Mon 24 Dec 07:30:54 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2avn-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2avn-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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 07:30:59 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 79.29 10328 reflections ( 99.56 % complete ) and 0 restraints for refining 4592 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3748 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3280 (Rfree = 0.000) for 4592 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 2.64 Search for helices and strands: 0 residues in 0 chains, 4713 seeds are put forward NCS extension: 0 residues added, 4713 seeds are put forward Round 1: 336 peptides, 45 chains. Longest chain 21 peptides. Score 0.465 Round 2: 347 peptides, 35 chains. Longest chain 22 peptides. Score 0.551 Round 3: 377 peptides, 39 chains. Longest chain 24 peptides. Score 0.566 Round 4: 366 peptides, 37 chains. Longest chain 22 peptides. Score 0.564 Round 5: 356 peptides, 39 chains. Longest chain 24 peptides. Score 0.537 Taking the results from Round 3 Chains 42, Residues 338, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8396 restraints for refining 3916 atoms. 6987 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 3916 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 2: After refmac, R = 0.2760 (Rfree = 0.000) for 3852 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 3: After refmac, R = 0.2718 (Rfree = 0.000) for 3823 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 4: After refmac, R = 0.2735 (Rfree = 0.000) for 3812 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 5: After refmac, R = 0.2619 (Rfree = 0.000) for 3793 atoms. Found 20 (20 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, 3992 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4010 seeds are put forward Round 1: 349 peptides, 45 chains. Longest chain 17 peptides. Score 0.485 Round 2: 354 peptides, 37 chains. Longest chain 24 peptides. Score 0.548 Round 3: 354 peptides, 31 chains. Longest chain 31 peptides. Score 0.587 Round 4: 365 peptides, 34 chains. Longest chain 36 peptides. Score 0.582 Round 5: 357 peptides, 32 chains. Longest chain 26 peptides. Score 0.584 Taking the results from Round 3 Chains 32, Residues 323, Estimated correctness of the model 0.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7893 restraints for refining 3792 atoms. 6457 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2822 (Rfree = 0.000) for 3792 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 7: After refmac, R = 0.2685 (Rfree = 0.000) for 3778 atoms. Found 17 (20 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.2565 (Rfree = 0.000) for 3777 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2566 (Rfree = 0.000) for 3765 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2491 (Rfree = 0.000) for 3761 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 2.71 Search for helices and strands: 0 residues in 0 chains, 3901 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 3933 seeds are put forward Round 1: 345 peptides, 37 chains. Longest chain 19 peptides. Score 0.535 Round 2: 367 peptides, 36 chains. Longest chain 49 peptides. Score 0.572 Round 3: 352 peptides, 29 chains. Longest chain 33 peptides. Score 0.597 Round 4: 360 peptides, 33 chains. Longest chain 22 peptides. Score 0.582 Round 5: 344 peptides, 31 chains. Longest chain 27 peptides. Score 0.574 Taking the results from Round 3 Chains 30, Residues 323, Estimated correctness of the model 0.0 % 2 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7809 restraints for refining 3946 atoms. 6227 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2815 (Rfree = 0.000) for 3946 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 12: After refmac, R = 0.2627 (Rfree = 0.000) for 3919 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.2573 (Rfree = 0.000) for 3889 atoms. Found 17 (21 requested) and removed 13 (10 requested) atoms. Cycle 14: After refmac, R = 0.2480 (Rfree = 0.000) for 3877 atoms. Found 8 (21 requested) and removed 17 (10 requested) atoms. Cycle 15: After refmac, R = 0.2442 (Rfree = 0.000) for 3853 atoms. Found 13 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 4004 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4028 seeds are put forward Round 1: 344 peptides, 39 chains. Longest chain 22 peptides. Score 0.520 Round 2: 350 peptides, 36 chains. Longest chain 33 peptides. Score 0.549 Round 3: 361 peptides, 38 chains. Longest chain 24 peptides. Score 0.551 Round 4: 356 peptides, 38 chains. Longest chain 32 peptides. Score 0.544 Round 5: 341 peptides, 33 chains. Longest chain 28 peptides. Score 0.556 Taking the results from Round 5 Chains 34, Residues 308, Estimated correctness of the model 0.0 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8319 restraints for refining 3881 atoms. 6981 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2709 (Rfree = 0.000) for 3881 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 17: After refmac, R = 0.2555 (Rfree = 0.000) for 3841 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 18: After refmac, R = 0.2525 (Rfree = 0.000) for 3833 atoms. Found 17 (21 requested) and removed 19 (10 requested) atoms. Cycle 19: After refmac, R = 0.2464 (Rfree = 0.000) for 3826 atoms. Found 14 (21 requested) and removed 18 (10 requested) atoms. Cycle 20: After refmac, R = 0.2385 (Rfree = 0.000) for 3816 atoms. Found 6 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 3980 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3999 seeds are put forward Round 1: 322 peptides, 37 chains. Longest chain 28 peptides. Score 0.501 Round 2: 330 peptides, 32 chains. Longest chain 35 peptides. Score 0.548 Round 3: 340 peptides, 35 chains. Longest chain 32 peptides. Score 0.541 Round 4: 351 peptides, 33 chains. Longest chain 39 peptides. Score 0.570 Round 5: 338 peptides, 34 chains. Longest chain 31 peptides. Score 0.545 Taking the results from Round 4 Chains 33, Residues 318, Estimated correctness of the model 0.0 % 1 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7626 restraints for refining 3793 atoms. 