Mon 24 Dec 01:05:19 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 2ajr-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.4-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/2ajr-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.4-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 01:05:24 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/2ajr-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.4-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 575 and 0 Target number of residues in the AU: 575 Target solvent content: 0.6276 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-3.4-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.65 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 3.400 Wilson plot Bfac: 65.12 12126 reflections ( 99.61 % complete ) and 0 restraints for refining 5860 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3579 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3519 (Rfree = 0.000) for 5860 atoms. Found 44 (44 requested) and removed 51 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 5967 seeds are put forward NCS extension: 0 residues added, 5967 seeds are put forward Round 1: 234 peptides, 45 chains. Longest chain 12 peptides. Score 0.297 Round 2: 328 peptides, 56 chains. Longest chain 14 peptides. Score 0.394 Round 3: 351 peptides, 53 chains. Longest chain 17 peptides. Score 0.462 Round 4: 374 peptides, 54 chains. Longest chain 16 peptides. Score 0.494 Round 5: 347 peptides, 43 chains. Longest chain 16 peptides. Score 0.532 Taking the results from Round 5 Chains 46, Residues 304, Estimated correctness of the model 4.9 % 8 chains (61 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10514 restraints for refining 4815 atoms. 9179 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2991 (Rfree = 0.000) for 4815 atoms. Found 36 (36 requested) and removed 42 (18 requested) atoms. Cycle 2: After refmac, R = 0.2743 (Rfree = 0.000) for 4755 atoms. Found 26 (36 requested) and removed 29 (18 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2677 (Rfree = 0.000) for 4724 atoms. Found 25 (35 requested) and removed 34 (17 requested) atoms. Cycle 4: After refmac, R = 0.2548 (Rfree = 0.000) for 4699 atoms. Found 16 (35 requested) and removed 28 (17 requested) atoms. Cycle 5: After refmac, R = 0.2570 (Rfree = 0.000) for 4679 atoms. Found 28 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 4882 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4899 seeds are put forward Round 1: 334 peptides, 60 chains. Longest chain 17 peptides. Score 0.372 Round 2: 368 peptides, 52 chains. Longest chain 17 peptides. Score 0.499 Round 3: 389 peptides, 57 chains. Longest chain 17 peptides. Score 0.497 Round 4: 400 peptides, 53 chains. Longest chain 18 peptides. Score 0.545 Round 5: 393 peptides, 52 chains. Longest chain 22 peptides. Score 0.541 Taking the results from Round 4 Chains 53, Residues 347, Estimated correctness of the model 9.7 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10589 restraints for refining 4813 atoms. 9231 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2600 (Rfree = 0.000) for 4813 atoms. Found 30 (36 requested) and removed 38 (18 requested) atoms. Cycle 7: After refmac, R = 0.2493 (Rfree = 0.000) for 4772 atoms. Found 20 (36 requested) and removed 25 (18 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 4752 atoms. Found 14 (35 requested) and removed 25 (17 requested) atoms. Cycle 9: After refmac, R = 0.2362 (Rfree = 0.000) for 4733 atoms. Found 16 (35 requested) and removed 29 (17 requested) atoms. Cycle 10: After refmac, R = 0.2352 (Rfree = 0.000) for 4710 atoms. Found 20 (35 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 4898 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4913 seeds are put forward Round 1: 351 peptides, 59 chains. Longest chain 14 peptides. Score 0.413 Round 2: 358 peptides, 52 chains. Longest chain 22 peptides. Score 0.482 Round 3: 363 peptides, 49 chains. Longest chain 24 peptides. Score 0.513 Round 4: 361 peptides, 51 chains. Longest chain 18 peptides. Score 0.495 Round 5: 365 peptides, 52 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 3 Chains 49, Residues 314, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10769 restraints for refining 4814 atoms. 