null Tue 25 Dec 19:27:55 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 2aml-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aml-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aml-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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/2aml-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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 ============================================================ Tue 25 Dec 19:28:05 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/2aml-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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 428 and 0 Target number of residues in the AU: 428 Target solvent content: 0.6624 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-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: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.65 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: 77.491 4.000 Wilson plot Bfac: 86.49 6170 reflections ( 99.66 % complete ) and 0 restraints for refining 6597 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3374 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3131 (Rfree = 0.000) for 6597 atoms. Found 31 (31 requested) and removed 126 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 4.20 Search for helices and strands: 0 residues in 0 chains, 6657 seeds are put forward NCS extension: 0 residues added, 6657 seeds are put forward Round 1: 186 peptides, 42 chains. Longest chain 9 peptides. Score 0.220 Round 2: 264 peptides, 52 chains. Longest chain 10 peptides. Score 0.318 Round 3: 277 peptides, 51 chains. Longest chain 14 peptides. Score 0.361 Round 4: 297 peptides, 53 chains. Longest chain 13 peptides. Score 0.388 Round 5: 299 peptides, 54 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 4 Chains 53, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 13057 restraints for refining 5389 atoms. 12134 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2320 (Rfree = 0.000) for 5389 atoms. Found 18 (25 requested) and removed 35 (12 requested) atoms. Cycle 2: After refmac, R = 0.2475 (Rfree = 0.000) for 5297 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 3: After refmac, R = 0.2334 (Rfree = 0.000) for 5241 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 4: After refmac, R = 0.2365 (Rfree = 0.000) for 5203 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 5: After refmac, R = 0.2382 (Rfree = 0.000) for 5157 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 4.26 Search for helices and strands: 0 residues in 0 chains, 5372 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5389 seeds are put forward Round 1: 240 peptides, 52 chains. Longest chain 7 peptides. Score 0.256 Round 2: 280 peptides, 50 chains. Longest chain 13 peptides. Score 0.378 Round 3: 289 peptides, 49 chains. Longest chain 12 peptides. Score 0.409 Round 4: 301 peptides, 50 chains. Longest chain 13 peptides. Score 0.427 Round 5: 303 peptides, 49 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 5 Chains 49, Residues 254, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 11903 restraints for refining 5064 atoms. 10901 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2234 (Rfree = 0.000) for 5064 atoms. Found 14 (24 requested) and removed 50 (12 requested) atoms. Cycle 7: After refmac, R = 0.1991 (Rfree = 0.000) for 4988 atoms. Found 16 (23 requested) and removed 43 (11 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 4936 atoms. Found 21 (23 requested) and removed 28 (11 requested) atoms. Cycle 9: After refmac, R = 0.1959 (Rfree = 0.000) for 4914 atoms. Found 17 (23 requested) and removed 27 (11 requested) atoms. Cycle 10: After refmac, R = 0.2031 (Rfree = 0.000) for 4893 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 4.30 Search for helices and strands: 0 residues in 0 chains, 5120 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5134 seeds are put forward Round 1: 262 peptides, 54 chains. Longest chain 11 peptides. Score 0.291 Round 2: 314 peptides, 56 chains. Longest chain 10 peptides. Score 0.398 Round 3: 305 peptides, 52 chains. Longest chain 11 peptides. Score 0.416 Round 4: 298 peptides, 52 chains. Longest chain 12 peptides. Score 0.400 Round 5: 302 peptides, 49 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 5 Chains 51, Residues 253, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12124 restraints for refining 5238 atoms. 