Tue 25 Dec 19:27:57 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 2avn-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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/2avn-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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/2avn-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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 627 and 0 Target number of residues in the AU: 627 Target solvent content: 0.6517 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 520 Adjusted target solvent content: 0.71 Input MTZ file: 2avn-3.8-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.20 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: 115.845 3.800 Wilson plot Bfac: 79.29 10328 reflections ( 99.56 % complete ) and 0 restraints for refining 4628 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3611 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3317 (Rfree = 0.000) for 4628 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 2.67 Search for helices and strands: 0 residues in 0 chains, 4748 seeds are put forward NCS extension: 0 residues added, 4748 seeds are put forward Round 1: 311 peptides, 42 chains. Longest chain 20 peptides. Score 0.447 Round 2: 380 peptides, 38 chains. Longest chain 24 peptides. Score 0.576 Round 3: 381 peptides, 37 chains. Longest chain 30 peptides. Score 0.584 Round 4: 363 peptides, 30 chains. Longest chain 38 peptides. Score 0.605 Round 5: 364 peptides, 34 chains. Longest chain 30 peptides. Score 0.581 Taking the results from Round 4 Chains 35, Residues 333, Estimated correctness of the model 1.2 % 3 chains (65 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10328 reflections ( 99.56 % complete ) and 7897 restraints for refining 4011 atoms. 6322 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2752 (Rfree = 0.000) for 4011 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 2: After refmac, R = 0.2597 (Rfree = 0.000) for 3950 atoms. Found 20 (22 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2497 (Rfree = 0.000) for 3930 atoms. Found 9 (21 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2429 (Rfree = 0.000) for 3907 atoms. Found 7 (21 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2383 (Rfree = 0.000) for 3892 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 4041 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 4078 seeds are put forward Round 1: 364 peptides, 37 chains. Longest chain 40 peptides. Score 0.561 Round 2: 382 peptides, 39 chains. Longest chain 28 peptides. Score 0.573 Round 3: 376 peptides, 34 chains. Longest chain 42 peptides. Score 0.597 Round 4: 362 peptides, 33 chains. Longest chain 29 peptides. Score 0.585 Round 5: 367 peptides, 29 chains. Longest chain 42 peptides. Score 0.616 Taking the results from Round 5 Chains 31, Residues 338, Estimated correctness of the model 6.2 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10328 reflections ( 99.56 % complete ) and 8068 restraints for refining 3914 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2761 (Rfree = 0.000) for 3914 atoms. Found 21 (21 requested) and removed 76 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2613 (Rfree = 0.000) for 3818 atoms. Found 18 (21 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.2563 (Rfree = 0.000) for 3798 atoms. Found 19 (21 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2439 (Rfree = 0.000) for 3795 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2453 (Rfree = 0.000) for 3768 atoms. Found 12 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 2.66 Search for helices and strands: 0 residues in 0 chains, 3916 seeds are put forward NCS extension: 46 residues added (4 deleted due to clashes), 3962 seeds are put forward Round 1: 345 peptides, 42 chains. Longest chain 27 peptides. Score 0.500 Round 2: 363 peptides, 37 chains. Longest chain 27 peptides. Score 0.560 Round 3: 374 peptides, 38 chains. Longest chain 24 peptides. Score 0.568 Round 4: 377 peptides, 35 chains. Longest chain 32 peptides. Score 0.592 Round 5: 366 peptides, 33 chains. Longest chain 38 peptides. Score 0.590 Taking the results from Round 4 Chains 36, Residues 342, Estimated correctness of the model 0.0 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7785 restraints for refining 3875 atoms. 6175 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2779 (Rfree = 0.000) for 3875 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 12: After refmac, R = 0.2631 (Rfree = 0.000) for 3822 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2531 (Rfree = 0.000) for 3791 atoms. Found 16 (21 requested) and removed 19 (10 requested) atoms. Cycle 14: After refmac, R = 0.2426 (Rfree = 0.000) for 3777 atoms. Found 12 (20 requested) and removed 14 (10 requested) atoms. Cycle 15: After refmac, R = 0.2369 (Rfree = 0.000) for 3760 atoms. Found 12 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 3935 seeds are put forward Round 1: 352 peptides, 42 chains. Longest chain 24 peptides. Score 0.511 Round 2: 373 peptides, 33 chains. Longest chain 40 peptides. Score 0.599 Round 3: 376 peptides, 31 chains. Longest chain 37 peptides. Score 0.615 Round 4: 371 peptides, 32 chains. Longest chain 39 peptides. Score 0.603 Round 5: 365 peptides, 37 chains. Longest chain 31 peptides. Score 0.563 Taking the results from Round 3 Chains 33, Residues 345, Estimated correctness of the model 5.7 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7180 restraints for refining 3760 atoms. 5574 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2853 (Rfree = 0.000) for 3760 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 17: After refmac, R = 0.2633 (Rfree = 0.000) for 3724 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2519 (Rfree = 0.000) for 3708 atoms. Found 18 (20 requested) and removed 12 (10 requested) atoms. Cycle 19: After refmac, R = 0.2408 (Rfree = 0.000) for 3707 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2394 (Rfree = 0.000) for 3689 atoms. Found 17 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 3839 seeds are put forward NCS extension: 48 residues added (12 deleted due to clashes), 3887 seeds are put forward Round 1: 342 peptides, 39 chains. Longest chain 33 peptides. Score 0.517 Round 2: 361 peptides, 34 chains. Longest chain 37 peptides. Score 0.577 Round 3: 366 peptides, 33 chains. Longest chain 27 peptides. Score 0.590 Round 4: 360 peptides, 35 chains. Longest chain 31 peptides. Score 0.569 Round 5: 361 peptides, 30 chains. Longest chain 32 peptides. Score 0.603 Taking the results from Round 5 Chains 31, Residues 331, Estimated correctness of the model 0.3 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7950 restraints for refining 3831 atoms. 