null Mon 24 Dec 00:38:45 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 2i5i-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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/2i5i-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 ============================================================ Mon 24 Dec 00:38:51 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/2i5i-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6670 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 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: 29.446 4.002 Wilson plot Bfac: 89.81 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4552 reflections ( 98.94 % complete ) and 0 restraints for refining 4697 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3463 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2808 (Rfree = 0.000) for 4697 atoms. Found 8 (22 requested) and removed 33 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.89 3.94 Search for helices and strands: 0 residues in 0 chains, 4720 seeds are put forward NCS extension: 0 residues added, 4720 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.191 Round 2: 95 peptides, 22 chains. Longest chain 5 peptides. Score 0.197 Round 3: 108 peptides, 25 chains. Longest chain 6 peptides. Score 0.199 Round 4: 136 peptides, 29 chains. Longest chain 8 peptides. Score 0.242 Round 5: 137 peptides, 29 chains. Longest chain 7 peptides. Score 0.246 Taking the results from Round 5 Chains 29, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 9673 restraints for refining 3799 atoms. 9270 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2477 (Rfree = 0.000) for 3799 atoms. Found 11 (18 requested) and removed 21 (9 requested) atoms. Cycle 2: After refmac, R = 0.2234 (Rfree = 0.000) for 3758 atoms. Found 3 (17 requested) and removed 18 (8 requested) atoms. Cycle 3: After refmac, R = 0.2076 (Rfree = 0.000) for 3730 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2050 (Rfree = 0.000) for 3710 atoms. Found 2 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2022 (Rfree = 0.000) for 3690 atoms. Found 1 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 3751 seeds are put forward NCS extension: 0 residues added, 3751 seeds are put forward Round 1: 103 peptides, 25 chains. Longest chain 5 peptides. Score 0.179 Round 2: 130 peptides, 29 chains. Longest chain 6 peptides. Score 0.220 Round 3: 142 peptides, 30 chains. Longest chain 8 peptides. Score 0.248 Round 4: 153 peptides, 31 chains. Longest chain 8 peptides. Score 0.272 Round 5: 149 peptides, 31 chains. Longest chain 7 peptides. Score 0.258 Taking the results from Round 4 Chains 31, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8292 restraints for refining 3416 atoms. 7835 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2208 (Rfree = 0.000) for 3416 atoms. Found 10 (16 requested) and removed 25 (8 requested) atoms. Cycle 7: After refmac, R = 0.2097 (Rfree = 0.000) for 3384 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2048 (Rfree = 0.000) for 3370 atoms. Found 2 (16 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.2010 (Rfree = 0.000) for 3352 atoms. Found 3 (15 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.1890 (Rfree = 0.000) for 3337 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 3382 seeds are put forward NCS extension: 0 residues added, 3382 seeds are put forward Round 1: 165 peptides, 38 chains. Longest chain 8 peptides. Score 0.213 Round 2: 187 peptides, 38 chains. Longest chain 7 peptides. Score 0.287 Round 3: 181 peptides, 37 chains. Longest chain 9 peptides. Score 0.281 Round 4: 176 peptides, 34 chains. Longest chain 11 peptides. Score 0.306 Round 5: 188 peptides, 36 chains. Longest chain 11 peptides. Score 0.317 Taking the results from Round 5 Chains 36, Residues 152, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8027 restraints for refining 3444 atoms. 7442 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2148 (Rfree = 0.000) for 3444 atoms. Found 15 (16 requested) and removed 33 (8 requested) atoms. Cycle 12: After refmac, R = 0.1990 (Rfree = 0.000) for 3415 atoms. Found 3 (16 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.1999 (Rfree = 0.000) for 3402 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.1834 (Rfree = 0.000) for 3391 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.1835 (Rfree = 0.000) for 3374 atoms. Found 6 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 3444 seeds are put forward NCS extension: 0 residues added, 3444 seeds are put forward Round 1: 129 peptides, 30 chains. Longest chain 6 peptides. Score 0.201 Round 2: 170 peptides, 35 chains. Longest chain 9 peptides. Score 0.272 Round 3: 164 peptides, 35 chains. Longest chain 8 peptides. Score 0.252 Round 4: 170 peptides, 35 chains. Longest chain 9 peptides. Score 0.272 Round 5: 162 peptides, 32 chains. Longest chain 9 peptides. Score 0.288 Taking the results from Round 5 Chains 32, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8337 restraints for refining 3502 atoms. 7849 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2125 (Rfree = 0.000) for 3502 atoms. Found 13 (16 requested) and removed 26 (8 requested) atoms. Cycle 17: After refmac, R = 0.1935 (Rfree = 0.000) for 3474 atoms. Found 4 (16 requested) and removed 25 (8 requested) atoms. Cycle 18: After refmac, R = 0.1811 (Rfree = 0.000) for 3442 atoms. Found 2 (16 requested) and removed 15 (8 requested) atoms. Cycle 19: After refmac, R = 0.1870 (Rfree = 0.000) for 3416 atoms. Found 4 (16 requested) and removed 17 (8 requested) atoms. Cycle 20: After refmac, R = 0.1739 (Rfree = 0.000) for 3397 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 3459 seeds are put forward NCS extension: 0 residues added, 3459 seeds are put forward Round 1: 158 peptides, 37 chains. Longest chain 6 peptides. Score 0.203 Round 2: 180 peptides, 37 chains. Longest chain 8 peptides. Score 0.278 Round 3: 186 peptides, 37 chains. Longest chain 10 peptides. Score 0.297 Round 4: 192 peptides, 39 chains. Longest chain 8 peptides. Score 0.289 Round 5: 201 peptides, 37 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 5 Chains 37, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7714 restraints for refining 3400 atoms. 