null Mon 24 Dec 07:50:28 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-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2avn-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2avn-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-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-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-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 07:50:32 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-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-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 616 and 0 Target number of residues in the AU: 616 Target solvent content: 0.6578 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-4.0-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-4.0-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 4.000 Wilson plot Bfac: 83.40 8899 reflections ( 99.49 % complete ) and 0 restraints for refining 4621 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3726 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3578 (Rfree = 0.000) for 4621 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 2.76 Search for helices and strands: 0 residues in 0 chains, 4732 seeds are put forward NCS extension: 0 residues added, 4732 seeds are put forward Round 1: 274 peptides, 41 chains. Longest chain 18 peptides. Score 0.392 Round 2: 310 peptides, 31 chains. Longest chain 26 peptides. Score 0.526 Round 3: 309 peptides, 34 chains. Longest chain 19 peptides. Score 0.503 Round 4: 335 peptides, 34 chains. Longest chain 24 peptides. Score 0.541 Round 5: 317 peptides, 31 chains. Longest chain 25 peptides. Score 0.536 Taking the results from Round 4 Chains 34, Residues 301, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8984 restraints for refining 3934 atoms. 7814 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3108 (Rfree = 0.000) for 3934 atoms. Found 18 (18 requested) and removed 69 (9 requested) atoms. Cycle 2: After refmac, R = 0.2976 (Rfree = 0.000) for 3813 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2866 (Rfree = 0.000) for 3770 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2793 (Rfree = 0.000) for 3742 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2745 (Rfree = 0.000) for 3724 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 2.73 Search for helices and strands: 0 residues in 0 chains, 3895 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 3911 seeds are put forward Round 1: 337 peptides, 45 chains. Longest chain 18 peptides. Score 0.466 Round 2: 342 peptides, 32 chains. Longest chain 25 peptides. Score 0.564 Round 3: 343 peptides, 35 chains. Longest chain 29 peptides. Score 0.546 Round 4: 340 peptides, 31 chains. Longest chain 27 peptides. Score 0.568 Round 5: 329 peptides, 29 chains. Longest chain 31 peptides. Score 0.567 Taking the results from Round 4 Chains 32, Residues 309, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7921 restraints for refining 3777 atoms. 6583 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2946 (Rfree = 0.000) for 3777 atoms. Found 17 (17 requested) and removed 94 (8 requested) atoms. Cycle 7: After refmac, R = 0.2753 (Rfree = 0.000) for 3666 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2673 (Rfree = 0.000) for 3661 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 9: After refmac, R = 0.2579 (Rfree = 0.000) for 3662 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.2562 (Rfree = 0.000) for 3660 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 2.76 Search for helices and strands: 0 residues in 0 chains, 3805 seeds are put forward NCS extension: 0 residues added, 3805 seeds are put forward Round 1: 315 peptides, 32 chains. Longest chain 27 peptides. Score 0.526 Round 2: 338 peptides, 32 chains. Longest chain 32 peptides. Score 0.559 Round 3: 323 peptides, 35 chains. Longest chain 20 peptides. Score 0.517 Round 4: 345 peptides, 36 chains. Longest chain 26 peptides. Score 0.542 Round 5: 334 peptides, 33 chains. Longest chain 21 peptides. Score 0.546 Taking the results from Round 2 Chains 35, Residues 306, Estimated correctness of the model 0.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7654 restraints for refining 3755 atoms. 6279 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2968 (Rfree = 0.000) for 3755 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 12: After refmac, R = 0.2699 (Rfree = 0.000) for 3738 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2575 (Rfree = 0.000) for 3731 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.2611 (Rfree = 0.000) for 3722 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2474 (Rfree = 0.000) for 3720 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 2.81 Search for helices and strands: 0 residues in 0 chains, 3878 seeds are put forward NCS extension: 0 residues added, 3878 seeds are put forward Round 1: 312 peptides, 40 chains. Longest chain 16 peptides. Score 0.464 Round 2: 340 peptides, 34 chains. Longest chain 24 peptides. Score 0.548 Round 3: 346 peptides, 31 chains. Longest chain 29 peptides. Score 0.576 Round 4: 338 peptides, 30 chains. Longest chain 45 peptides. Score 0.572 Round 5: 344 peptides, 26 chains. Longest chain 41 peptides. Score 0.606 Taking the results from Round 5 Chains 29, Residues 318, Estimated correctness of the model 0.0 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7352 restraints for refining 3774 atoms. 5813 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3185 (Rfree = 0.000) for 3774 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.2953 (Rfree = 0.000) for 3742 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2905 (Rfree = 0.000) for 3725 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 19: After refmac, R = 0.2722 (Rfree = 0.000) for 3702 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.2734 (Rfree = 0.000) for 3700 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 2.81 Search for helices and strands: 0 residues in 0 chains, 3836 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3855 seeds are put forward Round 1: 301 peptides, 34 chains. Longest chain 25 peptides. Score 0.491 Round 2: 325 peptides, 34 chains. Longest chain 23 peptides. Score 0.527 Round 3: 320 peptides, 27 chains. Longest chain 28 peptides. Score 0.568 Round 4: 334 peptides, 29 chains. Longest chain 36 peptides. Score 0.574 Round 5: 317 peptides, 31 chains. Longest chain 25 peptides. Score 0.536 Taking the results from Round 4 Chains 31, Residues 305, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8196 restraints for refining 3756 atoms. 