null Mon 24 Dec 01:09:56 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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/2i5i-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 01:10:01 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/2i5i-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6594 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-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.8-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 3.800 Wilson plot Bfac: 83.92 5326 reflections ( 99.05 % complete ) and 0 restraints for refining 4654 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3428 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3144 (Rfree = 0.000) for 4654 atoms. Found 25 (25 requested) and removed 51 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 4674 seeds are put forward NCS extension: 0 residues added, 4674 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 8 peptides. Score 0.207 Round 2: 126 peptides, 25 chains. Longest chain 10 peptides. Score 0.267 Round 3: 135 peptides, 27 chains. Longest chain 10 peptides. Score 0.269 Round 4: 153 peptides, 31 chains. Longest chain 11 peptides. Score 0.272 Round 5: 159 peptides, 33 chains. Longest chain 9 peptides. Score 0.264 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 ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 9328 restraints for refining 3805 atoms. 8871 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2851 (Rfree = 0.000) for 3805 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 2: After refmac, R = 0.2728 (Rfree = 0.000) for 3741 atoms. Found 18 (20 requested) and removed 44 (10 requested) atoms. Cycle 3: After refmac, R = 0.2232 (Rfree = 0.000) for 3693 atoms. Found 8 (20 requested) and removed 34 (10 requested) atoms. Cycle 4: After refmac, R = 0.2613 (Rfree = 0.000) for 3648 atoms. Found 20 (20 requested) and removed 35 (10 requested) atoms. Cycle 5: After refmac, R = 0.2663 (Rfree = 0.000) for 3614 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 3656 seeds are put forward NCS extension: 0 residues added, 3656 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 7 peptides. Score 0.218 Round 2: 152 peptides, 32 chains. Longest chain 9 peptides. Score 0.254 Round 3: 179 peptides, 36 chains. Longest chain 13 peptides. Score 0.288 Round 4: 179 peptides, 36 chains. Longest chain 9 peptides. Score 0.288 Round 5: 177 peptides, 34 chains. Longest chain 11 peptides. Score 0.309 Taking the results from Round 5 Chains 34, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7239 restraints for refining 3218 atoms. 6701 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2542 (Rfree = 0.000) for 3218 atoms. Found 17 (17 requested) and removed 42 (8 requested) atoms. Cycle 7: After refmac, R = 0.2338 (Rfree = 0.000) for 3165 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 8: After refmac, R = 0.2259 (Rfree = 0.000) for 3130 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 9: After refmac, R = 0.1836 (Rfree = 0.000) for 3110 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.1694 (Rfree = 0.000) for 3102 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 3175 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3189 seeds are put forward Round 1: 172 peptides, 38 chains. Longest chain 7 peptides. Score 0.237 Round 2: 197 peptides, 36 chains. Longest chain 10 peptides. Score 0.345 Round 3: 203 peptides, 37 chains. Longest chain 15 peptides. Score 0.350 Round 4: 198 peptides, 33 chains. Longest chain 10 peptides. Score 0.387 Round 5: 197 peptides, 33 chains. Longest chain 15 peptides. Score 0.384 Taking the results from Round 4 Chains 33, Residues 165, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7111 restraints for refining 3281 atoms. 6467 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2207 (Rfree = 0.000) for 3281 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 12: After refmac, R = 0.2180 (Rfree = 0.000) for 3254 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 13: After refmac, R = 0.2212 (Rfree = 0.000) for 3221 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2197 (Rfree = 0.000) for 3210 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 15: After refmac, R = 0.2269 (Rfree = 0.000) for 3195 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 3281 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3287 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 7 peptides. Score 0.258 Round 2: 166 peptides, 30 chains. Longest chain 10 peptides. Score 0.329 Round 3: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.358 Round 4: 188 peptides, 32 chains. Longest chain 12 peptides. Score 0.370 Round 5: 190 peptides, 32 chains. Longest chain 17 peptides. Score 0.376 Taking the results from Round 5 Chains 32, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7228 restraints for refining 3308 atoms. 6628 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2402 (Rfree = 0.000) for 3308 atoms. Found 18 (18 requested) and removed 43 (9 requested) atoms. Cycle 17: After refmac, R = 0.2214 (Rfree = 0.000) for 3258 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 18: After refmac, R = 0.2434 (Rfree = 0.000) for 3221 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 19: After refmac, R = 0.2199 (Rfree = 0.000) for 3198 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 20: After refmac, R = 0.1851 (Rfree = 0.000) for 3183 atoms. Found 15 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3266 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 11 peptides. Score 0.268 Round 2: 183 peptides, 32 chains. Longest chain 12 peptides. Score 0.355 Round 3: 174 peptides, 29 chains. Longest chain 16 peptides. Score 0.368 Round 4: 198 peptides, 31 chains. Longest chain 16 peptides. Score 0.413 Round 5: 194 peptides, 33 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 4 Chains 31, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7271 restraints for refining 3341 atoms. 