null Tue 25 Dec 19:27:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aj7-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-parrot-hancs/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 401 and 0 Target number of residues in the AU: 401 Target solvent content: 0.6165 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: 2aj7-3.4-parrot-hancs.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: 2aj7-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.10 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 3.400 Wilson plot Bfac: 59.71 7776 reflections ( 99.94 % complete ) and 0 restraints for refining 2895 atoms. Observations/parameters ratio is 0.67 ------------------------------------------------------ Starting model: R = 0.3271 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2901 (Rfree = 0.000) for 2895 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 2.49 Search for helices and strands: 0 residues in 0 chains, 2943 seeds are put forward NCS extension: 0 residues added, 2943 seeds are put forward Round 1: 190 peptides, 26 chains. Longest chain 21 peptides. Score 0.453 Round 2: 235 peptides, 22 chains. Longest chain 26 peptides. Score 0.609 Round 3: 251 peptides, 18 chains. Longest chain 50 peptides. Score 0.680 Round 4: 248 peptides, 19 chains. Longest chain 50 peptides. Score 0.665 Round 5: 240 peptides, 18 chains. Longest chain 33 peptides. Score 0.659 Taking the results from Round 3 Chains 19, Residues 233, Estimated correctness of the model 52.6 % 3 chains (80 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4099 restraints for refining 2423 atoms. 2838 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2872 (Rfree = 0.000) for 2423 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 2: After refmac, R = 0.2730 (Rfree = 0.000) for 2385 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2624 (Rfree = 0.000) for 2375 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2587 (Rfree = 0.000) for 2375 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2477 (Rfree = 0.000) for 2373 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 2.48 Search for helices and strands: 0 residues in 0 chains, 2443 seeds are put forward NCS extension: 31 residues added (45 deleted due to clashes), 2474 seeds are put forward Round 1: 236 peptides, 22 chains. Longest chain 29 peptides. Score 0.611 Round 2: 243 peptides, 19 chains. Longest chain 37 peptides. Score 0.656 Round 3: 242 peptides, 18 chains. Longest chain 43 peptides. Score 0.663 Round 4: 252 peptides, 16 chains. Longest chain 47 peptides. Score 0.700 Round 5: 256 peptides, 18 chains. Longest chain 41 peptides. Score 0.689 Taking the results from Round 4 Chains 17, Residues 236, Estimated correctness of the model 57.9 % 3 chains (88 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3953 restraints for refining 2371 atoms. 2646 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2909 (Rfree = 0.000) for 2371 atoms. Found 10 (17 requested) and removed 20 (8 requested) atoms. Cycle 7: After refmac, R = 0.2651 (Rfree = 0.000) for 2350 atoms. Found 12 (17 requested) and removed 19 (8 requested) atoms. Cycle 8: After refmac, R = 0.2543 (Rfree = 0.000) for 2339 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2515 (Rfree = 0.000) for 2329 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.2523 (Rfree = 0.000) for 2323 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.45 Search for helices and strands: 0 residues in 0 chains, 2380 seeds are put forward NCS extension: 43 residues added (26 deleted due to clashes), 2423 seeds are put forward Round 1: 253 peptides, 17 chains. Longest chain 55 peptides. Score 0.693 Round 2: 256 peptides, 20 chains. Longest chain 41 peptides. Score 0.671 Round 3: 262 peptides, 18 chains. Longest chain 51 peptides. Score 0.700 Round 4: 267 peptides, 17 chains. Longest chain 54 peptides. Score 0.717 Round 5: 250 peptides, 17 chains. Longest chain 44 peptides. Score 0.688 Taking the results from Round 4 Chains 21, Residues 250, Estimated correctness of the model 62.1 % 5 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 141 A and 149 A 20 chains (257 residues) following loop building 4 chains (141 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3544 restraints for refining 2453 atoms. 