6893 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3121 (Rfree = 0.000) for 3756 atoms. Found 16 (17 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.2807 (Rfree = 0.000) for 3739 atoms. Found 10 (17 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2817 (Rfree = 0.000) for 3728 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.2870 (Rfree = 0.000) for 3721 atoms. Found 1 (17 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.3127 (Rfree = 0.000) for 3706 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 2.81 Search for helices and strands: 0 residues in 0 chains, 3840 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3863 seeds are put forward Round 1: 296 peptides, 32 chains. Longest chain 23 peptides. Score 0.498 Round 2: 305 peptides, 28 chains. Longest chain 37 peptides. Score 0.540 Round 3: 322 peptides, 34 chains. Longest chain 21 peptides. Score 0.522 Round 4: 320 peptides, 34 chains. Longest chain 24 peptides. Score 0.519 Round 5: 311 peptides, 31 chains. Longest chain 32 peptides. Score 0.527 Taking the results from Round 2 Chains 28, Residues 277, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8372 restraints for refining 3756 atoms. 7292 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2958 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2646 (Rfree = 0.000) for 3750 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.2522 (Rfree = 0.000) for 3741 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2483 (Rfree = 0.000) for 3739 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.2472 (Rfree = 0.000) for 3732 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 2.78 Search for helices and strands: 0 residues in 0 chains, 3916 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3949 seeds are put forward Round 1: 286 peptides, 39 chains. Longest chain 20 peptides. Score 0.429 Round 2: 306 peptides, 32 chains. Longest chain 26 peptides. Score 0.513 Round 3: 320 peptides, 36 chains. Longest chain 26 peptides. Score 0.505 Round 4: 306 peptides, 31 chains. Longest chain 32 peptides. Score 0.520 Round 5: 311 peptides, 31 chains. Longest chain 39 peptides. Score 0.527 Taking the results from Round 5 Chains 32, Residues 280, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7883 restraints for refining 3756 atoms. 6626 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2725 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 32: After refmac, R = 0.2538 (Rfree = 0.000) for 3739 atoms. Found 14 (17 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2492 (Rfree = 0.000) for 3728 atoms. Found 13 (17 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.2467 (Rfree = 0.000) for 3720 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2432 (Rfree = 0.000) for 3718 atoms. Found 15 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 2.75 Search for helices and strands: 0 residues in 0 chains, 3886 seeds are put forward NCS extension: 51 residues added (4 deleted due to clashes), 3937 seeds are put forward Round 1: 318 peptides, 46 chains. Longest chain 17 peptides. Score 0.429 Round 2: 301 peptides, 35 chains. Longest chain 23 peptides. Score 0.483 Round 3: 297 peptides, 37 chains. Longest chain 20 peptides. Score 0.462 Round 4: 307 peptides, 37 chains. Longest chain 18 peptides. Score 0.478 Round 5: 305 peptides, 36 chains. Longest chain 25 peptides. Score 0.482 Taking the results from Round 2 Chains 35, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8458 restraints for refining 3755 atoms. 7429 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2589 (Rfree = 0.000) for 3755 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.2518 (Rfree = 0.000) for 3741 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2455 (Rfree = 0.000) for 3743 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.2374 (Rfree = 0.000) for 3740 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2099 (Rfree = 0.000) for 3731 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 2.75 Search for helices and strands: 0 residues in 0 chains, 3916 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3940 seeds are put forward Round 1: 271 peptides, 44 chains. Longest chain 13 peptides. Score 0.363 Round 2: 300 peptides, 45 chains. Longest chain 20 peptides. Score 0.406 Round 3: 294 peptides, 38 chains. Longest chain 16 peptides. Score 0.450 Round 4: 298 peptides, 41 chains. Longest chain 15 peptides. Score 0.433 Round 5: 305 peptides, 41 chains. Longest chain 23 peptides. Score 0.445 Taking the results from Round 3 Chains 38, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8723 restraints for refining 3757 atoms. 7737 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2592 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 130 (8 requested) atoms. Cycle 42: After refmac, R = 0.2400 (Rfree = 0.000) for 3621 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.2324 (Rfree = 0.000) for 3619 atoms. Found 14 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2318 (Rfree = 0.000) for 3616 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2257 (Rfree = 0.000) for 3605 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 3780 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3793 seeds are put forward Round 1: 255 peptides, 43 chains. Longest chain 12 peptides. Score 0.342 Round 2: 282 peptides, 37 chains. Longest chain 18 peptides. Score 0.438 Round 3: 304 peptides, 42 chains. Longest chain 14 peptides. Score 0.436 Round 4: 303 peptides, 35 chains. Longest chain 23 peptides. Score 0.486 Round 5: 307 peptides, 34 chains. Longest chain 27 peptides. Score 0.500 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 273, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2avn-4_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (273 residues) following loop building 2 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8899 reflections ( 99.49 % complete ) and 7990 restraints for refining 3755 atoms. 6787 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2754 (Rfree = 0.000) for 3755 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2609 (Rfree = 0.000) for 3701 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2550 (Rfree = 0.000) for 3676 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2456 (Rfree = 0.000) for 3654 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:43:30 GMT 2018 Job finished. TimeTaking 53.03 Used memory is bytes: 9901144