9529 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2519 (Rfree = 0.000) for 4814 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. Cycle 12: After refmac, R = 0.2436 (Rfree = 0.000) for 4793 atoms. Found 29 (36 requested) and removed 25 (18 requested) atoms. Cycle 13: After refmac, R = 0.2366 (Rfree = 0.000) for 4778 atoms. Found 27 (36 requested) and removed 30 (18 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2225 (Rfree = 0.000) for 4762 atoms. Found 16 (36 requested) and removed 24 (18 requested) atoms. Cycle 15: After refmac, R = 0.2132 (Rfree = 0.000) for 4747 atoms. Found 18 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 4908 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 4940 seeds are put forward Round 1: 331 peptides, 59 chains. Longest chain 15 peptides. Score 0.374 Round 2: 340 peptides, 50 chains. Longest chain 19 peptides. Score 0.466 Round 3: 355 peptides, 48 chains. Longest chain 27 peptides. Score 0.508 Round 4: 359 peptides, 49 chains. Longest chain 20 peptides. Score 0.507 Round 5: 360 peptides, 46 chains. Longest chain 30 peptides. Score 0.531 Taking the results from Round 5 Chains 49, Residues 314, Estimated correctness of the model 4.6 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10452 restraints for refining 4814 atoms. 9123 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2542 (Rfree = 0.000) for 4814 atoms. Found 32 (36 requested) and removed 33 (18 requested) atoms. Cycle 17: After refmac, R = 0.2384 (Rfree = 0.000) for 4796 atoms. Found 17 (36 requested) and removed 24 (18 requested) atoms. Cycle 18: After refmac, R = 0.2295 (Rfree = 0.000) for 4777 atoms. Found 15 (36 requested) and removed 26 (18 requested) atoms. Cycle 19: After refmac, R = 0.2247 (Rfree = 0.000) for 4757 atoms. Found 6 (35 requested) and removed 21 (17 requested) atoms. Cycle 20: After refmac, R = 0.2203 (Rfree = 0.000) for 4737 atoms. Found 11 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.00 Search for helices and strands: 0 residues in 0 chains, 4875 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4895 seeds are put forward Round 1: 348 peptides, 58 chains. Longest chain 14 peptides. Score 0.416 Round 2: 364 peptides, 53 chains. Longest chain 16 peptides. Score 0.485 Round 3: 385 peptides, 53 chains. Longest chain 20 peptides. Score 0.520 Round 4: 374 peptides, 50 chains. Longest chain 16 peptides. Score 0.524 Round 5: 385 peptides, 47 chains. Longest chain 23 peptides. Score 0.564 Taking the results from Round 5 Chains 47, Residues 338, Estimated correctness of the model 16.5 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12126 reflections ( 99.61 % complete ) and 10338 restraints for refining 4815 atoms. 8938 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2620 (Rfree = 0.000) for 4815 atoms. Found 34 (36 requested) and removed 30 (18 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 4791 atoms. Found 24 (36 requested) and removed 26 (18 requested) atoms. Cycle 23: After refmac, R = 0.2319 (Rfree = 0.000) for 4771 atoms. Found 9 (36 requested) and removed 23 (18 requested) atoms. Cycle 24: After refmac, R = 0.2293 (Rfree = 0.000) for 4748 atoms. Found 15 (35 requested) and removed 24 (17 requested) atoms. Cycle 25: After refmac, R = 0.2251 (Rfree = 0.000) for 4727 atoms. Found 11 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 4860 seeds are put forward NCS extension: 42 residues added (3 deleted due to clashes), 4902 seeds are put forward Round 1: 345 peptides, 62 chains. Longest chain 12 peptides. Score 0.377 Round 2: 374 peptides, 56 chains. Longest chain 15 peptides. Score 0.479 Round 3: 361 peptides, 52 chains. Longest chain 20 peptides. Score 0.487 Round 4: 378 peptides, 52 chains. Longest chain 20 peptides. Score 0.516 Round 5: 379 peptides, 51 chains. Longest chain 21 peptides. Score 0.525 Taking the results from Round 5 Chains 52, Residues 328, Estimated correctness of the model 2.3 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10522 restraints for refining 4815 atoms. 9203 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2570 (Rfree = 0.000) for 4815 atoms. Found 32 (36 requested) and removed 26 (18 requested) atoms. Cycle 27: After refmac, R = 0.2454 (Rfree = 0.000) for 4803 atoms. Found 23 (36 requested) and removed 28 (18 requested) atoms. Cycle 28: After refmac, R = 0.2408 (Rfree = 0.000) for 4790 atoms. Found 26 (36 requested) and removed 23 (18 requested) atoms. Cycle 29: After refmac, R = 0.2360 (Rfree = 0.000) for 4786 atoms. Found 17 (36 requested) and removed 26 (18 requested) atoms. Cycle 30: After refmac, R = 0.2272 (Rfree = 0.000) for 4766 atoms. Found 15 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4913 seeds are put forward Round 1: 325 peptides, 58 chains. Longest chain 14 peptides. Score 0.371 Round 2: 361 peptides, 56 chains. Longest chain 21 peptides. Score 0.456 Round 3: 352 peptides, 53 chains. Longest chain 15 peptides. Score 0.463 Round 4: 351 peptides, 48 chains. Longest chain 17 peptides. Score 0.501 Round 5: 363 peptides, 52 chains. Longest chain 20 peptides. Score 0.491 Taking the results from Round 4 Chains 48, Residues 303, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10624 restraints for refining 4813 atoms. 