null Sun 23 Dec 22:22:59 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 2gfg-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-4.0-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/2gfg-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-4.0-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 22:23:08 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/2gfg-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-4.0-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 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-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: 19 Cell parameters: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-4.0-parrot-hancs.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 5163 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3672 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3383 (Rfree = 0.000) for 5163 atoms. Found 24 (24 requested) and removed 68 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 5201 seeds are put forward NCS extension: 0 residues added, 5201 seeds are put forward Round 1: 145 peptides, 29 chains. Longest chain 11 peptides. Score 0.269 Round 2: 180 peptides, 34 chains. Longest chain 11 peptides. Score 0.311 Round 3: 211 peptides, 39 chains. Longest chain 13 peptides. Score 0.339 Round 4: 217 peptides, 41 chains. Longest chain 10 peptides. Score 0.332 Round 5: 230 peptides, 39 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 39, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10267 restraints for refining 4181 atoms. 9542 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2588 (Rfree = 0.000) for 4181 atoms. Found 10 (19 requested) and removed 39 (9 requested) atoms. Cycle 2: After refmac, R = 0.2425 (Rfree = 0.000) for 4113 atoms. Found 15 (19 requested) and removed 27 (9 requested) atoms. Cycle 3: After refmac, R = 0.1952 (Rfree = 0.000) for 4079 atoms. Found 1 (19 requested) and removed 25 (9 requested) atoms. Cycle 4: After refmac, R = 0.1801 (Rfree = 0.000) for 4046 atoms. Found 4 (19 requested) and removed 17 (9 requested) atoms. Cycle 5: After refmac, R = 0.1751 (Rfree = 0.000) for 4030 atoms. Found 3 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 4163 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4185 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 8 peptides. Score 0.271 Round 2: 225 peptides, 39 chains. Longest chain 16 peptides. Score 0.378 Round 3: 234 peptides, 40 chains. Longest chain 11 peptides. Score 0.391 Round 4: 219 peptides, 33 chains. Longest chain 16 peptides. Score 0.433 Round 5: 219 peptides, 37 chains. Longest chain 14 peptides. Score 0.386 Taking the results from Round 4 Chains 33, Residues 186, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10200 restraints for refining 4183 atoms. 9462 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2370 (Rfree = 0.000) for 4183 atoms. Found 7 (19 requested) and removed 38 (9 requested) atoms. Cycle 7: After refmac, R = 0.2290 (Rfree = 0.000) for 4117 atoms. Found 17 (19 requested) and removed 35 (9 requested) atoms. Cycle 8: After refmac, R = 0.2064 (Rfree = 0.000) for 4079 atoms. Found 18 (19 requested) and removed 26 (9 requested) atoms. Cycle 9: After refmac, R = 0.2103 (Rfree = 0.000) for 4062 atoms. Found 13 (19 requested) and removed 18 (9 requested) atoms. Cycle 10: After refmac, R = 0.1969 (Rfree = 0.000) for 4047 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 4192 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4215 seeds are put forward Round 1: 193 peptides, 38 chains. Longest chain 11 peptides. Score 0.299 Round 2: 210 peptides, 35 chains. Longest chain 12 peptides. Score 0.385 Round 3: 216 peptides, 35 chains. Longest chain 16 peptides. Score 0.401 Round 4: 218 peptides, 34 chains. Longest chain 17 peptides. Score 0.419 Round 5: 226 peptides, 36 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 4 Chains 34, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10226 restraints for refining 4183 atoms. 9524 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1970 (Rfree = 0.000) for 4183 atoms. Found 13 (19 requested) and removed 27 (9 requested) atoms. Cycle 12: After refmac, R = 0.1934 (Rfree = 0.000) for 4151 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 13: After refmac, R = 0.1894 (Rfree = 0.000) for 4127 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 14: After refmac, R = 0.1948 (Rfree = 0.000) for 4106 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 15: After refmac, R = 0.1921 (Rfree = 0.000) for 4091 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 4230 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4250 seeds are put forward Round 1: 201 peptides, 40 chains. Longest chain 10 peptides. Score 0.297 Round 2: 211 peptides, 37 chains. Longest chain 13 peptides. Score 0.363 Round 3: 227 peptides, 38 chains. Longest chain 11 peptides. Score 0.396 Round 4: 240 peptides, 38 chains. Longest chain 15 peptides. Score 0.430 Round 5: 222 peptides, 36 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 4 Chains 38, Residues 202, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9649 restraints for refining 4182 atoms. 8849 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2016 (Rfree = 0.000) for 4182 atoms. Found 15 (19 requested) and removed 29 (9 requested) atoms. Cycle 17: After refmac, R = 0.2077 (Rfree = 0.000) for 4146 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 18: After refmac, R = 0.1843 (Rfree = 0.000) for 4128 atoms. Found 11 (19 requested) and removed 19 (9 requested) atoms. Cycle 19: After refmac, R = 0.1827 (Rfree = 0.000) for 4111 atoms. Found 11 (19 requested) and removed 19 (9 requested) atoms. Cycle 20: After refmac, R = 0.1805 (Rfree = 0.000) for 4093 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 4224 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4246 seeds are put forward Round 1: 186 peptides, 40 chains. Longest chain 8 peptides. Score 0.252 Round 2: 219 peptides, 40 chains. Longest chain 12 peptides. Score 0.349 Round 3: 200 peptides, 33 chains. Longest chain 12 peptides. Score 0.382 Round 4: 216 peptides, 37 chains. Longest chain 14 peptides. Score 0.377 Round 5: 202 peptides, 32 chains. Longest chain 13 peptides. Score 0.399 Taking the results from Round 5 Chains 32, Residues 170, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9983 restraints for refining 4183 atoms. 