null Mon 24 Dec 08:02:39 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2otm-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-parrot-noncs ############### 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 08:02:43 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-parrot-noncs/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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6391 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-3.8-parrot-noncs.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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3696 target number of atoms Had to go as low as 0.75 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: 78.536 3.800 Wilson plot Bfac: 71.40 5499 reflections ( 99.73 % complete ) and 0 restraints for refining 4094 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3032 (Rfree = 0.000) for 4094 atoms. Found 22 (22 requested) and removed 48 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 4151 seeds are put forward NCS extension: 0 residues added, 4151 seeds are put forward Round 1: 227 peptides, 40 chains. Longest chain 13 peptides. Score 0.386 Round 2: 258 peptides, 38 chains. Longest chain 18 peptides. Score 0.495 Round 3: 254 peptides, 32 chains. Longest chain 17 peptides. Score 0.552 Round 4: 271 peptides, 33 chains. Longest chain 18 peptides. Score 0.581 Round 5: 278 peptides, 33 chains. Longest chain 17 peptides. Score 0.596 Taking the results from Round 5 Chains 35, Residues 245, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7018 restraints for refining 3343 atoms. 5920 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2369 (Rfree = 0.000) for 3343 atoms. Found 15 (18 requested) and removed 20 (9 requested) atoms. Cycle 2: After refmac, R = 0.2224 (Rfree = 0.000) for 3263 atoms. Found 10 (18 requested) and removed 21 (9 requested) atoms. Cycle 3: After refmac, R = 0.2224 (Rfree = 0.000) for 3223 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 4: After refmac, R = 0.2262 (Rfree = 0.000) for 3201 atoms. Found 5 (17 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2485 (Rfree = 0.000) for 3185 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3294 seeds are put forward Round 1: 257 peptides, 41 chains. Longest chain 18 peptides. Score 0.458 Round 2: 263 peptides, 34 chains. Longest chain 21 peptides. Score 0.552 Round 3: 271 peptides, 36 chains. Longest chain 23 peptides. Score 0.549 Round 4: 264 peptides, 31 chains. Longest chain 25 peptides. Score 0.586 Round 5: 273 peptides, 28 chains. Longest chain 23 peptides. Score 0.635 Taking the results from Round 5 Chains 30, Residues 245, Estimated correctness of the model 14.5 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7278 restraints for refining 3343 atoms. 6258 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2555 (Rfree = 0.000) for 3343 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 7: After refmac, R = 0.2327 (Rfree = 0.000) for 3294 atoms. Found 13 (18 requested) and removed 22 (9 requested) atoms. Cycle 8: After refmac, R = 0.2312 (Rfree = 0.000) for 3269 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.2001 (Rfree = 0.000) for 3250 atoms. Found 6 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2054 (Rfree = 0.000) for 3236 atoms. Found 0 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3292 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3310 seeds are put forward Round 1: 244 peptides, 37 chains. Longest chain 19 peptides. Score 0.470 Round 2: 264 peptides, 34 chains. Longest chain 16 peptides. Score 0.554 Round 3: 265 peptides, 34 chains. Longest chain 18 peptides. Score 0.556 Round 4: 287 peptides, 36 chains. Longest chain 40 peptides. Score 0.586 Round 5: 274 peptides, 37 chains. Longest chain 13 peptides. Score 0.546 Taking the results from Round 4 Chains 38, Residues 251, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7234 restraints for refining 3342 atoms. 