9392 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2542 (Rfree = 0.000) for 4813 atoms. Found 36 (36 requested) and removed 37 (18 requested) atoms. Cycle 32: After refmac, R = 0.2407 (Rfree = 0.000) for 4790 atoms. Found 26 (36 requested) and removed 23 (18 requested) atoms. Cycle 33: After refmac, R = 0.2298 (Rfree = 0.000) for 4781 atoms. Found 23 (36 requested) and removed 22 (18 requested) atoms. Cycle 34: After refmac, R = 0.2208 (Rfree = 0.000) for 4773 atoms. Found 22 (36 requested) and removed 19 (18 requested) atoms. Cycle 35: After refmac, R = 0.2131 (Rfree = 0.000) for 4772 atoms. Found 13 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 4894 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4919 seeds are put forward Round 1: 298 peptides, 54 chains. Longest chain 13 peptides. Score 0.351 Round 2: 333 peptides, 48 chains. Longest chain 17 peptides. Score 0.469 Round 3: 332 peptides, 47 chains. Longest chain 15 peptides. Score 0.475 Round 4: 350 peptides, 48 chains. Longest chain 19 peptides. Score 0.499 Round 5: 353 peptides, 47 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 5 Chains 48, Residues 306, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10451 restraints for refining 4815 atoms. 9207 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2595 (Rfree = 0.000) for 4815 atoms. Found 30 (36 requested) and removed 33 (18 requested) atoms. Cycle 37: After refmac, R = 0.2465 (Rfree = 0.000) for 4801 atoms. Found 27 (36 requested) and removed 23 (18 requested) atoms. Cycle 38: After refmac, R = 0.2439 (Rfree = 0.000) for 4795 atoms. Found 23 (36 requested) and removed 23 (18 requested) atoms. Cycle 39: After refmac, R = 0.2410 (Rfree = 0.000) for 4790 atoms. Found 19 (36 requested) and removed 25 (18 requested) atoms. Cycle 40: After refmac, R = 0.2363 (Rfree = 0.000) for 4782 atoms. Found 14 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 4885 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 4914 seeds are put forward Round 1: 283 peptides, 52 chains. Longest chain 14 peptides. Score 0.338 Round 2: 327 peptides, 49 chains. Longest chain 14 peptides. Score 0.450 Round 3: 344 peptides, 50 chains. Longest chain 20 peptides. Score 0.473 Round 4: 337 peptides, 49 chains. Longest chain 18 peptides. Score 0.468 Round 5: 329 peptides, 45 chains. Longest chain 19 peptides. Score 0.486 Taking the results from Round 5 Chains 46, Residues 284, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10720 restraints for refining 4812 atoms. 9604 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2425 (Rfree = 0.000) for 4812 atoms. Found 26 (36 requested) and removed 22 (18 requested) atoms. Cycle 42: After refmac, R = 0.2412 (Rfree = 0.000) for 4806 atoms. Found 30 (36 requested) and removed 23 (18 requested) atoms. Cycle 43: After refmac, R = 0.2356 (Rfree = 0.000) for 4808 atoms. Found 22 (36 requested) and removed 23 (18 requested) atoms. Cycle 44: After refmac, R = 0.2379 (Rfree = 0.000) for 4802 atoms. Found 27 (36 requested) and removed 20 (18 requested) atoms. Cycle 45: After refmac, R = 0.2365 (Rfree = 0.000) for 4803 atoms. Found 23 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 4896 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4913 seeds are put forward Round 1: 296 peptides, 58 chains. Longest chain 12 peptides. Score 0.312 Round 2: 326 peptides, 56 chains. Longest chain 17 peptides. Score 0.390 Round 3: 351 peptides, 56 chains. Longest chain 17 peptides. Score 0.437 Round 4: 332 peptides, 53 chains. Longest chain 16 peptides. Score 0.427 Round 5: 339 peptides, 49 chains. Longest chain 18 peptides. Score 0.472 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 290, 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 2ajr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12126 reflections ( 99.61 % complete ) and 10725 restraints for refining 4813 atoms. 9614 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2525 (Rfree = 0.000) for 4813 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2428 (Rfree = 0.000) for 4777 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2426 (Rfree = 0.000) for 4748 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2362 (Rfree = 0.000) for 4729 atoms. TimeTaking 63.17