null Sun 23 Dec 22:23:02 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 2ajr-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.6-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/2ajr-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.6-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 ============================================================ Sun 23 Dec 22:23:12 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/2ajr-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.6-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 559 and 0 Target number of residues in the AU: 559 Target solvent content: 0.6380 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-3.6-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.70 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: 29.168 3.600 Wilson plot Bfac: 70.60 10268 reflections ( 99.54 % complete ) and 0 restraints for refining 5900 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3625 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3536 (Rfree = 0.000) for 5900 atoms. Found 37 (37 requested) and removed 56 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 5978 seeds are put forward NCS extension: 0 residues added, 5978 seeds are put forward Round 1: 240 peptides, 49 chains. Longest chain 11 peptides. Score 0.272 Round 2: 310 peptides, 52 chains. Longest chain 13 peptides. Score 0.393 Round 3: 329 peptides, 49 chains. Longest chain 17 peptides. Score 0.454 Round 4: 344 peptides, 49 chains. Longest chain 20 peptides. Score 0.481 Round 5: 334 peptides, 48 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 4 Chains 51, Residues 295, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10775 restraints for refining 4797 atoms. 9594 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3088 (Rfree = 0.000) for 4797 atoms. Found 27 (30 requested) and removed 41 (15 requested) atoms. Cycle 2: After refmac, R = 0.2930 (Rfree = 0.000) for 4684 atoms. Found 26 (30 requested) and removed 34 (15 requested) atoms. Cycle 3: After refmac, R = 0.2679 (Rfree = 0.000) for 4641 atoms. Found 12 (29 requested) and removed 26 (14 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 4586 atoms. Found 9 (29 requested) and removed 30 (14 requested) atoms. Cycle 5: After refmac, R = 0.2436 (Rfree = 0.000) for 4551 atoms. Found 4 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 4684 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4710 seeds are put forward Round 1: 305 peptides, 55 chains. Longest chain 13 peptides. Score 0.357 Round 2: 326 peptides, 46 chains. Longest chain 18 peptides. Score 0.473 Round 3: 360 peptides, 47 chains. Longest chain 29 peptides. Score 0.524 Round 4: 352 peptides, 48 chains. Longest chain 16 peptides. Score 0.502 Round 5: 344 peptides, 47 chains. Longest chain 23 peptides. Score 0.496 Taking the results from Round 3 Chains 49, Residues 313, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10443 restraints for refining 4778 atoms. 9162 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2711 (Rfree = 0.000) for 4778 atoms. Found 23 (30 requested) and removed 52 (15 requested) atoms. Cycle 7: After refmac, R = 0.2564 (Rfree = 0.000) for 4705 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 8: After refmac, R = 0.2490 (Rfree = 0.000) for 4673 atoms. Found 29 (30 requested) and removed 31 (15 requested) atoms. Cycle 9: After refmac, R = 0.2394 (Rfree = 0.000) for 4649 atoms. Found 28 (29 requested) and removed 27 (14 requested) atoms. Cycle 10: After refmac, R = 0.2383 (Rfree = 0.000) for 4639 atoms. Found 26 (29 requested) and removed 26 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 4881 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4902 seeds are put forward Round 1: 319 peptides, 59 chains. Longest chain 13 peptides. Score 0.350 Round 2: 340 peptides, 54 chains. Longest chain 18 peptides. Score 0.433 Round 3: 347 peptides, 51 chains. Longest chain 18 peptides. Score 0.470 Round 4: 374 peptides, 55 chains. Longest chain 18 peptides. Score 0.487 Round 5: 347 peptides, 49 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 4 Chains 58, Residues 319, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10311 restraints for refining 4801 atoms. 