null Mon 24 Dec 00:50:38 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-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 00:50:43 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-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 638 and 0 Target number of residues in the AU: 638 Target solvent content: 0.6456 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 75.33 12083 reflections ( 99.62 % complete ) and 0 restraints for refining 4591 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3608 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3233 (Rfree = 0.000) for 4591 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.61 Search for helices and strands: 0 residues in 0 chains, 4707 seeds are put forward NCS extension: 0 residues added, 4707 seeds are put forward Round 1: 338 peptides, 48 chains. Longest chain 18 peptides. Score 0.446 Round 2: 364 peptides, 37 chains. Longest chain 22 peptides. Score 0.561 Round 3: 367 peptides, 41 chains. Longest chain 22 peptides. Score 0.539 Round 4: 386 peptides, 33 chains. Longest chain 27 peptides. Score 0.615 Round 5: 366 peptides, 29 chains. Longest chain 29 peptides. Score 0.615 Taking the results from Round 5 Chains 35, Residues 337, Estimated correctness of the model 20.4 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7952 restraints for refining 3889 atoms. 6489 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2952 (Rfree = 0.000) for 3889 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 2: After refmac, R = 0.2770 (Rfree = 0.000) for 3860 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 3: After refmac, R = 0.2595 (Rfree = 0.000) for 3837 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2534 (Rfree = 0.000) for 3819 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 5: After refmac, R = 0.2485 (Rfree = 0.000) for 3821 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.52 Search for helices and strands: 0 residues in 0 chains, 3978 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 4012 seeds are put forward Round 1: 368 peptides, 35 chains. Longest chain 23 peptides. Score 0.580 Round 2: 376 peptides, 33 chains. Longest chain 32 peptides. Score 0.603 Round 3: 375 peptides, 34 chains. Longest chain 34 peptides. Score 0.595 Round 4: 369 peptides, 36 chains. Longest chain 29 peptides. Score 0.575 Round 5: 357 peptides, 30 chains. Longest chain 37 peptides. Score 0.597 Taking the results from Round 2 Chains 38, Residues 343, Estimated correctness of the model 15.8 % 5 chains (90 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7163 restraints for refining 3857 atoms. 5411 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2802 (Rfree = 0.000) for 3857 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 7: After refmac, R = 0.2653 (Rfree = 0.000) for 3826 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2610 (Rfree = 0.000) for 3806 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2491 (Rfree = 0.000) for 3798 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. Cycle 10: After refmac, R = 0.2469 (Rfree = 0.000) for 3779 atoms. Found 7 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 3901 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3934 seeds are put forward Round 1: 355 peptides, 35 chains. Longest chain 25 peptides. Score 0.562 Round 2: 379 peptides, 33 chains. Longest chain 31 peptides. Score 0.607 Round 3: 389 peptides, 33 chains. Longest chain 43 peptides. Score 0.619 Round 4: 382 peptides, 36 chains. Longest chain 33 peptides. Score 0.592 Round 5: 375 peptides, 36 chains. Longest chain 33 peptides. Score 0.583 Taking the results from Round 3 Chains 40, Residues 356, Estimated correctness of the model 21.9 % 6 chains (115 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7008 restraints for refining 3908 atoms. 