Tue 25 Dec 19:30:29 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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/2otm-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 ============================================================ Tue 25 Dec 19:30:39 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 359 and 0 Target number of residues in the AU: 359 Target solvent content: 0.6489 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-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-4.0-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 4.001 Wilson plot Bfac: 77.35 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4718 reflections ( 99.68 % complete ) and 0 restraints for refining 4098 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3152 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 4098 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.46 Search for helices and strands: 0 residues in 0 chains, 4150 seeds are put forward NCS extension: 0 residues added, 4150 seeds are put forward Round 1: 208 peptides, 38 chains. Longest chain 10 peptides. Score 0.354 Round 2: 260 peptides, 40 chains. Longest chain 16 peptides. Score 0.477 Round 3: 263 peptides, 37 chains. Longest chain 14 peptides. Score 0.519 Round 4: 278 peptides, 34 chains. Longest chain 25 peptides. Score 0.586 Round 5: 266 peptides, 31 chains. Longest chain 20 peptides. Score 0.590 Taking the results from Round 5 Chains 31, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7823 restraints for refining 3338 atoms. 6914 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2368 (Rfree = 0.000) for 3338 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2328 (Rfree = 0.000) for 3289 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2141 (Rfree = 0.000) for 3253 atoms. Found 5 (15 requested) and removed 21 (7 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2119 (Rfree = 0.000) for 3222 atoms. Found 5 (15 requested) and removed 20 (7 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2025 (Rfree = 0.000) for 3190 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.41 Search for helices and strands: 0 residues in 0 chains, 3268 seeds are put forward NCS extension: 14 residues added (9 deleted due to clashes), 3282 seeds are put forward Round 1: 231 peptides, 40 chains. Longest chain 16 peptides. Score 0.397 Round 2: 258 peptides, 35 chains. Longest chain 16 peptides. Score 0.529 Round 3: 255 peptides, 30 chains. Longest chain 17 peptides. Score 0.576 Round 4: 280 peptides, 34 chains. Longest chain 18 peptides. Score 0.591 Round 5: 279 peptides, 33 chains. Longest chain 15 peptides. Score 0.598 Taking the results from Round 5 Chains 35, Residues 246, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7342 restraints for refining 3338 atoms. 6342 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2192 (Rfree = 0.000) for 3338 atoms. Found 7 (15 requested) and removed 20 (7 requested) atoms. Cycle 7: After refmac, R = 0.2043 (Rfree = 0.000) for 3302 atoms. Found 7 (15 requested) and removed 17 (7 requested) atoms. Cycle 8: After refmac, R = 0.2036 (Rfree = 0.000) for 3278 atoms. Found 8 (15 requested) and removed 17 (7 requested) atoms. Cycle 9: After refmac, R = 0.1861 (Rfree = 0.000) for 3262 atoms. Found 1 (15 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.1951 (Rfree = 0.000) for 3240 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 3367 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3380 seeds are put forward Round 1: 223 peptides, 37 chains. Longest chain 14 peptides. Score 0.412 Round 2: 226 peptides, 31 chains. Longest chain 18 peptides. Score 0.493 Round 3: 243 peptides, 31 chains. Longest chain 26 peptides. Score 0.536 Round 4: 249 peptides, 28 chains. Longest chain 24 peptides. Score 0.583 Round 5: 263 peptides, 32 chains. Longest chain 17 peptides. Score 0.573 Taking the results from Round 4 Chains 30, Residues 221, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7550 restraints for refining 3338 atoms. 6632 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 3338 atoms. Found 7 (15 requested) and removed 19 (7 requested) atoms. Cycle 12: After refmac, R = 0.2004 (Rfree = 0.000) for 3295 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. Cycle 13: After refmac, R = 0.1807 (Rfree = 0.000) for 3275 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.1770 (Rfree = 0.000) for 3259 atoms. Found 2 (15 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.1911 (Rfree = 0.000) for 3244 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 3329 seeds are put forward NCS extension: 0 residues added, 3329 seeds are put forward Round 1: 230 peptides, 38 chains. Longest chain 13 peptides. Score 0.419 Round 2: 243 peptides, 34 chains. Longest chain 26 peptides. Score 0.502 Round 3: 250 peptides, 31 chains. Longest chain 21 peptides. Score 0.553 Round 4: 263 peptides, 32 chains. Longest chain 24 peptides. Score 0.573 Round 5: 256 peptides, 36 chains. Longest chain 14 peptides. Score 0.513 Taking the results from Round 4 Chains 35, Residues 231, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7188 restraints for refining 3337 atoms. 6184 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2285 (Rfree = 0.000) for 3337 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 17: After refmac, R = 0.2069 (Rfree = 0.000) for 3313 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.2188 (Rfree = 0.000) for 3294 atoms. Found 9 (15 requested) and removed 18 (7 requested) atoms. Cycle 19: After refmac, R = 0.2069 (Rfree = 0.000) for 3277 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. Cycle 20: After refmac, R = 0.1809 (Rfree = 0.000) for 3263 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.41 Search for helices and strands: 0 residues in 0 chains, 3348 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3363 seeds are put forward Round 1: 214 peptides, 33 chains. Longest chain 20 peptides. Score 0.436 Round 2: 246 peptides, 37 chains. Longest chain 16 peptides. Score 0.475 Round 3: 253 peptides, 31 chains. Longest chain 34 peptides. Score 0.560 Round 4: 255 peptides, 28 chains. Longest chain 28 peptides. Score 0.596 Round 5: 252 peptides, 27 chains. Longest chain 36 peptides. Score 0.600 Taking the results from Round 5 Chains 29, Residues 225, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7496 restraints for refining 3338 atoms. 