Mon 24 Dec 01:00:06 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 2aj7-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.8-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/2aj7-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.8-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 01:00:10 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/2aj7-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.8-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 373 and 0 Target number of residues in the AU: 373 Target solvent content: 0.6433 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-3.8-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.15 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: 94.224 3.800 Wilson plot Bfac: 73.84 5579 reflections ( 99.91 % complete ) and 0 restraints for refining 2905 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3350 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3694 (Rfree = 0.000) for 2905 atoms. Found 15 (15 requested) and removed 65 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 2.87 Search for helices and strands: 0 residues in 0 chains, 2892 seeds are put forward NCS extension: 0 residues added, 2892 seeds are put forward Round 1: 153 peptides, 28 chains. Longest chain 13 peptides. Score 0.314 Round 2: 190 peptides, 23 chains. Longest chain 20 peptides. Score 0.490 Round 3: 208 peptides, 25 chains. Longest chain 19 peptides. Score 0.513 Round 4: 197 peptides, 23 chains. Longest chain 19 peptides. Score 0.508 Round 5: 202 peptides, 25 chains. Longest chain 20 peptides. Score 0.497 Taking the results from Round 3 Chains 25, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5245 restraints for refining 2358 atoms. 4538 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3400 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.3193 (Rfree = 0.000) for 2293 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.3279 (Rfree = 0.000) for 2260 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 4: After refmac, R = 0.3169 (Rfree = 0.000) for 2236 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 5: After refmac, R = 0.2947 (Rfree = 0.000) for 2215 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 2.80 Search for helices and strands: 0 residues in 0 chains, 2286 seeds are put forward NCS extension: 0 residues added, 2286 seeds are put forward Round 1: 214 peptides, 27 chains. Longest chain 20 peptides. Score 0.504 Round 2: 223 peptides, 26 chains. Longest chain 30 peptides. Score 0.538 Round 3: 219 peptides, 22 chains. Longest chain 37 peptides. Score 0.573 Round 4: 224 peptides, 25 chains. Longest chain 26 peptides. Score 0.552 Round 5: 235 peptides, 23 chains. Longest chain 39 peptides. Score 0.599 Taking the results from Round 5 Chains 25, Residues 212, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4917 restraints for refining 2359 atoms. 3997 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3077 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.3005 (Rfree = 0.000) for 2326 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.3005 (Rfree = 0.000) for 2284 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2895 (Rfree = 0.000) for 2253 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.2855 (Rfree = 0.000) for 2236 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 2.77 Search for helices and strands: 0 residues in 0 chains, 2288 seeds are put forward NCS extension: 49 residues added (0 deleted due to clashes), 2337 seeds are put forward Round 1: 219 peptides, 32 chains. Longest chain 18 peptides. Score 0.458 Round 2: 235 peptides, 27 chains. Longest chain 33 peptides. Score 0.556 Round 3: 228 peptides, 25 chains. Longest chain 30 peptides. Score 0.561 Round 4: 233 peptides, 25 chains. Longest chain 25 peptides. Score 0.573 Round 5: 242 peptides, 29 chains. Longest chain 32 peptides. Score 0.550 Taking the results from Round 4 Chains 25, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5057 restraints for refining 2359 atoms. 4250 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3362 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 12: After refmac, R = 0.3129 (Rfree = 0.000) for 2331 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 13: After refmac, R = 0.3096 (Rfree = 0.000) for 2299 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.2929 (Rfree = 0.000) for 2278 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 15: After refmac, R = 0.2853 (Rfree = 0.000) for 2259 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 2.85 Search for helices and strands: 0 residues in 0 chains, 2325 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2346 seeds are put forward Round 1: 205 peptides, 29 chains. Longest chain 26 peptides. Score 0.456 Round 2: 220 peptides, 21 chains. Longest chain 33 peptides. Score 0.587 Round 3: 218 peptides, 26 chains. Longest chain 18 peptides. Score 0.526 Round 4: 219 peptides, 25 chains. Longest chain 19 peptides. Score 0.540 Round 5: 225 peptides, 23 chains. Longest chain 24 peptides. Score 0.576 Taking the results from Round 2 Chains 23, Residues 199, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4942 restraints for refining 2358 atoms. 4094 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3144 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.2862 (Rfree = 0.000) for 2336 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.2779 (Rfree = 0.000) for 2316 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 19: After refmac, R = 0.2730 (Rfree = 0.000) for 2300 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. Cycle 20: After refmac, R = 0.2475 (Rfree = 0.000) for 2292 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 2.79 Search for helices and strands: 0 residues in 0 chains, 2357 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 2378 seeds are put forward Round 1: 208 peptides, 29 chains. Longest chain 16 peptides. Score 0.465 Round 2: 215 peptides, 25 chains. Longest chain 25 peptides. Score 0.530 Round 3: 228 peptides, 24 chains. Longest chain 36 peptides. Score 0.572 Round 4: 227 peptides, 25 chains. Longest chain 26 peptides. Score 0.559 Round 5: 237 peptides, 23 chains. Longest chain 32 peptides. Score 0.603 Taking the results from Round 5 Chains 25, Residues 214, Estimated correctness of the model 0.3 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4826 restraints for refining 2358 atoms. 