7095 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1920 (Rfree = 0.000) for 3400 atoms. Found 12 (16 requested) and removed 31 (8 requested) atoms. Cycle 22: After refmac, R = 0.2155 (Rfree = 0.000) for 3357 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 23: After refmac, R = 0.1911 (Rfree = 0.000) for 3329 atoms. Found 9 (15 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.1950 (Rfree = 0.000) for 3311 atoms. Found 12 (15 requested) and removed 18 (7 requested) atoms. Cycle 25: After refmac, R = 0.1877 (Rfree = 0.000) for 3292 atoms. Found 11 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 3364 seeds are put forward NCS extension: 0 residues added, 3364 seeds are put forward Round 1: 138 peptides, 30 chains. Longest chain 7 peptides. Score 0.234 Round 2: 156 peptides, 32 chains. Longest chain 7 peptides. Score 0.268 Round 3: 157 peptides, 30 chains. Longest chain 10 peptides. Score 0.300 Round 4: 142 peptides, 26 chains. Longest chain 10 peptides. Score 0.307 Round 5: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.291 Taking the results from Round 4 Chains 26, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7552 restraints for refining 3330 atoms. 7114 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2164 (Rfree = 0.000) for 3330 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 27: After refmac, R = 0.1805 (Rfree = 0.000) for 3286 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 28: After refmac, R = 0.1569 (Rfree = 0.000) for 3273 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.1628 (Rfree = 0.000) for 3267 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.1519 (Rfree = 0.000) for 3262 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 3305 seeds are put forward NCS extension: 0 residues added, 3305 seeds are put forward Round 1: 137 peptides, 32 chains. Longest chain 7 peptides. Score 0.201 Round 2: 164 peptides, 34 chains. Longest chain 8 peptides. Score 0.266 Round 3: 160 peptides, 33 chains. Longest chain 9 peptides. Score 0.267 Round 4: 163 peptides, 29 chains. Longest chain 12 peptides. Score 0.333 Round 5: 161 peptides, 30 chains. Longest chain 10 peptides. Score 0.313 Taking the results from Round 4 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7208 restraints for refining 3267 atoms. 6701 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2047 (Rfree = 0.000) for 3267 atoms. Found 14 (15 requested) and removed 28 (7 requested) atoms. Cycle 32: After refmac, R = 0.1758 (Rfree = 0.000) for 3244 atoms. Found 6 (15 requested) and removed 18 (7 requested) atoms. Cycle 33: After refmac, R = 0.1576 (Rfree = 0.000) for 3225 atoms. Found 5 (15 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.1556 (Rfree = 0.000) for 3214 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1448 (Rfree = 0.000) for 3201 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 3264 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3279 seeds are put forward Round 1: 147 peptides, 34 chains. Longest chain 6 peptides. Score 0.207 Round 2: 172 peptides, 32 chains. Longest chain 15 peptides. Score 0.320 Round 3: 181 peptides, 35 chains. Longest chain 9 peptides. Score 0.308 Round 4: 174 peptides, 30 chains. Longest chain 12 peptides. Score 0.354 Round 5: 175 peptides, 29 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Chains 29, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7579 restraints for refining 3346 atoms. 7024 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1962 (Rfree = 0.000) for 3346 atoms. Found 9 (15 requested) and removed 22 (7 requested) atoms. Cycle 37: After refmac, R = 0.1850 (Rfree = 0.000) for 3316 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1655 (Rfree = 0.000) for 3305 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.1708 (Rfree = 0.000) for 3296 atoms. Found 10 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1541 (Rfree = 0.000) for 3292 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.87 Search for helices and strands: 0 residues in 0 chains, 3348 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3364 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 9 peptides. Score 0.225 Round 2: 150 peptides, 31 chains. Longest chain 7 peptides. Score 0.262 Round 3: 158 peptides, 30 chains. Longest chain 10 peptides. Score 0.303 Round 4: 166 peptides, 31 chains. Longest chain 10 peptides. Score 0.315 Round 5: 162 peptides, 31 chains. Longest chain 10 peptides. Score 0.302 Taking the results from Round 4 Chains 31, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7703 restraints for refining 3362 atoms. 7194 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1850 (Rfree = 0.000) for 3362 atoms. Found 9 (15 requested) and removed 17 (7 requested) atoms. Cycle 42: After refmac, R = 0.1727 (Rfree = 0.000) for 3338 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1554 (Rfree = 0.000) for 3323 atoms. Found 1 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.1616 (Rfree = 0.000) for 3307 atoms. Found 9 (15 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.1468 (Rfree = 0.000) for 3301 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 3351 seeds are put forward NCS extension: 0 residues added, 3351 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 7 peptides. Score 0.218 Round 2: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.272 Round 3: 161 peptides, 29 chains. Longest chain 14 peptides. Score 0.327 Round 4: 158 peptides, 30 chains. Longest chain 10 peptides. Score 0.303 Round 5: 144 peptides, 28 chains. Longest chain 10 peptides. Score 0.285 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 132, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2i5i-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4552 reflections ( 98.94 % complete ) and 7554 restraints for refining 3353 atoms. 7005 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1892 (Rfree = 0.000) for 3353 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1679 (Rfree = 0.000) for 3333 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1649 (Rfree = 0.000) for 3314 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1596 (Rfree = 0.000) for 3302 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:23:52 GMT 2018 Job finished. TimeTaking 45.11 Used memory is bytes: 19006688