Sun 23 Dec 23:50:50 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 2otm-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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/2otm-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 ============================================================ Sun 23 Dec 23:51:01 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/2otm-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 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-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.8-parrot-mrncs.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 4105 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3140 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2983 (Rfree = 0.000) for 4105 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.23 Search for helices and strands: 0 residues in 0 chains, 4169 seeds are put forward NCS extension: 0 residues added, 4169 seeds are put forward Round 1: 232 peptides, 39 chains. Longest chain 13 peptides. Score 0.413 Round 2: 286 peptides, 41 chains. Longest chain 15 peptides. Score 0.532 Round 3: 290 peptides, 38 chains. Longest chain 16 peptides. Score 0.573 Round 4: 290 peptides, 36 chains. Longest chain 19 peptides. Score 0.593 Round 5: 301 peptides, 39 chains. Longest chain 17 peptides. Score 0.587 Taking the results from Round 4 Chains 40, Residues 254, Estimated correctness of the model 0.0 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 6852 restraints for refining 3342 atoms. 5672 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2278 (Rfree = 0.000) for 3342 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 2: After refmac, R = 0.2167 (Rfree = 0.000) for 3270 atoms. Found 9 (18 requested) and removed 19 (9 requested) atoms. Cycle 3: After refmac, R = 0.1977 (Rfree = 0.000) for 3236 atoms. Found 5 (17 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2076 (Rfree = 0.000) for 3213 atoms. Found 6 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2138 (Rfree = 0.000) for 3192 atoms. Found 9 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3293 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3309 seeds are put forward Round 1: 263 peptides, 46 chains. Longest chain 16 peptides. Score 0.415 Round 2: 290 peptides, 37 chains. Longest chain 25 peptides. Score 0.583 Round 3: 291 peptides, 35 chains. Longest chain 24 peptides. Score 0.605 Round 4: 290 peptides, 32 chains. Longest chain 24 peptides. Score 0.631 Round 5: 298 peptides, 36 chains. Longest chain 22 peptides. Score 0.610 Taking the results from Round 4 Chains 34, Residues 258, Estimated correctness of the model 12.8 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7212 restraints for refining 3341 atoms. 6135 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2625 (Rfree = 0.000) for 3341 atoms. Found 10 (18 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.2307 (Rfree = 0.000) for 3298 atoms. Found 11 (18 requested) and removed 13 (9 requested) atoms. Cycle 8: After refmac, R = 0.2180 (Rfree = 0.000) for 3281 atoms. Found 6 (18 requested) and removed 16 (9 requested) atoms. Cycle 9: After refmac, R = 0.2182 (Rfree = 0.000) for 3259 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.2134 (Rfree = 0.000) for 3249 atoms. Found 7 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 3322 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 3332 seeds are put forward Round 1: 264 peptides, 43 chains. Longest chain 11 peptides. Score 0.453 Round 2: 287 peptides, 36 chains. Longest chain 19 peptides. Score 0.586 Round 3: 290 peptides, 33 chains. Longest chain 19 peptides. Score 0.622 Round 4: 292 peptides, 34 chains. Longest chain 19 peptides. Score 0.616 Round 5: 287 peptides, 35 chains. Longest chain 20 peptides. Score 0.596 Taking the results from Round 3 Chains 33, Residues 257, Estimated correctness of the model 8.8 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7396 restraints for refining 3343 atoms. 6375 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2492 (Rfree = 0.000) for 3343 atoms. Found 15 (18 requested) and removed 30 (9 requested) atoms. Cycle 12: After refmac, R = 0.2329 (Rfree = 0.000) for 3312 atoms. Found 13 (18 requested) and removed 26 (9 requested) atoms. Cycle 13: After refmac, R = 0.1996 (Rfree = 0.000) for 3290 atoms. Found 6 (18 requested) and removed 17 (9 requested) atoms. Cycle 14: After refmac, R = 0.1909 (Rfree = 0.000) for 3276 atoms. Found 13 (18 requested) and removed 24 (9 requested) atoms. Cycle 15: After refmac, R = 0.2044 (Rfree = 0.000) for 3262 atoms. Found 16 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 3366 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3383 seeds are put forward Round 1: 218 peptides, 40 chains. Longest chain 11 peptides. Score 0.359 Round 2: 261 peptides, 37 chains. Longest chain 18 peptides. Score 0.514 Round 3: 254 peptides, 35 chains. Longest chain 19 peptides. Score 0.519 Round 4: 267 peptides, 35 chains. Longest chain 23 peptides. Score 0.550 Round 5: 269 peptides, 31 chains. Longest chain 34 peptides. Score 0.597 Taking the results from Round 5 Chains 33, Residues 238, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7326 restraints for refining 3342 atoms. 6303 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2279 (Rfree = 0.000) for 3342 atoms. Found 13 (18 requested) and removed 15 (9 requested) atoms. Cycle 17: After refmac, R = 0.2051 (Rfree = 0.000) for 3314 atoms. Found 8 (18 requested) and removed 17 (9 requested) atoms. Cycle 18: After refmac, R = 0.1900 (Rfree = 0.000) for 3291 atoms. Found 4 (18 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.1997 (Rfree = 0.000) for 3278 atoms. Found 6 (18 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1854 (Rfree = 0.000) for 3262 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 3363 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3376 seeds are put forward Round 1: 231 peptides, 41 chains. Longest chain 17 peptides. Score 0.385 Round 2: 259 peptides, 42 chains. Longest chain 12 peptides. Score 0.451 Round 3: 253 peptides, 36 chains. Longest chain 17 peptides. Score 0.505 Round 4: 248 peptides, 35 chains. Longest chain 22 peptides. Score 0.503 Round 5: 262 peptides, 38 chains. Longest chain 16 peptides. Score 0.505 Taking the results from Round 5 Chains 39, Residues 224, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7486 restraints for refining 3343 atoms. 