null Mon 24 Dec 08:01:48 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2avn-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2avn-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2avn-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-parrot-noncs ############### 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 08:01:53 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/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.6-parrot-noncs/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-noncs.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-noncs.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 4613 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3685 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3060 (Rfree = 0.000) for 4613 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 2.59 Search for helices and strands: 0 residues in 0 chains, 4723 seeds are put forward NCS extension: 0 residues added, 4723 seeds are put forward Round 1: 331 peptides, 43 chains. Longest chain 19 peptides. Score 0.472 Round 2: 371 peptides, 36 chains. Longest chain 32 peptides. Score 0.577 Round 3: 376 peptides, 36 chains. Longest chain 31 peptides. Score 0.584 Round 4: 380 peptides, 32 chains. Longest chain 43 peptides. Score 0.614 Round 5: 381 peptides, 36 chains. Longest chain 28 peptides. Score 0.590 Taking the results from Round 4 Chains 36, Residues 348, Estimated correctness of the model 20.0 % 5 chains (100 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7496 restraints for refining 4051 atoms. 5706 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2939 (Rfree = 0.000) for 4051 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 2: After refmac, R = 0.2841 (Rfree = 0.000) for 3996 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2695 (Rfree = 0.000) for 3972 atoms. Found 18 (25 requested) and removed 18 (12 requested) atoms. Cycle 4: After refmac, R = 0.2686 (Rfree = 0.000) for 3949 atoms. Found 21 (25 requested) and removed 16 (12 requested) atoms. Cycle 5: After refmac, R = 0.2648 (Rfree = 0.000) for 3929 atoms. Found 22 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 2.55 Search for helices and strands: 0 residues in 0 chains, 4097 seeds are put forward NCS extension: 41 residues added (10 deleted due to clashes), 4138 seeds are put forward Round 1: 357 peptides, 40 chains. Longest chain 31 peptides. Score 0.532 Round 2: 380 peptides, 35 chains. Longest chain 25 peptides. Score 0.595 Round 3: 371 peptides, 31 chains. Longest chain 69 peptides. Score 0.609 Round 4: 375 peptides, 32 chains. Longest chain 29 peptides. Score 0.608 Round 5: 368 peptides, 33 chains. Longest chain 31 peptides. Score 0.592 Taking the results from Round 3 Chains 34, Residues 340, Estimated correctness of the model 18.1 % 3 chains (82 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7006 restraints for refining 3884 atoms. 5264 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2809 (Rfree = 0.000) for 3884 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 7: After refmac, R = 0.2661 (Rfree = 0.000) for 3835 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2560 (Rfree = 0.000) for 3816 atoms. Found 14 (24 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2503 (Rfree = 0.000) for 3795 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2444 (Rfree = 0.000) for 3780 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 3921 seeds are put forward NCS extension: 27 residues added (13 deleted due to clashes), 3948 seeds are put forward Round 1: 383 peptides, 39 chains. Longest chain 24 peptides. Score 0.574 Round 2: 407 peptides, 36 chains. Longest chain 33 peptides. Score 0.623 Round 3: 386 peptides, 30 chains. Longest chain 31 peptides. Score 0.633 Round 4: 397 peptides, 31 chains. Longest chain 31 peptides. Score 0.641 Round 5: 392 peptides, 36 chains. Longest chain 28 peptides. Score 0.604 Taking the results from Round 4 Chains 36, Residues 366, Estimated correctness of the model 30.0 % 5 chains (104 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7297 restraints for refining 4004 atoms. 