9006 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2508 (Rfree = 0.000) for 4801 atoms. Found 23 (30 requested) and removed 36 (15 requested) atoms. Cycle 12: After refmac, R = 0.2430 (Rfree = 0.000) for 4749 atoms. Found 25 (30 requested) and removed 38 (15 requested) atoms. Cycle 13: After refmac, R = 0.2314 (Rfree = 0.000) for 4707 atoms. Found 18 (30 requested) and removed 33 (15 requested) atoms. Cycle 14: After refmac, R = 0.2340 (Rfree = 0.000) for 4684 atoms. Found 20 (30 requested) and removed 26 (15 requested) atoms. Cycle 15: After refmac, R = 0.2413 (Rfree = 0.000) for 4666 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 4836 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 4854 seeds are put forward Round 1: 319 peptides, 57 chains. Longest chain 19 peptides. Score 0.368 Round 2: 326 peptides, 53 chains. Longest chain 13 peptides. Score 0.415 Round 3: 350 peptides, 53 chains. Longest chain 17 peptides. Score 0.460 Round 4: 359 peptides, 54 chains. Longest chain 18 peptides. Score 0.468 Round 5: 371 peptides, 55 chains. Longest chain 20 peptides. Score 0.481 Taking the results from Round 5 Chains 57, Residues 316, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10454 restraints for refining 4801 atoms. 9162 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2692 (Rfree = 0.000) for 4801 atoms. Found 30 (30 requested) and removed 55 (15 requested) atoms. Cycle 17: After refmac, R = 0.2497 (Rfree = 0.000) for 4738 atoms. Found 28 (30 requested) and removed 30 (15 requested) atoms. Cycle 18: After refmac, R = 0.2391 (Rfree = 0.000) for 4724 atoms. Found 27 (30 requested) and removed 33 (15 requested) atoms. Cycle 19: After refmac, R = 0.2284 (Rfree = 0.000) for 4708 atoms. Found 21 (30 requested) and removed 26 (15 requested) atoms. Cycle 20: After refmac, R = 0.2213 (Rfree = 0.000) for 4696 atoms. Found 20 (30 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 4835 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 4853 seeds are put forward Round 1: 318 peptides, 61 chains. Longest chain 15 peptides. Score 0.331 Round 2: 361 peptides, 59 chains. Longest chain 15 peptides. Score 0.432 Round 3: 383 peptides, 60 chains. Longest chain 14 peptides. Score 0.464 Round 4: 374 peptides, 53 chains. Longest chain 20 peptides. Score 0.502 Round 5: 375 peptides, 52 chains. Longest chain 20 peptides. Score 0.511 Taking the results from Round 5 Chains 54, Residues 323, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10442 restraints for refining 4800 atoms. 9139 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2610 (Rfree = 0.000) for 4800 atoms. Found 16 (30 requested) and removed 48 (15 requested) atoms. Cycle 22: After refmac, R = 0.2421 (Rfree = 0.000) for 4743 atoms. Found 9 (30 requested) and removed 26 (15 requested) atoms. Cycle 23: After refmac, R = 0.2306 (Rfree = 0.000) for 4715 atoms. Found 11 (30 requested) and removed 29 (15 requested) atoms. Cycle 24: After refmac, R = 0.2273 (Rfree = 0.000) for 4688 atoms. Found 14 (30 requested) and removed 19 (15 requested) atoms. Cycle 25: After refmac, R = 0.2196 (Rfree = 0.000) for 4672 atoms. Found 12 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 4784 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4802 seeds are put forward Round 1: 307 peptides, 52 chains. Longest chain 15 peptides. Score 0.387 Round 2: 349 peptides, 58 chains. Longest chain 17 peptides. Score 0.417 Round 3: 353 peptides, 51 chains. Longest chain 19 peptides. Score 0.481 Round 4: 355 peptides, 51 chains. Longest chain 21 peptides. Score 0.484 Round 5: 358 peptides, 52 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 4 Chains 51, Residues 304, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10746 restraints for refining 4801 atoms. 9557 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2548 (Rfree = 0.000) for 4801 atoms. Found 28 (30 requested) and removed 23 (15 requested) atoms. Cycle 27: After refmac, R = 0.2337 (Rfree = 0.000) for 4777 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2232 (Rfree = 0.000) for 4782 atoms. Found 21 (30 requested) and removed 24 (15 requested) atoms. Cycle 29: After refmac, R = 0.2217 (Rfree = 0.000) for 4775 atoms. Found 21 (30 requested) and removed 28 (15 requested) atoms. Cycle 30: After refmac, R = 0.2133 (Rfree = 0.000) for 4762 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 4953 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4982 seeds are put forward Round 1: 290 peptides, 53 chains. Longest chain 11 peptides. Score 0.344 Round 2: 337 peptides, 51 chains. Longest chain 18 peptides. Score 0.452 Round 3: 341 peptides, 52 chains. Longest chain 14 peptides. Score 0.451 Round 4: 345 peptides, 50 chains. Longest chain 14 peptides. Score 0.475 Round 5: 361 peptides, 54 chains. Longest chain 16 peptides. Score 0.471 Taking the results from Round 4 Chains 50, Residues 295, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10712 restraints for refining 4801 atoms. 