Mon 24 Dec 00:22:20 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 2pke-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-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/2pke-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-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 ============================================================ Mon 24 Dec 00:22:24 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/2pke-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-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 283 and 0 Target number of residues in the AU: 283 Target solvent content: 0.6592 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 3.800 Wilson plot Bfac: 84.18 4203 reflections ( 95.76 % complete ) and 0 restraints for refining 4422 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3067 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 4422 atoms. Found 24 (24 requested) and removed 49 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 4.19 Search for helices and strands: 0 residues in 0 chains, 4535 seeds are put forward NCS extension: 0 residues added, 4535 seeds are put forward Round 1: 140 peptides, 26 chains. Longest chain 13 peptides. Score 0.323 Round 2: 197 peptides, 34 chains. Longest chain 13 peptides. Score 0.408 Round 3: 197 peptides, 29 chains. Longest chain 16 peptides. Score 0.481 Round 4: 205 peptides, 33 chains. Longest chain 13 peptides. Score 0.450 Round 5: 207 peptides, 29 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 5 Chains 30, Residues 178, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 8629 restraints for refining 3632 atoms. 7862 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2225 (Rfree = 0.000) for 3632 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 2: After refmac, R = 0.2376 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 3: After refmac, R = 0.2310 (Rfree = 0.000) for 3519 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 4: After refmac, R = 0.2396 (Rfree = 0.000) for 3474 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 5: After refmac, R = 0.2420 (Rfree = 0.000) for 3427 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3609 seeds are put forward Round 1: 132 peptides, 29 chains. Longest chain 10 peptides. Score 0.238 Round 2: 189 peptides, 32 chains. Longest chain 14 peptides. Score 0.410 Round 3: 207 peptides, 35 chains. Longest chain 13 peptides. Score 0.427 Round 4: 199 peptides, 35 chains. Longest chain 11 peptides. Score 0.399 Round 5: 207 peptides, 33 chains. Longest chain 12 peptides. Score 0.457 Taking the results from Round 5 Chains 33, Residues 174, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4203 reflections ( 95.76 % complete ) and 7851 restraints for refining 3401 atoms. 7128 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2255 (Rfree = 0.000) for 3401 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. Cycle 7: After refmac, R = 0.2205 (Rfree = 0.000) for 3340 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 8: After refmac, R = 0.1631 (Rfree = 0.000) for 3298 atoms. Found 17 (18 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.2204 (Rfree = 0.000) for 3278 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 10: After refmac, R = 0.2331 (Rfree = 0.000) for 3262 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 3404 seeds are put forward NCS extension: 0 residues added, 3404 seeds are put forward Round 1: 158 peptides, 34 chains. Longest chain 10 peptides. Score 0.260 Round 2: 174 peptides, 33 chains. Longest chain 11 peptides. Score 0.339 Round 3: 195 peptides, 31 chains. Longest chain 15 peptides. Score 0.446 Round 4: 203 peptides, 32 chains. Longest chain 15 peptides. Score 0.458 Round 5: 191 peptides, 30 chains. Longest chain 13 peptides. Score 0.447 Taking the results from Round 4 Chains 32, Residues 171, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7401 restraints for refining 3226 atoms. 6733 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2369 (Rfree = 0.000) for 3226 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 12: After refmac, R = 0.2359 (Rfree = 0.000) for 3197 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2414 (Rfree = 0.000) for 3175 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 14: After refmac, R = 0.2277 (Rfree = 0.000) for 3158 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 15: After refmac, R = 0.2254 (Rfree = 0.000) for 3141 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.88 Search for helices and strands: 0 residues in 0 chains, 3305 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3328 seeds are put forward Round 1: 144 peptides, 29 chains. Longest chain 13 peptides. Score 0.288 Round 2: 176 peptides, 31 chains. Longest chain 10 peptides. Score 0.378 Round 3: 185 peptides, 30 chains. Longest chain 17 peptides. Score 0.426 Round 4: 190 peptides, 32 chains. Longest chain 13 peptides. Score 0.413 Round 5: 202 peptides, 32 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 5 Chains 32, Residues 170, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7329 restraints for refining 3247 atoms. 6649 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2159 (Rfree = 0.000) for 3247 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 17: After refmac, R = 0.2139 (Rfree = 0.000) for 3219 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 18: After refmac, R = 0.2077 (Rfree = 0.000) for 3202 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 19: After refmac, R = 0.2153 (Rfree = 0.000) for 3179 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 20: After refmac, R = 0.2052 (Rfree = 0.000) for 3166 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 3321 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3340 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 9 peptides. Score 0.279 Round 2: 183 peptides, 29 chains. Longest chain 18 peptides. Score 0.434 Round 3: 185 peptides, 32 chains. Longest chain 18 peptides. Score 0.396 Round 4: 191 peptides, 30 chains. Longest chain 18 peptides. Score 0.447 Round 5: 186 peptides, 30 chains. Longest chain 12 peptides. Score 0.430 Taking the results from Round 4 Chains 32, Residues 161, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7397 restraints for refining 3260 atoms. 