11069 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2181 (Rfree = 0.000) for 5238 atoms. Found 24 (24 requested) and removed 66 (12 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 5164 atoms. Found 19 (24 requested) and removed 72 (12 requested) atoms. Cycle 13: After refmac, R = 0.2029 (Rfree = 0.000) for 5090 atoms. Found 20 (24 requested) and removed 27 (12 requested) atoms. Cycle 14: After refmac, R = 0.1898 (Rfree = 0.000) for 5052 atoms. Found 15 (24 requested) and removed 37 (12 requested) atoms. Cycle 15: After refmac, R = 0.1927 (Rfree = 0.000) for 5008 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 4.22 Search for helices and strands: 0 residues in 0 chains, 5177 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5188 seeds are put forward Round 1: 255 peptides, 55 chains. Longest chain 10 peptides. Score 0.262 Round 2: 287 peptides, 54 chains. Longest chain 14 peptides. Score 0.354 Round 3: 278 peptides, 50 chains. Longest chain 10 peptides. Score 0.373 Round 4: 289 peptides, 48 chains. Longest chain 12 peptides. Score 0.419 Round 5: 285 peptides, 51 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 4 Chains 49, Residues 241, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12160 restraints for refining 5226 atoms. 11170 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1979 (Rfree = 0.000) for 5226 atoms. Found 18 (24 requested) and removed 58 (12 requested) atoms. Cycle 17: After refmac, R = 0.1958 (Rfree = 0.000) for 5148 atoms. Found 23 (24 requested) and removed 27 (12 requested) atoms. Cycle 18: After refmac, R = 0.2028 (Rfree = 0.000) for 5122 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 19: After refmac, R = 0.1968 (Rfree = 0.000) for 5102 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 20: After refmac, R = 0.1848 (Rfree = 0.000) for 5088 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 5288 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5303 seeds are put forward Round 1: 224 peptides, 49 chains. Longest chain 9 peptides. Score 0.246 Round 2: 268 peptides, 54 chains. Longest chain 9 peptides. Score 0.307 Round 3: 265 peptides, 49 chains. Longest chain 12 peptides. Score 0.352 Round 4: 269 peptides, 47 chains. Longest chain 13 peptides. Score 0.383 Round 5: 269 peptides, 50 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 4 Chains 47, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12329 restraints for refining 5191 atoms. 11488 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2081 (Rfree = 0.000) for 5191 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 22: After refmac, R = 0.1833 (Rfree = 0.000) for 5150 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 23: After refmac, R = 0.2032 (Rfree = 0.000) for 5134 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 24: After refmac, R = 0.1846 (Rfree = 0.000) for 5103 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 25: After refmac, R = 0.2035 (Rfree = 0.000) for 5098 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 4.23 Search for helices and strands: 0 residues in 0 chains, 5255 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5268 seeds are put forward Round 1: 193 peptides, 43 chains. Longest chain 8 peptides. Score 0.229 Round 2: 252 peptides, 49 chains. Longest chain 10 peptides. Score 0.320 Round 3: 261 peptides, 46 chains. Longest chain 11 peptides. Score 0.374 Round 4: 259 peptides, 44 chains. Longest chain 19 peptides. Score 0.390 Round 5: 262 peptides, 42 chains. Longest chain 14 peptides. Score 0.417 Taking the results from Round 5 Chains 42, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12322 restraints for refining 5217 atoms. 11484 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1975 (Rfree = 0.000) for 5217 atoms. Found 24 (24 requested) and removed 42 (12 requested) atoms. Cycle 27: After refmac, R = 0.1976 (Rfree = 0.000) for 5182 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 28: After refmac, R = 0.1859 (Rfree = 0.000) for 5156 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 29: After refmac, R = 0.1297 (Rfree = 0.000) for 5134 atoms. Found 11 (24 requested) and removed 22 (12 requested) atoms. Cycle 30: After refmac, R = 0.1185 (Rfree = 0.000) for 5114 atoms. Found 4 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 4.22 Search for helices and strands: 0 residues in 0 chains, 5250 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 5275 seeds are put forward Round 1: 220 peptides, 47 chains. Longest chain 10 peptides. Score 0.258 Round 2: 235 peptides, 41 chains. Longest chain 11 peptides. Score 0.363 Round 3: 227 peptides, 40 chains. Longest chain 11 peptides. Score 0.354 Round 4: 234 peptides, 40 chains. Longest chain 11 peptides. Score 0.371 Round 5: 226 peptides, 35 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 5 Chains 36, Residues 191, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12484 restraints for refining 5310 atoms. 