Mon 24 Dec 01:04:51 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 2aj7-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-4.0-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/2aj7-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-4.0-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 01:04:56 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/2aj7-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-4.0-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 357 and 0 Target number of residues in the AU: 357 Target solvent content: 0.6586 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: 2aj7-4.0-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-4.0-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 4.000 Wilson plot Bfac: 83.62 4804 reflections ( 99.90 % complete ) and 0 restraints for refining 2891 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2456 (Rfree = 0.000) for 2891 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 2.88 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 0 residues added, 2942 seeds are put forward Round 1: 206 peptides, 30 chains. Longest chain 14 peptides. Score 0.447 Round 2: 220 peptides, 22 chains. Longest chain 29 peptides. Score 0.576 Round 3: 224 peptides, 24 chains. Longest chain 30 peptides. Score 0.563 Round 4: 227 peptides, 20 chains. Longest chain 37 peptides. Score 0.613 Round 5: 227 peptides, 20 chains. Longest chain 36 peptides. Score 0.613 Taking the results from Round 5 Chains 22, Residues 207, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4936 restraints for refining 2355 atoms. 4052 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2957 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.2827 (Rfree = 0.000) for 2328 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2638 (Rfree = 0.000) for 2324 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2679 (Rfree = 0.000) for 2318 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2611 (Rfree = 0.000) for 2313 atoms. Found 2 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 2.93 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2397 seeds are put forward Round 1: 209 peptides, 27 chains. Longest chain 15 peptides. Score 0.491 Round 2: 225 peptides, 18 chains. Longest chain 25 peptides. Score 0.629 Round 3: 218 peptides, 19 chains. Longest chain 33 peptides. Score 0.604 Round 4: 223 peptides, 21 chains. Longest chain 24 peptides. Score 0.593 Round 5: 224 peptides, 22 chains. Longest chain 23 peptides. Score 0.585 Taking the results from Round 2 Chains 18, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4992 restraints for refining 2355 atoms. 4182 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 2355 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 7: After refmac, R = 0.2726 (Rfree = 0.000) for 2351 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.2652 (Rfree = 0.000) for 2337 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 9: After refmac, R = 0.2577 (Rfree = 0.000) for 2331 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2565 (Rfree = 0.000) for 2319 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 2.90 Search for helices and strands: 0 residues in 0 chains, 2374 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 2401 seeds are put forward Round 1: 204 peptides, 24 chains. Longest chain 22 peptides. Score 0.514 Round 2: 213 peptides, 19 chains. Longest chain 24 peptides. Score 0.593 Round 3: 229 peptides, 23 chains. Longest chain 25 peptides. Score 0.585 Round 4: 238 peptides, 21 chains. Longest chain 32 peptides. Score 0.626 Round 5: 239 peptides, 17 chains. Longest chain 37 peptides. Score 0.667 Taking the results from Round 5 Chains 18, Residues 222, Estimated correctness of the model 15.1 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4561 restraints for refining 2354 atoms. 3552 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2980 (Rfree = 0.000) for 2354 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2748 (Rfree = 0.000) for 2341 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2676 (Rfree = 0.000) for 2330 atoms. Found 4 (11 requested) and removed 19 (5 requested) atoms. Cycle 14: After refmac, R = 0.2614 (Rfree = 0.000) for 2309 atoms. Found 5 (10 requested) and removed 14 (5 requested) atoms. Cycle 15: After refmac, R = 0.2582 (Rfree = 0.000) for 2300 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.92 3.00 Search for helices and strands: 0 residues in 0 chains, 2359 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 2399 seeds are put forward Round 1: 200 peptides, 26 chains. Longest chain 15 peptides. Score 0.480 Round 2: 228 peptides, 20 chains. Longest chain 27 peptides. Score 0.615 Round 3: 221 peptides, 24 chains. Longest chain 21 peptides. Score 0.556 Round 4: 224 peptides, 21 chains. Longest chain 28 peptides. Score 0.596 Round 5: 217 peptides, 19 chains. Longest chain 22 peptides. Score 0.602 Taking the results from Round 2 Chains 21, Residues 208, Estimated correctness of the model 0.0 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4566 restraints for refining 2354 atoms. 3608 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2664 (Rfree = 0.000) for 2354 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2531 (Rfree = 0.000) for 2321 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2515 (Rfree = 0.000) for 2304 atoms. Found 9 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2356 (Rfree = 0.000) for 2286 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.2304 (Rfree = 0.000) for 2265 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 2.93 Search for helices and strands: 0 residues in 0 chains, 2306 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 2337 seeds are put forward Round 1: 205 peptides, 27 chains. Longest chain 19 peptides. Score 0.481 Round 2: 223 peptides, 22 chains. Longest chain 34 peptides. Score 0.583 Round 3: 223 peptides, 25 chains. Longest chain 25 peptides. Score 0.549 Round 4: 221 peptides, 24 chains. Longest chain 34 peptides. Score 0.556 Round 5: 233 peptides, 24 chains. Longest chain 34 peptides. Score 0.584 Taking the results from Round 5 Chains 26, Residues 209, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4850 restraints for refining 2354 atoms. 