Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2avn-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2avn-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2avn-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-parrot-hancs/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-hancs.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-hancs.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 4581 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3683 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3619 (Rfree = 0.000) for 4581 atoms. Found 21 (21 requested) and removed 102 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 2.81 Search for helices and strands: 0 residues in 0 chains, 4578 seeds are put forward NCS extension: 0 residues added, 4578 seeds are put forward Round 1: 255 peptides, 44 chains. Longest chain 19 peptides. Score 0.333 Round 2: 306 peptides, 44 chains. Longest chain 20 peptides. Score 0.424 Round 3: 304 peptides, 41 chains. Longest chain 29 peptides. Score 0.443 Round 4: 305 peptides, 42 chains. Longest chain 19 peptides. Score 0.437 Round 5: 320 peptides, 43 chains. Longest chain 17 peptides. Score 0.454 Taking the results from Round 5 Chains 43, Residues 277, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8289 restraints for refining 3756 atoms. 7224 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3401 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 2: After refmac, R = 0.3182 (Rfree = 0.000) for 3715 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.3069 (Rfree = 0.000) for 3700 atoms. Found 14 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2914 (Rfree = 0.000) for 3693 atoms. Found 8 (17 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2816 (Rfree = 0.000) for 3681 atoms. Found 9 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 2.75 Search for helices and strands: 0 residues in 0 chains, 3830 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3847 seeds are put forward Round 1: 292 peptides, 47 chains. Longest chain 15 peptides. Score 0.376 Round 2: 315 peptides, 41 chains. Longest chain 20 peptides. Score 0.461 Round 3: 334 peptides, 43 chains. Longest chain 21 peptides. Score 0.476 Round 4: 326 peptides, 37 chains. Longest chain 24 peptides. Score 0.507 Round 5: 325 peptides, 41 chains. Longest chain 31 peptides. Score 0.477 Taking the results from Round 4 Chains 37, Residues 289, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7866 restraints for refining 3755 atoms. 6641 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3371 (Rfree = 0.000) for 3755 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 7: After refmac, R = 0.3102 (Rfree = 0.000) for 3726 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2844 (Rfree = 0.000) for 3717 atoms. Found 14 (17 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.2851 (Rfree = 0.000) for 3708 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2726 (Rfree = 0.000) for 3702 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 2.75 Search for helices and strands: 0 residues in 0 chains, 3869 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 3903 seeds are put forward Round 1: 302 peptides, 38 chains. Longest chain 25 peptides. Score 0.462 Round 2: 321 peptides, 33 chains. Longest chain 34 peptides. Score 0.528 Round 3: 316 peptides, 32 chains. Longest chain 20 peptides. Score 0.528 Round 4: 331 peptides, 32 chains. Longest chain 29 peptides. Score 0.549 Round 5: 327 peptides, 36 chains. Longest chain 27 peptides. Score 0.515 Taking the results from Round 4 Chains 32, Residues 299, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8409 restraints for refining 3781 atoms. 7245 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3104 (Rfree = 0.000) for 3781 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 12: After refmac, R = 0.2949 (Rfree = 0.000) for 3739 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2872 (Rfree = 0.000) for 3720 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2542 (Rfree = 0.000) for 3701 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2539 (Rfree = 0.000) for 3677 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 2.81 Search for helices and strands: 0 residues in 0 chains, 3814 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3829 seeds are put forward Round 1: 306 peptides, 40 chains. Longest chain 14 peptides. Score 0.454 Round 2: 323 peptides, 37 chains. Longest chain 18 peptides. Score 0.502 Round 3: 309 peptides, 36 chains. Longest chain 21 peptides. Score 0.488 Round 4: 314 peptides, 35 chains. Longest chain 17 peptides. Score 0.503 Round 5: 312 peptides, 33 chains. Longest chain 21 peptides. Score 0.515 Taking the results from Round 5 Chains 33, Residues 279, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8426 restraints for refining 3757 atoms. 7343 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2986 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 17: After refmac, R = 0.2837 (Rfree = 0.000) for 3721 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2409 (Rfree = 0.000) for 3715 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2524 (Rfree = 0.000) for 3708 atoms. Found 14 (17 requested) and removed 9 (8 requested) atoms. Cycle 20: After refmac, R = 0.2649 (Rfree = 0.000) for 3699 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 2.75 Search for helices and strands: 0 residues in 0 chains, 3852 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3869 seeds are put forward Round 1: 293 peptides, 40 chains. Longest chain 15 peptides. Score 0.433 Round 2: 320 peptides, 34 chains. Longest chain 28 peptides. Score 0.519 Round 3: 329 peptides, 31 chains. Longest chain 29 peptides. Score 0.553 Round 4: 319 peptides, 34 chains. Longest chain 22 peptides. Score 0.518 Round 5: 320 peptides, 32 chains. Longest chain 23 peptides. Score 0.533 Taking the results from Round 3 Chains 31, Residues 298, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7859 restraints for refining 3757 atoms. 