 peptides, 35 chains. Longest chain 10 peptides. Score 0.298 Round 4: 186 peptides, 34 chains. Longest chain 12 peptides. Score 0.329 Round 5: 172 peptides, 31 chains. Longest chain 11 peptides. Score 0.326 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 152, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5507 reflections ( 99.30 % complete ) and 9831 restraints for refining 4182 atoms. 9257 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1698 (Rfree = 0.000) for 4182 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1787 (Rfree = 0.000) for 4162 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 4148 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1188 (Rfree = 0.000) for 4127 atoms. TimeTaking 45.87