5111 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2760 (Rfree = 0.000) for 3908 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 12: After refmac, R = 0.2561 (Rfree = 0.000) for 3878 atoms. Found 19 (25 requested) and removed 15 (12 requested) atoms. Cycle 13: After refmac, R = 0.2477 (Rfree = 0.000) for 3864 atoms. Found 21 (24 requested) and removed 16 (12 requested) atoms. Cycle 14: After refmac, R = 0.2407 (Rfree = 0.000) for 3858 atoms. Found 10 (24 requested) and removed 16 (12 requested) atoms. Cycle 15: After refmac, R = 0.2357 (Rfree = 0.000) for 3844 atoms. Found 11 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3963 seeds are put forward NCS extension: 37 residues added (13 deleted due to clashes), 4000 seeds are put forward Round 1: 357 peptides, 39 chains. Longest chain 30 peptides. Score 0.538 Round 2: 375 peptides, 31 chains. Longest chain 40 peptides. Score 0.614 Round 3: 366 peptides, 33 chains. Longest chain 31 peptides. Score 0.590 Round 4: 357 peptides, 37 chains. Longest chain 32 peptides. Score 0.552 Round 5: 367 peptides, 31 chains. Longest chain 34 peptides. Score 0.604 Taking the results from Round 2 Chains 35, Residues 344, Estimated correctness of the model 20.0 % 5 chains (82 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7186 restraints for refining 3860 atoms. 5482 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2695 (Rfree = 0.000) for 3860 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 17: After refmac, R = 0.2598 (Rfree = 0.000) for 3826 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2541 (Rfree = 0.000) for 3814 atoms. Found 23 (24 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.2470 (Rfree = 0.000) for 3812 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 20: After refmac, R = 0.2333 (Rfree = 0.000) for 3805 atoms. Found 17 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3940 seeds are put forward NCS extension: 11 residues added (13 deleted due to clashes), 3951 seeds are put forward Round 1: 363 peptides, 36 chains. Longest chain 27 peptides. Score 0.567 Round 2: 367 peptides, 33 chains. Longest chain 46 peptides. Score 0.591 Round 3: 384 peptides, 30 chains. Longest chain 32 peptides. Score 0.631 Round 4: 366 peptides, 31 chains. Longest chain 28 peptides. Score 0.603 Round 5: 363 peptides, 33 chains. Longest chain 26 peptides. Score 0.586 Taking the results from Round 3 Chains 35, Residues 354, Estimated correctness of the model 26.4 % 5 chains (109 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7239 restraints for refining 3932 atoms. 5402 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2717 (Rfree = 0.000) for 3932 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 22: After refmac, R = 0.2590 (Rfree = 0.000) for 3907 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 23: After refmac, R = 0.2549 (Rfree = 0.000) for 3891 atoms. Found 9 (25 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2559 (Rfree = 0.000) for 3881 atoms. Found 9 (24 requested) and removed 15 (12 requested) atoms. Cycle 25: After refmac, R = 0.2510 (Rfree = 0.000) for 3865 atoms. Found 3 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 3995 seeds are put forward NCS extension: 28 residues added (10 deleted due to clashes), 4023 seeds are put forward Round 1: 364 peptides, 42 chains. Longest chain 23 peptides. Score 0.528 Round 2: 392 peptides, 31 chains. Longest chain 43 peptides. Score 0.635 Round 3: 391 peptides, 33 chains. Longest chain 28 peptides. Score 0.621 Round 4: 394 peptides, 38 chains. Longest chain 32 peptides. Score 0.595 Round 5: 376 peptides, 33 chains. Longest chain 38 peptides. Score 0.603 Taking the results from Round 2 Chains 33, Residues 361, Estimated correctness of the model 27.8 % 3 chains (90 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7243 restraints for refining 3877 atoms. 5435 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2646 (Rfree = 0.000) for 3877 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 27: After refmac, R = 0.2462 (Rfree = 0.000) for 3855 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.2380 (Rfree = 0.000) for 3844 atoms. Found 11 (24 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.2321 (Rfree = 0.000) for 3831 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2306 (Rfree = 0.000) for 3818 atoms. Found 12 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 2.62 Search for helices and strands: 0 residues in 0 chains, 3929 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 3953 seeds are put forward Round 1: 369 peptides, 41 chains. Longest chain 28 peptides. Score 0.542 Round 2: 396 peptides, 39 chains. Longest chain 33 peptides. Score 0.591 Round 3: 390 peptides, 36 chains. Longest chain 34 peptides. Score 0.602 Round 4: 375 peptides, 38 chains. Longest chain 22 peptides. Score 0.570 Round 5: 372 peptides, 33 chains. Longest chain 25 peptides. Score 0.598 Taking the results from Round 3 Chains 40, Residues 354, Estimated correctness of the model 15.4 % 4 chains (82 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7313 restraints for refining 3842 atoms. 