6224 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2243 (Rfree = 0.000) for 3342 atoms. Found 10 (18 requested) and removed 53 (9 requested) atoms. Cycle 12: After refmac, R = 0.2114 (Rfree = 0.000) for 3268 atoms. Found 10 (18 requested) and removed 44 (9 requested) atoms. Cycle 13: After refmac, R = 0.1955 (Rfree = 0.000) for 3219 atoms. Found 4 (17 requested) and removed 28 (8 requested) atoms. Cycle 14: After refmac, R = 0.1950 (Rfree = 0.000) for 3187 atoms. Found 3 (17 requested) and removed 30 (8 requested) atoms. Cycle 15: After refmac, R = 0.1884 (Rfree = 0.000) for 3153 atoms. Found 3 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3253 seeds are put forward Round 1: 253 peptides, 46 chains. Longest chain 12 peptides. Score 0.387 Round 2: 276 peptides, 43 chains. Longest chain 20 peptides. Score 0.485 Round 3: 255 peptides, 36 chains. Longest chain 20 peptides. Score 0.510 Round 4: 261 peptides, 38 chains. Longest chain 19 peptides. Score 0.503 Round 5: 251 peptides, 35 chains. Longest chain 20 peptides. Score 0.511 Taking the results from Round 5 Chains 36, Residues 216, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7551 restraints for refining 3343 atoms. 6685 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2212 (Rfree = 0.000) for 3343 atoms. Found 8 (18 requested) and removed 37 (9 requested) atoms. Cycle 17: After refmac, R = 0.2158 (Rfree = 0.000) for 3287 atoms. Found 11 (18 requested) and removed 20 (9 requested) atoms. Cycle 18: After refmac, R = 0.2119 (Rfree = 0.000) for 3265 atoms. Found 13 (18 requested) and removed 20 (9 requested) atoms. Cycle 19: After refmac, R = 0.1820 (Rfree = 0.000) for 3250 atoms. Found 7 (17 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.1836 (Rfree = 0.000) for 3236 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 3301 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3320 seeds are put forward Round 1: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.397 Round 2: 263 peptides, 37 chains. Longest chain 20 peptides. Score 0.519 Round 3: 275 peptides, 40 chains. Longest chain 21 peptides. Score 0.516 Round 4: 268 peptides, 40 chains. Longest chain 19 peptides. Score 0.498 Round 5: 255 peptides, 35 chains. Longest chain 22 peptides. Score 0.521 Taking the results from Round 5 Chains 36, Residues 220, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7331 restraints for refining 3343 atoms. 6418 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2350 (Rfree = 0.000) for 3343 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 22: After refmac, R = 0.1965 (Rfree = 0.000) for 3305 atoms. Found 7 (18 requested) and removed 20 (9 requested) atoms. Cycle 23: After refmac, R = 0.1947 (Rfree = 0.000) for 3281 atoms. Found 4 (18 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.1877 (Rfree = 0.000) for 3261 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1885 (Rfree = 0.000) for 3247 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 3320 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3347 seeds are put forward Round 1: 189 peptides, 38 chains. Longest chain 12 peptides. Score 0.294 Round 2: 231 peptides, 37 chains. Longest chain 21 peptides. Score 0.434 Round 3: 239 peptides, 34 chains. Longest chain 17 peptides. Score 0.492 Round 4: 240 peptides, 35 chains. Longest chain 25 peptides. Score 0.483 Round 5: 244 peptides, 35 chains. Longest chain 22 peptides. Score 0.493 Taking the results from Round 5 Chains 36, Residues 209, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7449 restraints for refining 3343 atoms. 6558 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2259 (Rfree = 0.000) for 3343 atoms. Found 17 (18 requested) and removed 18 (9 requested) atoms. Cycle 27: After refmac, R = 0.2039 (Rfree = 0.000) for 3310 atoms. Found 17 (18 requested) and removed 18 (9 requested) atoms. Cycle 28: After refmac, R = 0.2023 (Rfree = 0.000) for 3300 atoms. Found 9 (18 requested) and removed 15 (9 requested) atoms. Cycle 29: After refmac, R = 0.1855 (Rfree = 0.000) for 3288 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.1983 (Rfree = 0.000) for 3267 atoms. Found 17 (18 requested) and removed 46 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 3305 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3331 seeds are put forward Round 1: 229 peptides, 45 chains. Longest chain 10 peptides. Score 0.328 Round 2: 245 peptides, 43 chains. Longest chain 11 peptides. Score 0.400 Round 3: 246 peptides, 41 chains. Longest chain 13 peptides. Score 0.428 Round 4: 246 peptides, 39 chains. Longest chain 19 peptides. Score 0.452 Round 5: 235 peptides, 38 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 4 Chains 39, Residues 207, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7364 restraints for refining 3343 atoms. 