6584 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2148 (Rfree = 0.000) for 3338 atoms. Found 14 (15 requested) and removed 21 (7 requested) atoms. Cycle 22: After refmac, R = 0.1992 (Rfree = 0.000) for 3311 atoms. Found 6 (15 requested) and removed 19 (7 requested) atoms. Cycle 23: After refmac, R = 0.1891 (Rfree = 0.000) for 3289 atoms. Found 4 (15 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.1887 (Rfree = 0.000) for 3273 atoms. Found 3 (15 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.1850 (Rfree = 0.000) for 3256 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 3324 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3339 seeds are put forward Round 1: 200 peptides, 36 chains. Longest chain 10 peptides. Score 0.356 Round 2: 216 peptides, 38 chains. Longest chain 14 peptides. Score 0.378 Round 3: 240 peptides, 34 chains. Longest chain 19 peptides. Score 0.494 Round 4: 230 peptides, 31 chains. Longest chain 22 peptides. Score 0.503 Round 5: 237 peptides, 34 chains. Longest chain 23 peptides. Score 0.487 Taking the results from Round 4 Chains 31, Residues 199, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7784 restraints for refining 3337 atoms. 6997 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2089 (Rfree = 0.000) for 3337 atoms. Found 13 (15 requested) and removed 13 (7 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1952 (Rfree = 0.000) for 3326 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1700 (Rfree = 0.000) for 3320 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.1799 (Rfree = 0.000) for 3309 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1853 (Rfree = 0.000) for 3305 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 3412 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 3449 seeds are put forward Round 1: 205 peptides, 37 chains. Longest chain 10 peptides. Score 0.358 Round 2: 214 peptides, 35 chains. Longest chain 14 peptides. Score 0.411 Round 3: 218 peptides, 35 chains. Longest chain 15 peptides. Score 0.422 Round 4: 229 peptides, 32 chains. Longest chain 13 peptides. Score 0.489 Round 5: 220 peptides, 33 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 4 Chains 32, Residues 197, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7845 restraints for refining 3338 atoms. 7065 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2032 (Rfree = 0.000) for 3338 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.1899 (Rfree = 0.000) for 3327 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1871 (Rfree = 0.000) for 3313 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1905 (Rfree = 0.000) for 3302 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1707 (Rfree = 0.000) for 3300 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 3378 seeds are put forward NCS extension: 0 residues added, 3378 seeds are put forward Round 1: 182 peptides, 35 chains. Longest chain 9 peptides. Score 0.313 Round 2: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.400 Round 3: 219 peptides, 32 chains. Longest chain 16 peptides. Score 0.462 Round 4: 237 peptides, 35 chains. Longest chain 14 peptides. Score 0.475 Round 5: 219 peptides, 33 chains. Longest chain 18 peptides. Score 0.450 Taking the results from Round 4 Chains 35, Residues 202, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7636 restraints for refining 3337 atoms. 6787 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1981 (Rfree = 0.000) for 3337 atoms. Found 7 (15 requested) and removed 18 (7 requested) atoms. Cycle 37: After refmac, R = 0.1801 (Rfree = 0.000) for 3292 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1789 (Rfree = 0.000) for 3278 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1832 (Rfree = 0.000) for 3266 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1657 (Rfree = 0.000) for 3252 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 3330 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3343 seeds are put forward Round 1: 178 peptides, 37 chains. Longest chain 9 peptides. Score 0.272 Round 2: 174 peptides, 31 chains. Longest chain 11 peptides. Score 0.342 Round 3: 199 peptides, 34 chains. Longest chain 11 peptides. Score 0.379 Round 4: 198 peptides, 32 chains. Longest chain 14 peptides. Score 0.402 Round 5: 185 peptides, 31 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 4 Chains 32, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7767 restraints for refining 3270 atoms. 7135 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1977 (Rfree = 0.000) for 3270 atoms. Found 10 (15 requested) and removed 23 (7 requested) atoms. Cycle 42: After refmac, R = 0.1877 (Rfree = 0.000) for 3238 atoms. Found 14 (15 requested) and removed 20 (7 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1803 (Rfree = 0.000) for 3220 atoms. Found 5 (15 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.1689 (Rfree = 0.000) for 3200 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1604 (Rfree = 0.000) for 3190 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 3260 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3273 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 8 peptides. Score 0.230 Round 2: 189 peptides, 31 chains. Longest chain 13 peptides. Score 0.389 Round 3: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.371 Round 4: 193 peptides, 33 chains. Longest chain 13 peptides. Score 0.374 Round 5: 202 peptides, 32 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 170, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2otm-4_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (170 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4718 reflections ( 99.68 % complete ) and 7567 restraints for refining 3276 atoms. 6893 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2149 (Rfree = 0.000) for 3276 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1875 (Rfree = 0.000) for 3237 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 3216 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1780 (Rfree = 0.000) for 3205 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:45:07 GMT 2018 Job finished. TimeTaking 74.64