6550 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2299 (Rfree = 0.000) for 3343 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.2188 (Rfree = 0.000) for 3323 atoms. Found 14 (18 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.2086 (Rfree = 0.000) for 3306 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1631 (Rfree = 0.000) for 3305 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.1593 (Rfree = 0.000) for 3290 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 3363 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3393 seeds are put forward Round 1: 202 peptides, 40 chains. Longest chain 12 peptides. Score 0.309 Round 2: 241 peptides, 39 chains. Longest chain 10 peptides. Score 0.438 Round 3: 239 peptides, 37 chains. Longest chain 13 peptides. Score 0.456 Round 4: 243 peptides, 39 chains. Longest chain 12 peptides. Score 0.443 Round 5: 261 peptides, 37 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 5 Chains 37, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7679 restraints for refining 3343 atoms. 6820 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2412 (Rfree = 0.000) for 3343 atoms. Found 14 (18 requested) and removed 19 (9 requested) atoms. Cycle 27: After refmac, R = 0.2242 (Rfree = 0.000) for 3321 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 28: After refmac, R = 0.2192 (Rfree = 0.000) for 3311 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.1900 (Rfree = 0.000) for 3301 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 30: After refmac, R = 0.1978 (Rfree = 0.000) for 3289 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 3424 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3437 seeds are put forward Round 1: 192 peptides, 39 chains. Longest chain 11 peptides. Score 0.291 Round 2: 215 peptides, 37 chains. Longest chain 14 peptides. Score 0.388 Round 3: 224 peptides, 36 chains. Longest chain 11 peptides. Score 0.427 Round 4: 218 peptides, 34 chains. Longest chain 16 peptides. Score 0.435 Round 5: 235 peptides, 34 chains. Longest chain 16 peptides. Score 0.481 Taking the results from Round 5 Chains 34, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7614 restraints for refining 3343 atoms. 6844 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2169 (Rfree = 0.000) for 3343 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 32: After refmac, R = 0.2095 (Rfree = 0.000) for 3310 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 33: After refmac, R = 0.1999 (Rfree = 0.000) for 3300 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.1935 (Rfree = 0.000) for 3289 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1845 (Rfree = 0.000) for 3283 atoms. Found 9 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3380 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3398 seeds are put forward Round 1: 172 peptides, 35 chains. Longest chain 9 peptides. Score 0.280 Round 2: 205 peptides, 35 chains. Longest chain 13 peptides. Score 0.384 Round 3: 215 peptides, 38 chains. Longest chain 13 peptides. Score 0.375 Round 4: 226 peptides, 35 chains. Longest chain 14 peptides. Score 0.445 Round 5: 227 peptides, 40 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 4 Chains 35, Residues 191, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7702 restraints for refining 3342 atoms. 6938 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2382 (Rfree = 0.000) for 3342 atoms. Found 15 (18 requested) and removed 14 (9 requested) atoms. Cycle 37: After refmac, R = 0.1943 (Rfree = 0.000) for 3325 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. Cycle 38: After refmac, R = 0.1972 (Rfree = 0.000) for 3302 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.1844 (Rfree = 0.000) for 3304 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 40: After refmac, R = 0.1490 (Rfree = 0.000) for 3305 atoms. Found 2 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 3385 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3403 seeds are put forward Round 1: 192 peptides, 41 chains. Longest chain 11 peptides. Score 0.263 Round 2: 237 peptides, 41 chains. Longest chain 13 peptides. Score 0.402 Round 3: 229 peptides, 39 chains. Longest chain 13 peptides. Score 0.404 Round 4: 236 peptides, 40 chains. Longest chain 14 peptides. Score 0.412 Round 5: 237 peptides, 39 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 5 Chains 39, Residues 198, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7611 restraints for refining 3342 atoms. 6828 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2083 (Rfree = 0.000) for 3342 atoms. Found 17 (18 requested) and removed 16 (9 requested) atoms. Cycle 42: After refmac, R = 0.1980 (Rfree = 0.000) for 3332 atoms. Found 4 (18 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.1861 (Rfree = 0.000) for 3314 atoms. Found 2 (18 requested) and removed 17 (9 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 3293 atoms. Found 4 (18 requested) and removed 16 (9 requested) atoms. Cycle 45: After refmac, R = 0.1661 (Rfree = 0.000) for 3275 atoms. Found 4 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 3342 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3359 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 8 peptides. Score 0.290 Round 2: 191 peptides, 34 chains. Longest chain 20 peptides. Score 0.355 Round 3: 212 peptides, 39 chains. Longest chain 10 peptides. Score 0.353 Round 4: 214 peptides, 37 chains. Longest chain 16 peptides. Score 0.385 Round 5: 215 peptides, 35 chains. Longest chain 19 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 180, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (180 residues) following loop building 2 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5499 reflections ( 99.73 % complete ) and 7546 restraints for refining 3342 atoms. 6826 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2121 (Rfree = 0.000) for 3342 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2010 (Rfree = 0.000) for 3313 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1853 (Rfree = 0.000) for 3292 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1919 (Rfree = 0.000) for 3278 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 47.4