11699 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1807 (Rfree = 0.000) for 5310 atoms. Found 25 (25 requested) and removed 48 (12 requested) atoms. Cycle 32: After refmac, R = 0.1991 (Rfree = 0.000) for 5265 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 33: After refmac, R = 0.1687 (Rfree = 0.000) for 5246 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 34: After refmac, R = 0.1313 (Rfree = 0.000) for 5237 atoms. Found 6 (24 requested) and removed 18 (12 requested) atoms. Cycle 35: After refmac, R = 0.1206 (Rfree = 0.000) for 5213 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 4.22 Search for helices and strands: 0 residues in 0 chains, 5345 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5359 seeds are put forward Round 1: 180 peptides, 37 chains. Longest chain 11 peptides. Score 0.263 Round 2: 218 peptides, 36 chains. Longest chain 14 peptides. Score 0.375 Round 3: 228 peptides, 37 chains. Longest chain 15 peptides. Score 0.389 Round 4: 218 peptides, 34 chains. Longest chain 12 peptides. Score 0.397 Round 5: 210 peptides, 34 chains. Longest chain 14 peptides. Score 0.377 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 ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12856 restraints for refining 5290 atoms. 12154 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1981 (Rfree = 0.000) for 5290 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 37: After refmac, R = 0.2000 (Rfree = 0.000) for 5264 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.1921 (Rfree = 0.000) for 5249 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 39: After refmac, R = 0.1966 (Rfree = 0.000) for 5236 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 40: After refmac, R = 0.1889 (Rfree = 0.000) for 5220 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 5401 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5416 seeds are put forward Round 1: 167 peptides, 37 chains. Longest chain 8 peptides. Score 0.225 Round 2: 189 peptides, 37 chains. Longest chain 10 peptides. Score 0.288 Round 3: 184 peptides, 34 chains. Longest chain 12 peptides. Score 0.310 Round 4: 187 peptides, 32 chains. Longest chain 16 peptides. Score 0.341 Round 5: 184 peptides, 34 chains. Longest chain 13 peptides. Score 0.310 Taking the results from Round 4 Chains 32, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6170 reflections ( 99.66 % complete ) and 12427 restraints for refining 5202 atoms. 11839 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2010 (Rfree = 0.000) for 5202 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 42: After refmac, R = 0.2185 (Rfree = 0.000) for 5162 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 43: After refmac, R = 0.1935 (Rfree = 0.000) for 5144 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 44: After refmac, R = 0.2103 (Rfree = 0.000) for 5134 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 45: After refmac, R = 0.2129 (Rfree = 0.000) for 5125 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 4.21 Search for helices and strands: 0 residues in 0 chains, 5278 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5292 seeds are put forward Round 1: 164 peptides, 37 chains. Longest chain 9 peptides. Score 0.216 Round 2: 192 peptides, 40 chains. Longest chain 9 peptides. Score 0.261 Round 3: 191 peptides, 37 chains. Longest chain 14 peptides. Score 0.294 Round 4: 189 peptides, 37 chains. Longest chain 11 peptides. Score 0.288 Round 5: 189 peptides, 33 chains. Longest chain 17 peptides. Score 0.335 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 156, 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 2aml-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6170 reflections ( 99.66 % complete ) and 11742 restraints for refining 4979 atoms. 11151 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1989 (Rfree = 0.000) for 4979 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2004 (Rfree = 0.000) for 4956 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1982 (Rfree = 0.000) for 4934 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1985 (Rfree = 0.000) for 4914 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:42:19 GMT 2018 Job finished. TimeTaking 74.41 Used memory is bytes: 3279544