6543 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2309 (Rfree = 0.000) for 3343 atoms. Found 14 (18 requested) and removed 30 (9 requested) atoms. Cycle 32: After refmac, R = 0.2119 (Rfree = 0.000) for 3314 atoms. Found 15 (18 requested) and removed 22 (9 requested) atoms. Cycle 33: After refmac, R = 0.1753 (Rfree = 0.000) for 3302 atoms. Found 2 (18 requested) and removed 22 (9 requested) atoms. Cycle 34: After refmac, R = 0.1807 (Rfree = 0.000) for 3278 atoms. Found 8 (18 requested) and removed 17 (9 requested) atoms. Cycle 35: After refmac, R = 0.2037 (Rfree = 0.000) for 3264 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 3359 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3381 seeds are put forward Round 1: 187 peptides, 38 chains. Longest chain 10 peptides. Score 0.288 Round 2: 211 peptides, 37 chains. Longest chain 10 peptides. Score 0.376 Round 3: 198 peptides, 34 chains. Longest chain 12 peptides. Score 0.376 Round 4: 227 peptides, 35 chains. Longest chain 13 peptides. Score 0.448 Round 5: 241 peptides, 36 chains. Longest chain 14 peptides. Score 0.474 Taking the results from Round 5 Chains 38, Residues 205, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7269 restraints for refining 3343 atoms. 6416 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2314 (Rfree = 0.000) for 3343 atoms. Found 10 (18 requested) and removed 33 (9 requested) atoms. Cycle 37: After refmac, R = 0.2170 (Rfree = 0.000) for 3297 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 38: After refmac, R = 0.2103 (Rfree = 0.000) for 3276 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 39: After refmac, R = 0.1943 (Rfree = 0.000) for 3258 atoms. Found 16 (17 requested) and removed 21 (8 requested) atoms. Cycle 40: After refmac, R = 0.1814 (Rfree = 0.000) for 3243 atoms. Found 10 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.27 Search for helices and strands: 0 residues in 0 chains, 3322 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3334 seeds are put forward Round 1: 209 peptides, 41 chains. Longest chain 11 peptides. Score 0.318 Round 2: 221 peptides, 37 chains. Longest chain 12 peptides. Score 0.406 Round 3: 223 peptides, 37 chains. Longest chain 19 peptides. Score 0.412 Round 4: 225 peptides, 36 chains. Longest chain 12 peptides. Score 0.430 Round 5: 230 peptides, 33 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 5 Chains 33, Residues 197, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7580 restraints for refining 3342 atoms. 6808 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2178 (Rfree = 0.000) for 3342 atoms. Found 13 (18 requested) and removed 26 (9 requested) atoms. Cycle 42: After refmac, R = 0.1934 (Rfree = 0.000) for 3315 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 43: After refmac, R = 0.1963 (Rfree = 0.000) for 3303 atoms. Found 15 (18 requested) and removed 20 (9 requested) atoms. Cycle 44: After refmac, R = 0.1863 (Rfree = 0.000) for 3291 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 45: After refmac, R = 0.1817 (Rfree = 0.000) for 3281 atoms. Found 17 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 3370 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3389 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.288 Round 2: 181 peptides, 33 chains. Longest chain 13 peptides. Score 0.337 Round 3: 183 peptides, 33 chains. Longest chain 11 peptides. Score 0.343 Round 4: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.362 Round 5: 171 peptides, 28 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 143, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (143 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5499 reflections ( 99.73 % complete ) and 7781 restraints for refining 3342 atoms. 7212 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1983 (Rfree = 0.000) for 3342 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1967 (Rfree = 0.000) for 3325 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1841 (Rfree = 0.000) for 3309 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1873 (Rfree = 0.000) for 3294 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:40:02 GMT 2018 Job finished. TimeTaking 37.4 Used memory is bytes: 19154576