3909 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3217 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.3090 (Rfree = 0.000) for 2314 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.2866 (Rfree = 0.000) for 2286 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2929 (Rfree = 0.000) for 2269 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2937 (Rfree = 0.000) for 2244 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 2.77 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2318 seeds are put forward Round 1: 189 peptides, 29 chains. Longest chain 16 peptides. Score 0.412 Round 2: 210 peptides, 25 chains. Longest chain 26 peptides. Score 0.518 Round 3: 219 peptides, 26 chains. Longest chain 26 peptides. Score 0.528 Round 4: 233 peptides, 30 chains. Longest chain 27 peptides. Score 0.518 Round 5: 215 peptides, 20 chains. Longest chain 30 peptides. Score 0.586 Taking the results from Round 5 Chains 20, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5171 restraints for refining 2358 atoms. 4411 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3223 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.3104 (Rfree = 0.000) for 2324 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.3056 (Rfree = 0.000) for 2299 atoms. Found 8 (12 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.3086 (Rfree = 0.000) for 2274 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 30: After refmac, R = 0.2768 (Rfree = 0.000) for 2244 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 2.72 Search for helices and strands: 0 residues in 0 chains, 2297 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2313 seeds are put forward Round 1: 192 peptides, 31 chains. Longest chain 23 peptides. Score 0.394 Round 2: 207 peptides, 32 chains. Longest chain 16 peptides. Score 0.425 Round 3: 212 peptides, 27 chains. Longest chain 26 peptides. Score 0.499 Round 4: 216 peptides, 29 chains. Longest chain 16 peptides. Score 0.486 Round 5: 228 peptides, 28 chains. Longest chain 32 peptides. Score 0.528 Taking the results from Round 5 Chains 30, Residues 200, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4857 restraints for refining 2358 atoms. 3978 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3375 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 32: After refmac, R = 0.2976 (Rfree = 0.000) for 2331 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.2870 (Rfree = 0.000) for 2318 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.2669 (Rfree = 0.000) for 2299 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2826 (Rfree = 0.000) for 2288 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 2.88 Search for helices and strands: 0 residues in 0 chains, 2357 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 2397 seeds are put forward Round 1: 200 peptides, 33 chains. Longest chain 16 peptides. Score 0.392 Round 2: 212 peptides, 28 chains. Longest chain 28 peptides. Score 0.487 Round 3: 208 peptides, 25 chains. Longest chain 39 peptides. Score 0.513 Round 4: 207 peptides, 27 chains. Longest chain 22 peptides. Score 0.486 Round 5: 216 peptides, 28 chains. Longest chain 31 peptides. Score 0.498 Taking the results from Round 3 Chains 25, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5236 restraints for refining 2359 atoms. 4529 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2972 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.2972 (Rfree = 0.000) for 2338 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 38: After refmac, R = 0.2629 (Rfree = 0.000) for 2325 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2520 (Rfree = 0.000) for 2311 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2489 (Rfree = 0.000) for 2301 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.87 2.96 Search for helices and strands: 0 residues in 0 chains, 2353 seeds are put forward NCS extension: 50 residues added (10 deleted due to clashes), 2403 seeds are put forward Round 1: 182 peptides, 29 chains. Longest chain 16 peptides. Score 0.391 Round 2: 206 peptides, 29 chains. Longest chain 16 peptides. Score 0.459 Round 3: 202 peptides, 25 chains. Longest chain 22 peptides. Score 0.497 Round 4: 210 peptides, 28 chains. Longest chain 22 peptides. Score 0.482 Round 5: 203 peptides, 22 chains. Longest chain 22 peptides. Score 0.535 Taking the results from Round 5 Chains 22, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5186 restraints for refining 2359 atoms. 4484 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3160 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.3079 (Rfree = 0.000) for 2337 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 43: After refmac, R = 0.2989 (Rfree = 0.000) for 2315 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.2681 (Rfree = 0.000) for 2293 atoms. Found 10 (12 requested) and removed 14 (6 requested) atoms. Cycle 45: After refmac, R = 0.2599 (Rfree = 0.000) for 2277 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 2.75 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2358 seeds are put forward Round 1: 160 peptides, 29 chains. Longest chain 10 peptides. Score 0.323 Round 2: 189 peptides, 26 chains. Longest chain 28 peptides. Score 0.450 Round 3: 207 peptides, 26 chains. Longest chain 21 peptides. Score 0.498 Round 4: 197 peptides, 26 chains. Longest chain 21 peptides. Score 0.472 Round 5: 192 peptides, 21 chains. Longest chain 31 peptides. Score 0.520 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 171, 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 2aj7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5579 reflections ( 99.91 % complete ) and 5276 restraints for refining 2359 atoms. 4613 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3212 (Rfree = 0.000) for 2359 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3066 (Rfree = 0.000) for 2325 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3046 (Rfree = 0.000) for 2282 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2944 (Rfree = 0.000) for 2263 atoms. TimeTaking 38.97