6732 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1972 (Rfree = 0.000) for 3260 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 22: After refmac, R = 0.2221 (Rfree = 0.000) for 3242 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 23: After refmac, R = 0.2116 (Rfree = 0.000) for 3228 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 24: After refmac, R = 0.1642 (Rfree = 0.000) for 3223 atoms. Found 10 (17 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1721 (Rfree = 0.000) for 3211 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 3349 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3370 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 11 peptides. Score 0.296 Round 2: 179 peptides, 30 chains. Longest chain 16 peptides. Score 0.405 Round 3: 171 peptides, 31 chains. Longest chain 12 peptides. Score 0.360 Round 4: 166 peptides, 29 chains. Longest chain 15 peptides. Score 0.373 Round 5: 167 peptides, 31 chains. Longest chain 13 peptides. Score 0.345 Taking the results from Round 2 Chains 30, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7796 restraints for refining 3295 atoms. 7230 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2228 (Rfree = 0.000) for 3295 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. Cycle 27: After refmac, R = 0.2147 (Rfree = 0.000) for 3262 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 28: After refmac, R = 0.1524 (Rfree = 0.000) for 3247 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.1377 (Rfree = 0.000) for 3238 atoms. Found 12 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1349 (Rfree = 0.000) for 3241 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 3368 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3386 seeds are put forward Round 1: 120 peptides, 27 chains. Longest chain 7 peptides. Score 0.222 Round 2: 136 peptides, 29 chains. Longest chain 8 peptides. Score 0.255 Round 3: 141 peptides, 28 chains. Longest chain 9 peptides. Score 0.293 Round 4: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.352 Round 5: 154 peptides, 28 chains. Longest chain 14 peptides. Score 0.344 Taking the results from Round 4 Chains 25, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 8181 restraints for refining 3341 atoms. 7734 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2001 (Rfree = 0.000) for 3341 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 32: After refmac, R = 0.2157 (Rfree = 0.000) for 3318 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 3307 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 34: After refmac, R = 0.1891 (Rfree = 0.000) for 3300 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 35: After refmac, R = 0.1932 (Rfree = 0.000) for 3296 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 4.07 Search for helices and strands: 0 residues in 0 chains, 3435 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3451 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 6 peptides. Score 0.197 Round 2: 134 peptides, 30 chains. Longest chain 7 peptides. Score 0.229 Round 3: 136 peptides, 28 chains. Longest chain 9 peptides. Score 0.272 Round 4: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.278 Round 5: 125 peptides, 24 chains. Longest chain 8 peptides. Score 0.297 Taking the results from Round 5 Chains 24, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7833 restraints for refining 3236 atoms. 7453 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1845 (Rfree = 0.000) for 3236 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.1966 (Rfree = 0.000) for 3230 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 38: After refmac, R = 0.2004 (Rfree = 0.000) for 3219 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 39: After refmac, R = 0.1423 (Rfree = 0.000) for 3208 atoms. Found 11 (17 requested) and removed 16 (8 requested) atoms. Cycle 40: After refmac, R = 0.1258 (Rfree = 0.000) for 3200 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 3332 seeds are put forward NCS extension: 0 residues added, 3332 seeds are put forward Round 1: 98 peptides, 23 chains. Longest chain 6 peptides. Score 0.196 Round 2: 118 peptides, 24 chains. Longest chain 9 peptides. Score 0.268 Round 3: 120 peptides, 24 chains. Longest chain 12 peptides. Score 0.276 Round 4: 119 peptides, 25 chains. Longest chain 9 peptides. Score 0.254 Round 5: 120 peptides, 23 chains. Longest chain 15 peptides. Score 0.294 Taking the results from Round 5 Chains 23, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7733 restraints for refining 3227 atoms. 7368 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1809 (Rfree = 0.000) for 3227 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.2053 (Rfree = 0.000) for 3214 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 43: After refmac, R = 0.1889 (Rfree = 0.000) for 3205 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.1424 (Rfree = 0.000) for 3203 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.1298 (Rfree = 0.000) for 3199 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 3328 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 3336 seeds are put forward Round 1: 93 peptides, 22 chains. Longest chain 5 peptides. Score 0.192 Round 2: 114 peptides, 26 chains. Longest chain 6 peptides. Score 0.213 Round 3: 112 peptides, 26 chains. Longest chain 5 peptides. Score 0.204 Round 4: 106 peptides, 23 chains. Longest chain 7 peptides. Score 0.233 Round 5: 104 peptides, 23 chains. Longest chain 8 peptides. Score 0.224 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 83, 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 2pke-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4203 reflections ( 95.76 % complete ) and 7727 restraints for refining 3159 atoms. 7418 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1856 (Rfree = 0.000) for 3159 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1918 (Rfree = 0.000) for 3144 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1804 (Rfree = 0.000) for 3133 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1771 (Rfree = 0.000) for 3122 atoms. TimeTaking 33