3928 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2982 (Rfree = 0.000) for 2354 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 22: After refmac, R = 0.2857 (Rfree = 0.000) for 2329 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2731 (Rfree = 0.000) for 2326 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2624 (Rfree = 0.000) for 2320 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2608 (Rfree = 0.000) for 2311 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.86 2.96 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 2410 seeds are put forward Round 1: 186 peptides, 22 chains. Longest chain 22 peptides. Score 0.492 Round 2: 209 peptides, 21 chains. Longest chain 22 peptides. Score 0.561 Round 3: 220 peptides, 22 chains. Longest chain 27 peptides. Score 0.576 Round 4: 223 peptides, 21 chains. Longest chain 32 peptides. Score 0.593 Round 5: 218 peptides, 17 chains. Longest chain 30 peptides. Score 0.625 Taking the results from Round 5 Chains 18, Residues 201, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4990 restraints for refining 2354 atoms. 4112 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2793 (Rfree = 0.000) for 2354 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 27: After refmac, R = 0.2626 (Rfree = 0.000) for 2347 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2485 (Rfree = 0.000) for 2340 atoms. Found 7 (11 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.2434 (Rfree = 0.000) for 2332 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2353 (Rfree = 0.000) for 2323 atoms. Found 1 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 2.88 Search for helices and strands: 0 residues in 0 chains, 2362 seeds are put forward NCS extension: 0 residues added, 2362 seeds are put forward Round 1: 202 peptides, 24 chains. Longest chain 19 peptides. Score 0.509 Round 2: 208 peptides, 22 chains. Longest chain 29 peptides. Score 0.547 Round 3: 211 peptides, 20 chains. Longest chain 29 peptides. Score 0.577 Round 4: 214 peptides, 24 chains. Longest chain 19 peptides. Score 0.539 Round 5: 212 peptides, 19 chains. Longest chain 24 peptides. Score 0.591 Taking the results from Round 5 Chains 19, Residues 193, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4966 restraints for refining 2355 atoms. 4102 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2982 (Rfree = 0.000) for 2355 atoms. Found 9 (11 requested) and removed 21 (5 requested) atoms. Cycle 32: After refmac, R = 0.2804 (Rfree = 0.000) for 2329 atoms. Found 4 (11 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.2824 (Rfree = 0.000) for 2312 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.2735 (Rfree = 0.000) for 2304 atoms. Found 1 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.2751 (Rfree = 0.000) for 2295 atoms. Found 1 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.86 2.96 Search for helices and strands: 0 residues in 0 chains, 2338 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 2372 seeds are put forward Round 1: 200 peptides, 27 chains. Longest chain 19 peptides. Score 0.467 Round 2: 196 peptides, 21 chains. Longest chain 21 peptides. Score 0.530 Round 3: 207 peptides, 24 chains. Longest chain 21 peptides. Score 0.522 Round 4: 196 peptides, 20 chains. Longest chain 23 peptides. Score 0.542 Round 5: 205 peptides, 24 chains. Longest chain 20 peptides. Score 0.517 Taking the results from Round 4 Chains 20, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5394 restraints for refining 2355 atoms. 4710 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2965 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 37: After refmac, R = 0.2781 (Rfree = 0.000) for 2334 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2734 (Rfree = 0.000) for 2330 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2624 (Rfree = 0.000) for 2325 atoms. Found 5 (11 requested) and removed 16 (5 requested) atoms. Cycle 40: After refmac, R = 0.2622 (Rfree = 0.000) for 2313 atoms. Found 6 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 2.96 Search for helices and strands: 0 residues in 0 chains, 2352 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2377 seeds are put forward Round 1: 167 peptides, 25 chains. Longest chain 11 peptides. Score 0.400 Round 2: 188 peptides, 23 chains. Longest chain 22 peptides. Score 0.485 Round 3: 180 peptides, 22 chains. Longest chain 14 peptides. Score 0.476 Round 4: 175 peptides, 23 chains. Longest chain 17 peptides. Score 0.449 Round 5: 179 peptides, 28 chains. Longest chain 14 peptides. Score 0.395 Taking the results from Round 2 Chains 23, Residues 165, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5290 restraints for refining 2354 atoms. 4636 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2885 (Rfree = 0.000) for 2354 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2781 (Rfree = 0.000) for 2350 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2846 (Rfree = 0.000) for 2340 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.2822 (Rfree = 0.000) for 2329 atoms. Found 11 (11 requested) and removed 55 (5 requested) atoms. Cycle 45: After refmac, R = 0.3043 (Rfree = 0.000) for 2283 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 2.89 Search for helices and strands: 0 residues in 0 chains, 2330 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2356 seeds are put forward Round 1: 166 peptides, 28 chains. Longest chain 13 peptides. Score 0.356 Round 2: 177 peptides, 25 chains. Longest chain 19 peptides. Score 0.429 Round 3: 180 peptides, 28 chains. Longest chain 18 peptides. Score 0.398 Round 4: 184 peptides, 27 chains. Longest chain 13 peptides. Score 0.423 Round 5: 181 peptides, 24 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 157, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2aj7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4804 reflections ( 99.90 % complete ) and 5179 restraints for refining 2354 atoms. 4528 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2868 (Rfree = 0.000) for 2354 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2653 (Rfree = 0.000) for 2341 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2615 (Rfree = 0.000) for 2328 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2550 (Rfree = 0.000) for 2319 atoms. TimeTaking 40.75