5380 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2910 (Rfree = 0.000) for 4004 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 12: After refmac, R = 0.2789 (Rfree = 0.000) for 3975 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 13: After refmac, R = 0.2693 (Rfree = 0.000) for 3942 atoms. Found 21 (25 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.2560 (Rfree = 0.000) for 3921 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.2508 (Rfree = 0.000) for 3918 atoms. Found 14 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.56 Search for helices and strands: 0 residues in 0 chains, 4065 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 4098 seeds are put forward Round 1: 379 peptides, 44 chains. Longest chain 26 peptides. Score 0.536 Round 2: 383 peptides, 33 chains. Longest chain 29 peptides. Score 0.612 Round 3: 383 peptides, 37 chains. Longest chain 27 peptides. Score 0.587 Round 4: 389 peptides, 37 chains. Longest chain 32 peptides. Score 0.595 Round 5: 371 peptides, 32 chains. Longest chain 34 peptides. Score 0.603 Taking the results from Round 2 Chains 35, Residues 350, Estimated correctness of the model 19.3 % 3 chains (69 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7139 restraints for refining 3801 atoms. 5453 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2686 (Rfree = 0.000) for 3801 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 17: After refmac, R = 0.2592 (Rfree = 0.000) for 3778 atoms. Found 15 (24 requested) and removed 20 (12 requested) atoms. Cycle 18: After refmac, R = 0.2537 (Rfree = 0.000) for 3746 atoms. Found 23 (24 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.2539 (Rfree = 0.000) for 3742 atoms. Found 23 (24 requested) and removed 15 (12 requested) atoms. Cycle 20: After refmac, R = 0.2431 (Rfree = 0.000) for 3739 atoms. Found 14 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 3871 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3888 seeds are put forward Round 1: 364 peptides, 39 chains. Longest chain 28 peptides. Score 0.548 Round 2: 364 peptides, 34 chains. Longest chain 41 peptides. Score 0.581 Round 3: 366 peptides, 32 chains. Longest chain 40 peptides. Score 0.596 Round 4: 377 peptides, 36 chains. Longest chain 41 peptides. Score 0.585 Round 5: 370 peptides, 37 chains. Longest chain 27 peptides. Score 0.570 Taking the results from Round 3 Chains 36, Residues 334, Estimated correctness of the model 13.1 % 5 chains (121 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 6802 restraints for refining 3831 atoms. 4968 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2756 (Rfree = 0.000) for 3831 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 22: After refmac, R = 0.2597 (Rfree = 0.000) for 3800 atoms. Found 17 (24 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.2509 (Rfree = 0.000) for 3787 atoms. Found 14 (24 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2408 (Rfree = 0.000) for 3769 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2454 (Rfree = 0.000) for 3757 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 2.59 Search for helices and strands: 0 residues in 0 chains, 3885 seeds are put forward NCS extension: 49 residues added (10 deleted due to clashes), 3934 seeds are put forward Round 1: 370 peptides, 44 chains. Longest chain 22 peptides. Score 0.523 Round 2: 384 peptides, 36 chains. Longest chain 22 peptides. Score 0.594 Round 3: 398 peptides, 42 chains. Longest chain 30 peptides. Score 0.575 Round 4: 384 peptides, 36 chains. Longest chain 28 peptides. Score 0.594 Round 5: 379 peptides, 37 chains. Longest chain 26 peptides. Score 0.582 Taking the results from Round 4 Chains 39, Residues 348, Estimated correctness of the model 12.3 % 4 chains (62 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7461 restraints for refining 3774 atoms. 5842 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2905 (Rfree = 0.000) for 3774 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 27: After refmac, R = 0.2593 (Rfree = 0.000) for 3759 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.2525 (Rfree = 0.000) for 3754 atoms. Found 23 (24 requested) and removed 16 (12 requested) atoms. Cycle 29: After refmac, R = 0.2461 (Rfree = 0.000) for 3746 atoms. Found 22 (24 requested) and removed 16 (12 requested) atoms. Cycle 30: After refmac, R = 0.2440 (Rfree = 0.000) for 3748 atoms. Found 20 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3909 seeds are put forward NCS extension: 19 residues added (10 deleted due to clashes), 3928 seeds are put forward Round 1: 351 peptides, 42 chains. Longest chain 23 peptides. Score 0.509 Round 2: 379 peptides, 33 chains. Longest chain 30 peptides. Score 0.607 Round 3: 357 peptides, 33 chains. Longest chain 41 peptides. Score 0.578 Round 4: 366 peptides, 34 chains. Longest chain 35 peptides. Score 0.584 Round 5: 354 peptides, 31 chains. Longest chain 33 peptides. Score 0.587 Taking the results from Round 2 Chains 35, Residues 346, Estimated correctness of the model 17.4 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7457 restraints for refining 3771 atoms. 