null Mon 24 Dec 00:58:59 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 2avn-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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/2avn-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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 00:59:04 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/2avn-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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 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-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.8-parrot-mrncs.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 4660 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3625 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3162 (Rfree = 0.000) for 4660 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 4769 seeds are put forward NCS extension: 0 residues added, 4769 seeds are put forward Round 1: 313 peptides, 45 chains. Longest chain 13 peptides. Score 0.428 Round 2: 351 peptides, 36 chains. Longest chain 26 peptides. Score 0.550 Round 3: 358 peptides, 32 chains. Longest chain 25 peptides. Score 0.586 Round 4: 357 peptides, 33 chains. Longest chain 44 peptides. Score 0.578 Round 5: 362 peptides, 32 chains. Longest chain 43 peptides. Score 0.591 Taking the results from Round 5 Chains 35, Residues 330, Estimated correctness of the model 0.0 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7558 restraints for refining 3826 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2920 (Rfree = 0.000) for 3826 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 2: After refmac, R = 0.2772 (Rfree = 0.000) for 3769 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 3: After refmac, R = 0.2660 (Rfree = 0.000) for 3742 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 4: After refmac, R = 0.2693 (Rfree = 0.000) for 3724 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 5: After refmac, R = 0.2712 (Rfree = 0.000) for 3717 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 2.71 Search for helices and strands: 0 residues in 0 chains, 3867 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 3899 seeds are put forward Round 1: 346 peptides, 36 chains. Longest chain 22 peptides. Score 0.543 Round 2: 361 peptides, 28 chains. Longest chain 45 peptides. Score 0.615 Round 3: 359 peptides, 32 chains. Longest chain 37 peptides. Score 0.587 Round 4: 357 peptides, 34 chains. Longest chain 29 peptides. Score 0.572 Round 5: 352 peptides, 30 chains. Longest chain 35 peptides. Score 0.591 Taking the results from Round 2 Chains 31, Residues 333, Estimated correctness of the model 5.7 % 3 chains (103 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 6693 restraints for refining 3822 atoms. 4876 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2863 (Rfree = 0.000) for 3822 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 7: After refmac, R = 0.2693 (Rfree = 0.000) for 3800 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 8: After refmac, R = 0.2698 (Rfree = 0.000) for 3797 atoms. Found 15 (20 requested) and removed 19 (10 requested) atoms. Cycle 9: After refmac, R = 0.2606 (Rfree = 0.000) for 3790 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 10: After refmac, R = 0.2644 (Rfree = 0.000) for 3781 atoms. Found 11 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 2.72 Search for helices and strands: 0 residues in 0 chains, 3939 seeds are put forward NCS extension: 58 residues added (13 deleted due to clashes), 3997 seeds are put forward Round 1: 332 peptides, 35 chains. Longest chain 22 peptides. Score 0.530 Round 2: 351 peptides, 35 chains. Longest chain 28 peptides. Score 0.557 Round 3: 353 peptides, 31 chains. Longest chain 39 peptides. Score 0.586 Round 4: 347 peptides, 34 chains. Longest chain 27 peptides. Score 0.558 Round 5: 360 peptides, 31 chains. Longest chain 35 peptides. Score 0.595 Taking the results from Round 5 Chains 34, Residues 329, Estimated correctness of the model 0.0 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8223 restraints for refining 3913 atoms. 6760 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2864 (Rfree = 0.000) for 3913 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 12: After refmac, R = 0.2664 (Rfree = 0.000) for 3880 atoms. Found 17 (21 requested) and removed 13 (10 requested) atoms. Cycle 13: After refmac, R = 0.2588 (Rfree = 0.000) for 3865 atoms. Found 14 (21 requested) and removed 11 (10 requested) atoms. Cycle 14: After refmac, R = 0.2576 (Rfree = 0.000) for 3850 atoms. Found 18 (21 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2425 (Rfree = 0.000) for 3846 atoms. Found 16 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 2.71 Search for helices and strands: 0 residues in 0 chains, 4015 seeds are put forward NCS extension: 57 residues added (0 deleted due to clashes), 4072 seeds are put forward Round 1: 349 peptides, 47 chains. Longest chain 17 peptides. Score 0.471 Round 2: 374 peptides, 37 chains. Longest chain 31 peptides. Score 0.575 Round 3: 351 peptides, 32 chains. Longest chain 27 peptides. Score 0.577 Round 4: 354 peptides, 35 chains. Longest chain 26 peptides. Score 0.561 Round 5: 349 peptides, 31 chains. Longest chain 24 peptides. Score 0.580 Taking the results from Round 5 Chains 32, Residues 318, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8128 restraints for refining 3816 atoms. 6833 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2720 (Rfree = 0.000) for 3816 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 17: After refmac, R = 0.2529 (Rfree = 0.000) for 3799 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2332 (Rfree = 0.000) for 3795 atoms. Found 18 (20 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2223 (Rfree = 0.000) for 3789 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 3773 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 3938 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3956 seeds are put forward Round 1: 337 peptides, 43 chains. Longest chain 21 peptides. Score 0.481 Round 2: 352 peptides, 33 chains. Longest chain 35 peptides. Score 0.571 Round 3: 362 peptides, 37 chains. Longest chain 29 peptides. Score 0.559 Round 4: 348 peptides, 35 chains. Longest chain 29 peptides. Score 0.553 Round 5: 366 peptides, 37 chains. Longest chain 27 peptides. Score 0.564 Taking the results from Round 2 Chains 33, Residues 319, Estimated correctness of the model 0.0 % 2 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7556 restraints for refining 3794 atoms. 