6192 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2822 (Rfree = 0.000) for 3793 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2619 (Rfree = 0.000) for 3771 atoms. Found 13 (20 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2534 (Rfree = 0.000) for 3756 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.2508 (Rfree = 0.000) for 3751 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.2450 (Rfree = 0.000) for 3739 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 2.74 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3920 seeds are put forward Round 1: 317 peptides, 40 chains. Longest chain 37 peptides. Score 0.471 Round 2: 333 peptides, 34 chains. Longest chain 36 peptides. Score 0.538 Round 3: 337 peptides, 34 chains. Longest chain 41 peptides. Score 0.544 Round 4: 326 peptides, 30 chains. Longest chain 32 peptides. Score 0.556 Round 5: 334 peptides, 31 chains. Longest chain 40 peptides. Score 0.560 Taking the results from Round 5 Chains 32, Residues 303, Estimated correctness of the model 0.0 % 3 chains (64 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7824 restraints for refining 3847 atoms. 6352 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2925 (Rfree = 0.000) for 3847 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 27: After refmac, R = 0.2656 (Rfree = 0.000) for 3828 atoms. Found 19 (21 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.2614 (Rfree = 0.000) for 3821 atoms. Found 8 (21 requested) and removed 17 (10 requested) atoms. Cycle 29: After refmac, R = 0.2493 (Rfree = 0.000) for 3800 atoms. Found 18 (20 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.2484 (Rfree = 0.000) for 3799 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 2.69 Search for helices and strands: 0 residues in 0 chains, 3944 seeds are put forward NCS extension: 43 residues added (2 deleted due to clashes), 3987 seeds are put forward Round 1: 323 peptides, 44 chains. Longest chain 18 peptides. Score 0.452 Round 2: 336 peptides, 36 chains. Longest chain 38 peptides. Score 0.529 Round 3: 324 peptides, 37 chains. Longest chain 26 peptides. Score 0.504 Round 4: 323 peptides, 31 chains. Longest chain 41 peptides. Score 0.545 Round 5: 343 peptides, 35 chains. Longest chain 30 peptides. Score 0.546 Taking the results from Round 5 Chains 35, Residues 308, Estimated correctness of the model 0.0 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 7967 restraints for refining 3815 atoms. 6605 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2936 (Rfree = 0.000) for 3815 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 32: After refmac, R = 0.2738 (Rfree = 0.000) for 3802 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2615 (Rfree = 0.000) for 3800 atoms. Found 18 (20 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2609 (Rfree = 0.000) for 3793 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.2442 (Rfree = 0.000) for 3790 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 2.67 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 53 residues added (4 deleted due to clashes), 4013 seeds are put forward Round 1: 324 peptides, 41 chains. Longest chain 24 peptides. Score 0.475 Round 2: 354 peptides, 35 chains. Longest chain 35 peptides. Score 0.561 Round 3: 341 peptides, 37 chains. Longest chain 23 peptides. Score 0.529 Round 4: 353 peptides, 37 chains. Longest chain 23 peptides. Score 0.546 Round 5: 338 peptides, 35 chains. Longest chain 30 peptides. Score 0.538 Taking the results from Round 2 Chains 36, Residues 319, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8069 restraints for refining 3761 atoms. 6781 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2789 (Rfree = 0.000) for 3761 atoms. Found 20 (20 requested) and removed 69 (10 requested) atoms. Cycle 37: After refmac, R = 0.2502 (Rfree = 0.000) for 3690 atoms. Found 18 (20 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.2402 (Rfree = 0.000) for 3691 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.2359 (Rfree = 0.000) for 3673 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2335 (Rfree = 0.000) for 3668 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 2.72 Search for helices and strands: 0 residues in 0 chains, 3816 seeds are put forward NCS extension: 49 residues added (8 deleted due to clashes), 3865 seeds are put forward Round 1: 321 peptides, 41 chains. Longest chain 20 peptides. Score 0.470 Round 2: 344 peptides, 36 chains. Longest chain 29 peptides. Score 0.540 Round 3: 335 peptides, 36 chains. Longest chain 28 peptides. Score 0.527 Round 4: 335 peptides, 31 chains. Longest chain 41 peptides. Score 0.561 Round 5: 345 peptides, 36 chains. Longest chain 24 peptides. Score 0.542 Taking the results from Round 4 Chains 32, Residues 304, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10328 reflections ( 99.56 % complete ) and 8120 restraints for refining 3759 atoms. 6894 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2990 (Rfree = 0.000) for 3759 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 42: After refmac, R = 0.2659 (Rfree = 0.000) for 3759 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.2562 (Rfree = 0.000) for 3757 atoms. Found 8 (20 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.2471 (Rfree = 0.000) for 3748 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2451 (Rfree = 0.000) for 3740 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 2.73 Search for helices and strands: 0 residues in 0 chains, 3913 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 3948 seeds are put forward Round 1: 308 peptides, 44 chains. Longest chain 16 peptides. Score 0.427 Round 2: 327 peptides, 36 chains. Longest chain 24 peptides. Score 0.515 Round 3: 337 peptides, 35 chains. Longest chain 36 peptides. Score 0.537 Round 4: 347 peptides, 35 chains. Longest chain 36 peptides. Score 0.551 Round 5: 334 peptides, 33 chains. Longest chain 37 peptides. Score 0.546 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 312, Estimated correctness of the model 0.0 % 2 chains (57 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (312 residues) following loop building 2 chains (57 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10328 reflections ( 99.56 % complete ) and 7933 restraints for refining 3865 atoms. 6456 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2885 (Rfree = 0.000) for 3865 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2732 (Rfree = 0.000) for 3836 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2668 (Rfree = 0.000) for 3821 atoms. Found 0 (21 requested) and removed 9 (10 requested) atoms. Cycle 49: After refmac, R = 0.2649 (Rfree = 0.000) for 3810 atoms. TimeTaking 60.48