6532 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2758 (Rfree = 0.000) for 3831 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.2599 (Rfree = 0.000) for 3800 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2498 (Rfree = 0.000) for 3779 atoms. Found 17 (20 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2432 (Rfree = 0.000) for 3763 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2381 (Rfree = 0.000) for 3743 atoms. Found 15 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3919 seeds are put forward NCS extension: 0 residues added, 3919 seeds are put forward Round 1: 335 peptides, 41 chains. Longest chain 21 peptides. Score 0.492 Round 2: 370 peptides, 33 chains. Longest chain 35 peptides. Score 0.595 Round 3: 357 peptides, 36 chains. Longest chain 27 peptides. Score 0.558 Round 4: 356 peptides, 35 chains. Longest chain 32 peptides. Score 0.564 Round 5: 349 peptides, 35 chains. Longest chain 28 peptides. Score 0.554 Taking the results from Round 2 Chains 37, Residues 337, Estimated correctness of the model 0.0 % 3 chains (69 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7275 restraints for refining 3761 atoms. 5652 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2668 (Rfree = 0.000) for 3761 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2535 (Rfree = 0.000) for 3732 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.2455 (Rfree = 0.000) for 3724 atoms. Found 17 (20 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.2413 (Rfree = 0.000) for 3719 atoms. Found 16 (20 requested) and removed 15 (10 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2383 (Rfree = 0.000) for 3714 atoms. Found 15 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 2.67 Search for helices and strands: 0 residues in 0 chains, 3857 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3879 seeds are put forward Round 1: 340 peptides, 42 chains. Longest chain 30 peptides. Score 0.493 Round 2: 365 peptides, 36 chains. Longest chain 35 peptides. Score 0.569 Round 3: 364 peptides, 36 chains. Longest chain 34 peptides. Score 0.568 Round 4: 378 peptides, 36 chains. Longest chain 31 peptides. Score 0.587 Round 5: 364 peptides, 36 chains. Longest chain 33 peptides. Score 0.568 Taking the results from Round 4 Chains 36, Residues 342, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7576 restraints for refining 3760 atoms. 6061 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2736 (Rfree = 0.000) for 3760 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.2620 (Rfree = 0.000) for 3741 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2482 (Rfree = 0.000) for 3738 atoms. Found 15 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.2424 (Rfree = 0.000) for 3740 atoms. Found 19 (20 requested) and removed 13 (10 requested) atoms. Cycle 35: After refmac, R = 0.2392 (Rfree = 0.000) for 3735 atoms. Found 19 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3915 seeds are put forward Round 1: 334 peptides, 43 chains. Longest chain 25 peptides. Score 0.476 Round 2: 359 peptides, 36 chains. Longest chain 38 peptides. Score 0.561 Round 3: 351 peptides, 36 chains. Longest chain 36 peptides. Score 0.550 Round 4: 360 peptides, 37 chains. Longest chain 26 peptides. Score 0.556 Round 5: 362 peptides, 38 chains. Longest chain 24 peptides. Score 0.552 Taking the results from Round 2 Chains 36, Residues 323, Estimated correctness of the model 0.0 % 1 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7670 restraints for refining 3761 atoms. 6224 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2700 (Rfree = 0.000) for 3761 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 37: After refmac, R = 0.2570 (Rfree = 0.000) for 3732 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 38: After refmac, R = 0.2545 (Rfree = 0.000) for 3719 atoms. Found 18 (20 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.2491 (Rfree = 0.000) for 3717 atoms. Found 10 (20 requested) and removed 18 (10 requested) atoms. Cycle 40: After refmac, R = 0.2466 (Rfree = 0.000) for 3697 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 3833 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 3874 seeds are put forward Round 1: 330 peptides, 44 chains. Longest chain 22 peptides. Score 0.463 Round 2: 337 peptides, 41 chains. Longest chain 22 peptides. Score 0.495 Round 3: 341 peptides, 40 chains. Longest chain 23 peptides. Score 0.508 Round 4: 354 peptides, 40 chains. Longest chain 22 peptides. Score 0.527 Round 5: 338 peptides, 41 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 4 Chains 41, Residues 314, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7747 restraints for refining 3762 atoms. 6355 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2756 (Rfree = 0.000) for 3762 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 42: After refmac, R = 0.2662 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 43: After refmac, R = 0.2589 (Rfree = 0.000) for 3724 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2586 (Rfree = 0.000) for 3707 atoms. Found 16 (20 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.2494 (Rfree = 0.000) for 3702 atoms. Found 8 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3857 seeds are put forward NCS extension: 29 residues added (6 deleted due to clashes), 3886 seeds are put forward Round 1: 321 peptides, 48 chains. Longest chain 14 peptides. Score 0.419 Round 2: 333 peptides, 41 chains. Longest chain 22 peptides. Score 0.489 Round 3: 314 peptides, 39 chains. Longest chain 27 peptides. Score 0.474 Round 4: 330 peptides, 34 chains. Longest chain 29 peptides. Score 0.534 Round 5: 327 peptides, 34 chains. Longest chain 26 peptides. Score 0.530 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 296, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 36 chains (296 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10328 reflections ( 99.56 % complete ) and 8123 restraints for refining 3761 atoms. 6873 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2698 (Rfree = 0.000) for 3761 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2562 (Rfree = 0.000) for 3723 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2497 (Rfree = 0.000) for 3693 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2438 (Rfree = 0.000) for 3678 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 81.18