5888 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2498 (Rfree = 0.000) for 3771 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.2451 (Rfree = 0.000) for 3762 atoms. Found 23 (24 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.2458 (Rfree = 0.000) for 3764 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2362 (Rfree = 0.000) for 3766 atoms. Found 18 (24 requested) and removed 17 (12 requested) atoms. Cycle 35: After refmac, R = 0.2304 (Rfree = 0.000) for 3761 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 3888 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3911 seeds are put forward Round 1: 356 peptides, 36 chains. Longest chain 23 peptides. Score 0.557 Round 2: 394 peptides, 35 chains. Longest chain 38 peptides. Score 0.613 Round 3: 393 peptides, 34 chains. Longest chain 54 peptides. Score 0.618 Round 4: 371 peptides, 33 chains. Longest chain 36 peptides. Score 0.596 Round 5: 387 peptides, 39 chains. Longest chain 40 peptides. Score 0.579 Taking the results from Round 3 Chains 36, Residues 359, Estimated correctness of the model 21.6 % 4 chains (114 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 6970 restraints for refining 3886 atoms. 5065 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2669 (Rfree = 0.000) for 3886 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 37: After refmac, R = 0.2482 (Rfree = 0.000) for 3861 atoms. Found 16 (24 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2480 (Rfree = 0.000) for 3843 atoms. Found 22 (24 requested) and removed 15 (12 requested) atoms. Cycle 39: After refmac, R = 0.2452 (Rfree = 0.000) for 3844 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 40: After refmac, R = 0.2465 (Rfree = 0.000) for 3828 atoms. Found 12 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 3920 seeds are put forward NCS extension: 37 residues added (23 deleted due to clashes), 3957 seeds are put forward Round 1: 346 peptides, 41 chains. Longest chain 21 peptides. Score 0.509 Round 2: 372 peptides, 33 chains. Longest chain 23 peptides. Score 0.598 Round 3: 393 peptides, 35 chains. Longest chain 29 peptides. Score 0.612 Round 4: 366 peptides, 31 chains. Longest chain 32 peptides. Score 0.603 Round 5: 373 peptides, 34 chains. Longest chain 25 peptides. Score 0.593 Taking the results from Round 3 Chains 35, Residues 358, Estimated correctness of the model 19.3 % 3 chains (54 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7362 restraints for refining 3773 atoms. 5726 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2835 (Rfree = 0.000) for 3773 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 42: After refmac, R = 0.2702 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 43: After refmac, R = 0.2521 (Rfree = 0.000) for 3734 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 44: After refmac, R = 0.2461 (Rfree = 0.000) for 3732 atoms. Found 22 (24 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.2381 (Rfree = 0.000) for 3740 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3877 seeds are put forward Round 1: 377 peptides, 46 chains. Longest chain 17 peptides. Score 0.520 Round 2: 379 peptides, 36 chains. Longest chain 29 peptides. Score 0.588 Round 3: 386 peptides, 36 chains. Longest chain 29 peptides. Score 0.597 Round 4: 375 peptides, 37 chains. Longest chain 29 peptides. Score 0.576 Round 5: 362 peptides, 40 chains. Longest chain 29 peptides. Score 0.539 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 350, Estimated correctness of the model 13.5 % 3 chains (36 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (350 residues) following loop building 3 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12083 reflections ( 99.62 % complete ) and 7603 restraints for refining 3770 atoms. 6098 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2533 (Rfree = 0.000) for 3770 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2451 (Rfree = 0.000) for 3738 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2440 (Rfree = 0.000) for 3722 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2453 (Rfree = 0.000) for 3710 atoms. Found 0 (23 requested) and removed 4 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:03:36 GMT 2018 Job finished. TimeTaking 61.8 Used memory is bytes: 14216672