6634 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2349 (Rfree = 0.000) for 3341 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 22: After refmac, R = 0.2288 (Rfree = 0.000) for 3295 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 23: After refmac, R = 0.2461 (Rfree = 0.000) for 3257 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 24: After refmac, R = 0.2251 (Rfree = 0.000) for 3243 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 25: After refmac, R = 0.2272 (Rfree = 0.000) for 3232 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 3315 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3333 seeds are put forward Round 1: 166 peptides, 37 chains. Longest chain 8 peptides. Score 0.231 Round 2: 201 peptides, 37 chains. Longest chain 13 peptides. Score 0.344 Round 3: 188 peptides, 33 chains. Longest chain 13 peptides. Score 0.357 Round 4: 191 peptides, 32 chains. Longest chain 13 peptides. Score 0.379 Round 5: 192 peptides, 31 chains. Longest chain 19 peptides. Score 0.395 Taking the results from Round 5 Chains 31, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7285 restraints for refining 3333 atoms. 6672 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2202 (Rfree = 0.000) for 3333 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 27: After refmac, R = 0.2215 (Rfree = 0.000) for 3303 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 28: After refmac, R = 0.2200 (Rfree = 0.000) for 3287 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 29: After refmac, R = 0.1792 (Rfree = 0.000) for 3277 atoms. Found 15 (18 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1718 (Rfree = 0.000) for 3267 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 3351 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 3384 seeds are put forward Round 1: 157 peptides, 35 chains. Longest chain 8 peptides. Score 0.228 Round 2: 184 peptides, 36 chains. Longest chain 8 peptides. Score 0.304 Round 3: 186 peptides, 32 chains. Longest chain 11 peptides. Score 0.364 Round 4: 187 peptides, 32 chains. Longest chain 10 peptides. Score 0.367 Round 5: 180 peptides, 33 chains. Longest chain 9 peptides. Score 0.332 Taking the results from Round 4 Chains 32, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7290 restraints for refining 3344 atoms. 6702 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2500 (Rfree = 0.000) for 3344 atoms. Found 18 (18 requested) and removed 38 (9 requested) atoms. Cycle 32: After refmac, R = 0.2314 (Rfree = 0.000) for 3307 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 33: After refmac, R = 0.2345 (Rfree = 0.000) for 3286 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 34: After refmac, R = 0.1843 (Rfree = 0.000) for 3277 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 35: After refmac, R = 0.1688 (Rfree = 0.000) for 3273 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 3305 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3317 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 8 peptides. Score 0.237 Round 2: 150 peptides, 30 chains. Longest chain 7 peptides. Score 0.276 Round 3: 164 peptides, 33 chains. Longest chain 7 peptides. Score 0.280 Round 4: 168 peptides, 33 chains. Longest chain 8 peptides. Score 0.294 Round 5: 170 peptides, 32 chains. Longest chain 9 peptides. Score 0.314 Taking the results from Round 5 Chains 32, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7610 restraints for refining 3375 atoms. 7090 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2431 (Rfree = 0.000) for 3375 atoms. Found 18 (18 requested) and removed 43 (9 requested) atoms. Cycle 37: After refmac, R = 0.2252 (Rfree = 0.000) for 3328 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 38: After refmac, R = 0.2173 (Rfree = 0.000) for 3307 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 39: After refmac, R = 0.1767 (Rfree = 0.000) for 3291 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.2178 (Rfree = 0.000) for 3287 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 3333 seeds are put forward NCS extension: 0 residues added, 3333 seeds are put forward Round 1: 119 peptides, 27 chains. Longest chain 7 peptides. Score 0.210 Round 2: 138 peptides, 29 chains. Longest chain 7 peptides. Score 0.249 Round 3: 136 peptides, 26 chains. Longest chain 8 peptides. Score 0.287 Round 4: 143 peptides, 26 chains. Longest chain 9 peptides. Score 0.311 Round 5: 144 peptides, 28 chains. Longest chain 10 peptides. Score 0.285 Taking the results from Round 4 Chains 26, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5326 reflections ( 99.05 % complete ) and 7278 restraints for refining 3288 atoms. 6836 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2558 (Rfree = 0.000) for 3288 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 42: After refmac, R = 0.2356 (Rfree = 0.000) for 3260 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. Cycle 43: After refmac, R = 0.2350 (Rfree = 0.000) for 3238 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 44: After refmac, R = 0.2499 (Rfree = 0.000) for 3218 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 45: After refmac, R = 0.2422 (Rfree = 0.000) for 3211 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 3252 seeds are put forward NCS extension: 0 residues added, 3252 seeds are put forward Round 1: 123 peptides, 29 chains. Longest chain 6 peptides. Score 0.194 Round 2: 144 peptides, 30 chains. Longest chain 10 peptides. Score 0.255 Round 3: 123 peptides, 25 chains. Longest chain 10 peptides. Score 0.256 Round 4: 128 peptides, 25 chains. Longest chain 10 peptides. Score 0.274 Round 5: 136 peptides, 25 chains. Longest chain 13 peptides. Score 0.302 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 111, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5326 reflections ( 99.05 % complete ) and 6913 restraints for refining 3194 atoms. 6467 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2416 (Rfree = 0.000) for 3194 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2360 (Rfree = 0.000) for 3175 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1888 (Rfree = 0.000) for 3155 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1758 (Rfree = 0.000) for 3140 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:56:25 GMT 2018 Job finished. TimeTaking 46.49 Used memory is bytes: 3579856