9563 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2475 (Rfree = 0.000) for 4801 atoms. Found 27 (30 requested) and removed 26 (15 requested) atoms. Cycle 32: After refmac, R = 0.2324 (Rfree = 0.000) for 4768 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 33: After refmac, R = 0.2259 (Rfree = 0.000) for 4749 atoms. Found 18 (30 requested) and removed 27 (15 requested) atoms. Cycle 34: After refmac, R = 0.2193 (Rfree = 0.000) for 4731 atoms. Found 29 (30 requested) and removed 24 (15 requested) atoms. Cycle 35: After refmac, R = 0.2161 (Rfree = 0.000) for 4730 atoms. Found 27 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 4892 seeds are put forward NCS extension: 9 residues added (4 deleted due to clashes), 4901 seeds are put forward Round 1: 306 peptides, 57 chains. Longest chain 11 peptides. Score 0.341 Round 2: 318 peptides, 56 chains. Longest chain 14 peptides. Score 0.374 Round 3: 326 peptides, 52 chains. Longest chain 13 peptides. Score 0.423 Round 4: 354 peptides, 54 chains. Longest chain 14 peptides. Score 0.459 Round 5: 339 peptides, 53 chains. Longest chain 15 peptides. Score 0.440 Taking the results from Round 4 Chains 55, Residues 300, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10649 restraints for refining 4801 atoms. 9456 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2536 (Rfree = 0.000) for 4801 atoms. Found 25 (30 requested) and removed 22 (15 requested) atoms. Cycle 37: After refmac, R = 0.2369 (Rfree = 0.000) for 4790 atoms. Found 26 (30 requested) and removed 19 (15 requested) atoms. Cycle 38: After refmac, R = 0.2320 (Rfree = 0.000) for 4787 atoms. Found 26 (30 requested) and removed 29 (15 requested) atoms. Cycle 39: After refmac, R = 0.2214 (Rfree = 0.000) for 4777 atoms. Found 23 (30 requested) and removed 21 (15 requested) atoms. Cycle 40: After refmac, R = 0.1967 (Rfree = 0.000) for 4764 atoms. Found 5 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 4901 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4922 seeds are put forward Round 1: 289 peptides, 59 chains. Longest chain 11 peptides. Score 0.288 Round 2: 330 peptides, 53 chains. Longest chain 21 peptides. Score 0.423 Round 3: 334 peptides, 53 chains. Longest chain 16 peptides. Score 0.430 Round 4: 327 peptides, 54 chains. Longest chain 21 peptides. Score 0.409 Round 5: 326 peptides, 52 chains. Longest chain 14 peptides. Score 0.423 Taking the results from Round 3 Chains 53, Residues 281, Estimated correctness of the model 0.0 % 7 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10644 restraints for refining 4800 atoms. 9508 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2446 (Rfree = 0.000) for 4800 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 42: After refmac, R = 0.2360 (Rfree = 0.000) for 4785 atoms. Found 27 (30 requested) and removed 29 (15 requested) atoms. Cycle 43: After refmac, R = 0.2346 (Rfree = 0.000) for 4770 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 44: After refmac, R = 0.2327 (Rfree = 0.000) for 4764 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 45: After refmac, R = 0.2281 (Rfree = 0.000) for 4761 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 4925 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4949 seeds are put forward Round 1: 225 peptides, 49 chains. Longest chain 9 peptides. Score 0.238 Round 2: 267 peptides, 48 chains. Longest chain 12 peptides. Score 0.341 Round 3: 286 peptides, 47 chains. Longest chain 20 peptides. Score 0.388 Round 4: 290 peptides, 48 chains. Longest chain 16 peptides. Score 0.388 Round 5: 296 peptides, 48 chains. Longest chain 17 peptides. Score 0.400 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 248, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input Building loops using Loopy2018 48 chains (248 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10268 reflections ( 99.54 % complete ) and 10895 restraints for refining 4801 atoms. 9890 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2402 (Rfree = 0.000) for 4801 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2381 (Rfree = 0.000) for 4755 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2462 (Rfree = 0.000) for 4724 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2335 (Rfree = 0.000) for 4701 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:34:51 GMT 2018 Job finished. TimeTaking 71.82 Used memory is bytes: 11197424