5522 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2696 (Rfree = 0.000) for 3842 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 32: After refmac, R = 0.2610 (Rfree = 0.000) for 3801 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.2560 (Rfree = 0.000) for 3786 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.2485 (Rfree = 0.000) for 3779 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2389 (Rfree = 0.000) for 3777 atoms. Found 21 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 2.61 Search for helices and strands: 0 residues in 0 chains, 3902 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3938 seeds are put forward Round 1: 358 peptides, 41 chains. Longest chain 20 peptides. Score 0.526 Round 2: 392 peptides, 38 chains. Longest chain 32 peptides. Score 0.592 Round 3: 395 peptides, 36 chains. Longest chain 35 peptides. Score 0.608 Round 4: 368 peptides, 31 chains. Longest chain 42 peptides. Score 0.605 Round 5: 356 peptides, 33 chains. Longest chain 27 peptides. Score 0.577 Taking the results from Round 3 Chains 40, Residues 359, Estimated correctness of the model 17.8 % 9 chains (178 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 6677 restraints for refining 4039 atoms. 4464 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2763 (Rfree = 0.000) for 4039 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 37: After refmac, R = 0.2653 (Rfree = 0.000) for 3992 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.2557 (Rfree = 0.000) for 3984 atoms. Found 20 (25 requested) and removed 19 (12 requested) atoms. Cycle 39: After refmac, R = 0.2524 (Rfree = 0.000) for 3966 atoms. Found 12 (25 requested) and removed 21 (12 requested) atoms. Cycle 40: After refmac, R = 0.2525 (Rfree = 0.000) for 3950 atoms. Found 13 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 4081 seeds are put forward NCS extension: 29 residues added (16 deleted due to clashes), 4110 seeds are put forward Round 1: 365 peptides, 41 chains. Longest chain 30 peptides. Score 0.536 Round 2: 388 peptides, 35 chains. Longest chain 36 peptides. Score 0.606 Round 3: 394 peptides, 35 chains. Longest chain 36 peptides. Score 0.613 Round 4: 389 peptides, 33 chains. Longest chain 39 peptides. Score 0.619 Round 5: 374 peptides, 34 chains. Longest chain 27 peptides. Score 0.594 Taking the results from Round 4 Chains 42, Residues 356, Estimated correctness of the model 21.9 % 7 chains (112 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7166 restraints for refining 3970 atoms. 5231 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2793 (Rfree = 0.000) for 3970 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 42: After refmac, R = 0.2602 (Rfree = 0.000) for 3933 atoms. Found 19 (25 requested) and removed 19 (12 requested) atoms. Cycle 43: After refmac, R = 0.2497 (Rfree = 0.000) for 3913 atoms. Found 14 (25 requested) and removed 17 (12 requested) atoms. Cycle 44: After refmac, R = 0.2405 (Rfree = 0.000) for 3897 atoms. Found 6 (25 requested) and removed 16 (12 requested) atoms. Cycle 45: After refmac, R = 0.2361 (Rfree = 0.000) for 3879 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 2.59 Search for helices and strands: 0 residues in 0 chains, 4021 seeds are put forward NCS extension: 8 residues added (4 deleted due to clashes), 4029 seeds are put forward Round 1: 350 peptides, 48 chains. Longest chain 19 peptides. Score 0.465 Round 2: 387 peptides, 31 chains. Longest chain 31 peptides. Score 0.629 Round 3: 382 peptides, 41 chains. Longest chain 28 peptides. Score 0.560 Round 4: 390 peptides, 32 chains. Longest chain 33 peptides. Score 0.626 Round 5: 386 peptides, 32 chains. Longest chain 36 peptides. Score 0.621 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 356, Estimated correctness of the model 25.6 % 1 chains (30 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12083 reflections ( 99.62 % complete ) and 7600 restraints for refining 3771 atoms. 6082 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2559 (Rfree = 0.000) for 3771 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2445 (Rfree = 0.000) for 3744 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2494 (Rfree = 0.000) for 3727 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2377 (Rfree = 0.000) for 3710 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:58:40 GMT 2018 Job finished. TimeTaking 68.04 Used memory is bytes: 14085544