9301 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1979 (Rfree = 0.000) for 4183 atoms. Found 14 (19 requested) and removed 21 (9 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 4160 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.1798 (Rfree = 0.000) for 4153 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 24: After refmac, R = 0.1365 (Rfree = 0.000) for 4142 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1539 (Rfree = 0.000) for 4127 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 4263 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4279 seeds are put forward Round 1: 180 peptides, 38 chains. Longest chain 10 peptides. Score 0.259 Round 2: 197 peptides, 39 chains. Longest chain 10 peptides. Score 0.298 Round 3: 210 peptides, 35 chains. Longest chain 12 peptides. Score 0.385 Round 4: 208 peptides, 35 chains. Longest chain 15 peptides. Score 0.379 Round 5: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 5 Chains 34, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10087 restraints for refining 4183 atoms. 9433 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2177 (Rfree = 0.000) for 4183 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 27: After refmac, R = 0.2129 (Rfree = 0.000) for 4155 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 28: After refmac, R = 0.1943 (Rfree = 0.000) for 4136 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 29: After refmac, R = 0.2120 (Rfree = 0.000) for 4128 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 30: After refmac, R = 0.1474 (Rfree = 0.000) for 4109 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 4230 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4246 seeds are put forward Round 1: 164 peptides, 34 chains. Longest chain 12 peptides. Score 0.261 Round 2: 204 peptides, 33 chains. Longest chain 13 peptides. Score 0.393 Round 3: 203 peptides, 32 chains. Longest chain 15 peptides. Score 0.402 Round 4: 219 peptides, 32 chains. Longest chain 18 peptides. Score 0.445 Round 5: 203 peptides, 31 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 4 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 9821 restraints for refining 4182 atoms. 9105 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2316 (Rfree = 0.000) for 4182 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 32: After refmac, R = 0.1912 (Rfree = 0.000) for 4147 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.1846 (Rfree = 0.000) for 4137 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 34: After refmac, R = 0.1869 (Rfree = 0.000) for 4132 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 35: After refmac, R = 0.1288 (Rfree = 0.000) for 4127 atoms. Found 8 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 4224 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4237 seeds are put forward Round 1: 165 peptides, 32 chains. Longest chain 12 peptides. Score 0.291 Round 2: 179 peptides, 34 chains. Longest chain 13 peptides. Score 0.308 Round 3: 199 peptides, 33 chains. Longest chain 14 peptides. Score 0.379 Round 4: 189 peptides, 32 chains. Longest chain 11 peptides. Score 0.363 Round 5: 215 peptides, 33 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 5 Chains 33, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10018 restraints for refining 4183 atoms. 9323 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2080 (Rfree = 0.000) for 4183 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 37: After refmac, R = 0.1840 (Rfree = 0.000) for 4165 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.1437 (Rfree = 0.000) for 4157 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.1313 (Rfree = 0.000) for 4143 atoms. Found 0 (19 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.1317 (Rfree = 0.000) for 4125 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 4247 seeds are put forward Round 1: 176 peptides, 38 chains. Longest chain 10 peptides. Score 0.246 Round 2: 192 peptides, 37 chains. Longest chain 14 peptides. Score 0.308 Round 3: 194 peptides, 36 chains. Longest chain 14 peptides. Score 0.327 Round 4: 192 peptides, 35 chains. Longest chain 9 peptides. Score 0.334 Round 5: 202 peptides, 36 chains. Longest chain 14 peptides. Score 0.350 Taking the results from Round 5 Chains 36, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 99.30 % complete ) and 10070 restraints for refining 4182 atoms. 9442 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1921 (Rfree = 0.000) for 4182 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 42: After refmac, R = 0.1780 (Rfree = 0.000) for 4158 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 43: After refmac, R = 0.1926 (Rfree = 0.000) for 4154 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 44: After refmac, R = 0.1338 (Rfree = 0.000) for 4150 atoms. Found 4 (19 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.1192 (Rfree = 0.000) for 4131 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 4258 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4274 seeds are put forward Round 1: 125 peptides, 28 chains. Longest chain 9 peptides. Score 0.215 Round 2: 139 peptides, 23 chains. Longest chain 16 peptides. Score 0.333 Round 3: 136 peptides, 21 chains. Longest chain 16 peptides. Score 0.352 Round 4: 136 peptides, 22 chains. Longest chain 13 peptides. Score 0.338 Round 5: 140 peptides, 22 chains. Longest chain 17 peptides. Score 0.351 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 115, 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 10288 restraints for refining 4177 atoms. 9849 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1899 (Rfree = 0.000) for 4177 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1856 (Rfree = 0.000) for 4161 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1567 (Rfree = 0.000) for 4149 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1722 (Rfree = 0.000) for 4136 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:24:31 GMT 2018 Job finished. TimeTaking 61.53 Used memory is bytes: 727600