1969 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2886 (Rfree = 0.000) for 2453 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 12: After refmac, R = 0.2633 (Rfree = 0.000) for 2424 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.2548 (Rfree = 0.000) for 2413 atoms. Found 6 (17 requested) and removed 13 (9 requested) atoms. Cycle 14: After refmac, R = 0.2452 (Rfree = 0.000) for 2405 atoms. Found 4 (17 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.2429 (Rfree = 0.000) for 2395 atoms. Found 1 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.44 Search for helices and strands: 0 residues in 0 chains, 2455 seeds are put forward NCS extension: 31 residues added (13 deleted due to clashes), 2486 seeds are put forward Round 1: 254 peptides, 22 chains. Longest chain 39 peptides. Score 0.648 Round 2: 250 peptides, 17 chains. Longest chain 52 peptides. Score 0.688 Round 3: 254 peptides, 20 chains. Longest chain 38 peptides. Score 0.667 Round 4: 260 peptides, 20 chains. Longest chain 45 peptides. Score 0.678 Round 5: 254 peptides, 22 chains. Longest chain 33 peptides. Score 0.648 Taking the results from Round 2 Chains 19, Residues 233, Estimated correctness of the model 54.7 % 2 chains (79 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4113 restraints for refining 2369 atoms. 2844 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2779 (Rfree = 0.000) for 2369 atoms. Found 11 (15 requested) and removed 14 (8 requested) atoms. Cycle 17: After refmac, R = 0.2648 (Rfree = 0.000) for 2358 atoms. Found 6 (15 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2581 (Rfree = 0.000) for 2348 atoms. Found 3 (15 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2549 (Rfree = 0.000) for 2339 atoms. Found 8 (15 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2543 (Rfree = 0.000) for 2332 atoms. Found 4 (15 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 2.45 Search for helices and strands: 0 residues in 0 chains, 2376 seeds are put forward NCS extension: 57 residues added (13 deleted due to clashes), 2433 seeds are put forward Round 1: 247 peptides, 21 chains. Longest chain 37 peptides. Score 0.644 Round 2: 250 peptides, 18 chains. Longest chain 41 peptides. Score 0.678 Round 3: 255 peptides, 24 chains. Longest chain 31 peptides. Score 0.631 Round 4: 254 peptides, 18 chains. Longest chain 45 peptides. Score 0.686 Round 5: 248 peptides, 17 chains. Longest chain 55 peptides. Score 0.684 Taking the results from Round 4 Chains 19, Residues 236, Estimated correctness of the model 54.2 % 2 chains (71 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4131 restraints for refining 2370 atoms. 2902 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2930 (Rfree = 0.000) for 2370 atoms. Found 15 (15 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2698 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 25 (8 requested) atoms. Cycle 23: After refmac, R = 0.2660 (Rfree = 0.000) for 2348 atoms. Found 15 (15 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2567 (Rfree = 0.000) for 2343 atoms. Found 15 (15 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2516 (Rfree = 0.000) for 2337 atoms. Found 10 (15 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 2.45 Search for helices and strands: 0 residues in 0 chains, 2403 seeds are put forward NCS extension: 46 residues added (30 deleted due to clashes), 2449 seeds are put forward Round 1: 243 peptides, 23 chains. Longest chain 47 peptides. Score 0.616 Round 2: 252 peptides, 23 chains. Longest chain 35 peptides. Score 0.635 Round 3: 261 peptides, 16 chains. Longest chain 48 peptides. Score 0.716 Round 4: 263 peptides, 22 chains. Longest chain 45 peptides. Score 0.665 Round 5: 270 peptides, 14 chains. Longest chain 51 peptides. Score 0.747 Taking the results from Round 5 Chains 14, Residues 256, Estimated correctness of the model 69.2 % 2 chains (97 residues) have been docked in sequence Building loops using Loopy2018 14 chains (256 residues) following loop building 2 chains (97 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3843 restraints for refining 2371 atoms. 2431 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2740 (Rfree = 0.000) for 2371 atoms. Found 15 (15 requested) and removed 22 (8 requested) atoms. Cycle 27: After refmac, R = 0.2700 (Rfree = 0.000) for 2358 atoms. Found 6 (15 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.2510 (Rfree = 0.000) for 2341 atoms. Found 11 (15 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2477 (Rfree = 0.000) for 2337 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2534 (Rfree = 0.000) for 2332 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 2.44 Search for helices and strands: 0 residues in 0 chains, 2382 seeds are put forward NCS extension: 57 residues added (11 deleted due to clashes), 2439 seeds are put forward Round 1: 245 peptides, 23 chains. Longest chain 46 peptides. Score 0.620 Round 2: 247 peptides, 17 chains. Longest chain 41 peptides. Score 0.682 Round 3: 249 peptides, 16 chains. Longest chain 51 peptides. Score 0.695 Round 4: 258 peptides, 18 chains. Longest chain 41 peptides. Score 0.693 Round 5: 256 peptides, 17 chains. Longest chain 49 peptides. Score 0.698 Taking the results from Round 5 Chains 17, Residues 239, Estimated correctness of the model 57.4 % 2 chains (75 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4084 restraints for refining 2371 atoms. 