6054 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2641 (Rfree = 0.000) for 3794 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.2501 (Rfree = 0.000) for 3770 atoms. Found 19 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.2365 (Rfree = 0.000) for 3768 atoms. Found 8 (20 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.2318 (Rfree = 0.000) for 3757 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.2285 (Rfree = 0.000) for 3751 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3877 seeds are put forward NCS extension: 46 residues added (2 deleted due to clashes), 3923 seeds are put forward Round 1: 333 peptides, 43 chains. Longest chain 20 peptides. Score 0.475 Round 2: 354 peptides, 40 chains. Longest chain 29 peptides. Score 0.527 Round 3: 360 peptides, 37 chains. Longest chain 31 peptides. Score 0.556 Round 4: 351 peptides, 35 chains. Longest chain 28 peptides. Score 0.557 Round 5: 371 peptides, 35 chains. Longest chain 38 peptides. Score 0.584 Taking the results from Round 5 Chains 40, Residues 336, Estimated correctness of the model 0.0 % 5 chains (77 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7678 restraints for refining 3971 atoms. 6009 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2931 (Rfree = 0.000) for 3971 atoms. Found 21 (21 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.2728 (Rfree = 0.000) for 3954 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.2668 (Rfree = 0.000) for 3956 atoms. Found 16 (21 requested) and removed 14 (10 requested) atoms. Cycle 29: After refmac, R = 0.2652 (Rfree = 0.000) for 3953 atoms. Found 15 (21 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.2530 (Rfree = 0.000) for 3948 atoms. Found 10 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 2.72 Search for helices and strands: 0 residues in 0 chains, 4101 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 4129 seeds are put forward Round 1: 334 peptides, 43 chains. Longest chain 31 peptides. Score 0.476 Round 2: 347 peptides, 36 chains. Longest chain 32 peptides. Score 0.544 Round 3: 328 peptides, 34 chains. Longest chain 30 peptides. Score 0.531 Round 4: 345 peptides, 32 chains. Longest chain 30 peptides. Score 0.569 Round 5: 335 peptides, 31 chains. Longest chain 30 peptides. Score 0.561 Taking the results from Round 4 Chains 32, Residues 313, Estimated correctness of the model 0.0 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8427 restraints for refining 3936 atoms. 7064 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2928 (Rfree = 0.000) for 3936 atoms. Found 21 (21 requested) and removed 61 (10 requested) atoms. Cycle 32: After refmac, R = 0.2734 (Rfree = 0.000) for 3876 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2620 (Rfree = 0.000) for 3871 atoms. Found 16 (21 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2571 (Rfree = 0.000) for 3869 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. Cycle 35: After refmac, R = 0.2511 (Rfree = 0.000) for 3855 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 2.69 Search for helices and strands: 0 residues in 0 chains, 3991 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 4028 seeds are put forward Round 1: 319 peptides, 43 chains. Longest chain 23 peptides. Score 0.453 Round 2: 345 peptides, 39 chains. Longest chain 24 peptides. Score 0.521 Round 3: 343 peptides, 38 chains. Longest chain 28 peptides. Score 0.525 Round 4: 339 peptides, 39 chains. Longest chain 24 peptides. Score 0.512 Round 5: 347 peptides, 39 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 3 Chains 40, Residues 305, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8187 restraints for refining 3761 atoms. 6964 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2774 (Rfree = 0.000) for 3761 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 37: After refmac, R = 0.2607 (Rfree = 0.000) for 3738 atoms. Found 16 (20 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2523 (Rfree = 0.000) for 3727 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2488 (Rfree = 0.000) for 3721 atoms. Found 13 (20 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.2476 (Rfree = 0.000) for 3713 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 3862 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 3899 seeds are put forward Round 1: 316 peptides, 47 chains. Longest chain 17 peptides. Score 0.418 Round 2: 332 peptides, 39 chains. Longest chain 18 peptides. Score 0.502 Round 3: 330 peptides, 41 chains. Longest chain 20 peptides. Score 0.484 Round 4: 337 peptides, 35 chains. Longest chain 23 peptides. Score 0.537 Round 5: 344 peptides, 33 chains. Longest chain 33 peptides. Score 0.560 Taking the results from Round 5 Chains 35, Residues 311, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8232 restraints for refining 3782 atoms. 6977 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2865 (Rfree = 0.000) for 3782 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 42: After refmac, R = 0.2639 (Rfree = 0.000) for 3767 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.2596 (Rfree = 0.000) for 3762 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 44: After refmac, R = 0.2488 (Rfree = 0.000) for 3746 atoms. Found 12 (20 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.2480 (Rfree = 0.000) for 3732 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 2.68 Search for helices and strands: 0 residues in 0 chains, 3879 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3903 seeds are put forward Round 1: 308 peptides, 45 chains. Longest chain 24 peptides. Score 0.419 Round 2: 341 peptides, 36 chains. Longest chain 40 peptides. Score 0.536 Round 3: 349 peptides, 34 chains. Longest chain 23 peptides. Score 0.561 Round 4: 331 peptides, 38 chains. Longest chain 18 peptides. Score 0.507 Round 5: 354 peptides, 38 chains. Longest chain 23 peptides. Score 0.541 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 315, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10328 reflections ( 99.56 % complete ) and 8159 restraints for refining 3762 atoms. 6897 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2851 (Rfree = 0.000) for 3762 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2705 (Rfree = 0.000) for 3726 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2725 (Rfree = 0.000) for 3695 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2572 (Rfree = 0.000) for 3671 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:02:44 GMT 2018 Job finished. TimeTaking 63.75 Used memory is bytes: 18996832