2828 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2736 (Rfree = 0.000) for 2371 atoms. Found 14 (14 requested) and removed 22 (8 requested) atoms. Cycle 32: After refmac, R = 0.2589 (Rfree = 0.000) for 2359 atoms. Found 12 (14 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.2571 (Rfree = 0.000) for 2358 atoms. Found 2 (14 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.2418 (Rfree = 0.000) for 2346 atoms. Found 4 (14 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2369 (Rfree = 0.000) for 2339 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 2.47 Search for helices and strands: 0 residues in 0 chains, 2398 seeds are put forward NCS extension: 15 residues added (14 deleted due to clashes), 2413 seeds are put forward Round 1: 234 peptides, 24 chains. Longest chain 31 peptides. Score 0.586 Round 2: 250 peptides, 18 chains. Longest chain 39 peptides. Score 0.678 Round 3: 254 peptides, 20 chains. Longest chain 36 peptides. Score 0.667 Round 4: 251 peptides, 20 chains. Longest chain 39 peptides. Score 0.661 Round 5: 250 peptides, 18 chains. Longest chain 41 peptides. Score 0.678 Taking the results from Round 5 Chains 20, Residues 232, Estimated correctness of the model 52.0 % 3 chains (87 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4017 restraints for refining 2371 atoms. 2746 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2644 (Rfree = 0.000) for 2371 atoms. Found 14 (14 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2599 (Rfree = 0.000) for 2365 atoms. Found 8 (14 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2482 (Rfree = 0.000) for 2356 atoms. Found 7 (14 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.2456 (Rfree = 0.000) for 2349 atoms. Found 6 (14 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2442 (Rfree = 0.000) for 2342 atoms. Found 8 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 2.45 Search for helices and strands: 0 residues in 0 chains, 2397 seeds are put forward NCS extension: 13 residues added (14 deleted due to clashes), 2410 seeds are put forward Round 1: 243 peptides, 26 chains. Longest chain 29 peptides. Score 0.585 Round 2: 257 peptides, 22 chains. Longest chain 38 peptides. Score 0.654 Round 3: 252 peptides, 21 chains. Longest chain 41 peptides. Score 0.654 Round 4: 246 peptides, 19 chains. Longest chain 41 peptides. Score 0.661 Round 5: 246 peptides, 20 chains. Longest chain 35 peptides. Score 0.652 Taking the results from Round 4 Chains 21, Residues 227, Estimated correctness of the model 47.3 % 2 chains (62 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4247 restraints for refining 2371 atoms. 3093 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2743 (Rfree = 0.000) for 2371 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.2649 (Rfree = 0.000) for 2363 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.2480 (Rfree = 0.000) for 2363 atoms. Found 10 (14 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2484 (Rfree = 0.000) for 2362 atoms. Found 11 (14 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2477 (Rfree = 0.000) for 2365 atoms. Found 4 (14 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 2.46 Search for helices and strands: 0 residues in 0 chains, 2416 seeds are put forward NCS extension: 15 residues added (15 deleted due to clashes), 2431 seeds are put forward Round 1: 228 peptides, 18 chains. Longest chain 40 peptides. Score 0.635 Round 2: 244 peptides, 21 chains. Longest chain 30 peptides. Score 0.638 Round 3: 239 peptides, 16 chains. Longest chain 47 peptides. Score 0.677 Round 4: 238 peptides, 19 chains. Longest chain 40 peptides. Score 0.646 Round 5: 246 peptides, 18 chains. Longest chain 42 peptides. Score 0.671 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 223, Estimated correctness of the model 51.8 % 4 chains (89 residues) have been docked in sequence Sequence coverage is 39 % Consider running further cycles of model building using 2aj7-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (223 residues) following loop building 4 chains (89 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7776 reflections ( 99.94 % complete ) and 4011 restraints for refining 2371 atoms. 2766 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2613 (Rfree = 0.000) for 2371 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2544 (Rfree = 0.000) for 2359 atoms. Found 0 (14 requested) and removed 4 (8 requested) atoms. Cycle 48: After refmac, R = 0.2550 (Rfree = 0.000) for 2350 atoms. Found 0 (14 requested) and removed 0 (8 requested) atoms. Cycle 49: After refmac, R = 0.2524 (Rfree = 0.000) for 2347 atoms. Found 0 (14 requested) and removed 0 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:35:58 GMT 2018 Job finished. TimeTaking 68.02 Used memory is bytes: 21001504