6571 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3012 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.2767 (Rfree = 0.000) for 3728 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2766 (Rfree = 0.000) for 3712 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 24: After refmac, R = 0.2472 (Rfree = 0.000) for 3702 atoms. Found 10 (17 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.2471 (Rfree = 0.000) for 3692 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 2.78 Search for helices and strands: 0 residues in 0 chains, 3841 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 3883 seeds are put forward Round 1: 294 peptides, 40 chains. Longest chain 17 peptides. Score 0.434 Round 2: 324 peptides, 37 chains. Longest chain 23 peptides. Score 0.504 Round 3: 328 peptides, 34 chains. Longest chain 32 peptides. Score 0.531 Round 4: 320 peptides, 33 chains. Longest chain 34 peptides. Score 0.526 Round 5: 339 peptides, 34 chains. Longest chain 36 peptides. Score 0.547 Taking the results from Round 5 Chains 34, Residues 305, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8462 restraints for refining 3756 atoms. 7276 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3026 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.2766 (Rfree = 0.000) for 3734 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2726 (Rfree = 0.000) for 3724 atoms. Found 10 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2550 (Rfree = 0.000) for 3718 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2544 (Rfree = 0.000) for 3708 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 3862 seeds are put forward NCS extension: 34 residues added (5 deleted due to clashes), 3896 seeds are put forward Round 1: 289 peptides, 39 chains. Longest chain 16 peptides. Score 0.434 Round 2: 310 peptides, 32 chains. Longest chain 27 peptides. Score 0.519 Round 3: 320 peptides, 33 chains. Longest chain 27 peptides. Score 0.526 Round 4: 334 peptides, 34 chains. Longest chain 27 peptides. Score 0.540 Round 5: 330 peptides, 32 chains. Longest chain 27 peptides. Score 0.548 Taking the results from Round 5 Chains 34, Residues 298, Estimated correctness of the model 0.0 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8232 restraints for refining 3817 atoms. 6940 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2801 (Rfree = 0.000) for 3817 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 32: After refmac, R = 0.2641 (Rfree = 0.000) for 3799 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2528 (Rfree = 0.000) for 3789 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2468 (Rfree = 0.000) for 3783 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2455 (Rfree = 0.000) for 3772 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 3919 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3946 seeds are put forward Round 1: 279 peptides, 41 chains. Longest chain 18 peptides. Score 0.401 Round 2: 297 peptides, 36 chains. Longest chain 16 peptides. Score 0.470 Round 3: 305 peptides, 33 chains. Longest chain 32 peptides. Score 0.504 Round 4: 313 peptides, 40 chains. Longest chain 16 peptides. Score 0.465 Round 5: 310 peptides, 39 chains. Longest chain 21 peptides. Score 0.468 Taking the results from Round 3 Chains 35, Residues 272, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8557 restraints for refining 3757 atoms. 7478 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2731 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 37: After refmac, R = 0.2605 (Rfree = 0.000) for 3751 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.2580 (Rfree = 0.000) for 3744 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2519 (Rfree = 0.000) for 3738 atoms. Found 15 (17 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2511 (Rfree = 0.000) for 3740 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 44 residues added (4 deleted due to clashes), 3936 seeds are put forward Round 1: 294 peptides, 45 chains. Longest chain 16 peptides. Score 0.396 Round 2: 303 peptides, 42 chains. Longest chain 16 peptides. Score 0.434 Round 3: 306 peptides, 37 chains. Longest chain 32 peptides. Score 0.476 Round 4: 311 peptides, 35 chains. Longest chain 23 peptides. Score 0.499 Round 5: 308 peptides, 35 chains. Longest chain 27 peptides. Score 0.494 Taking the results from Round 4 Chains 37, Residues 276, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8435 restraints for refining 3756 atoms. 7334 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3058 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2821 (Rfree = 0.000) for 3736 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 43: After refmac, R = 0.2759 (Rfree = 0.000) for 3722 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 44: After refmac, R = 0.2620 (Rfree = 0.000) for 3697 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2685 (Rfree = 0.000) for 3690 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 2.84 Search for helices and strands: 0 residues in 0 chains, 3853 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 3872 seeds are put forward Round 1: 266 peptides, 43 chains. Longest chain 15 peptides. Score 0.362 Round 2: 293 peptides, 37 chains. Longest chain 22 peptides. Score 0.456 Round 3: 300 peptides, 40 chains. Longest chain 18 peptides. Score 0.444 Round 4: 292 peptides, 38 chains. Longest chain 23 peptides. Score 0.446 Round 5: 308 peptides, 34 chains. Longest chain 22 peptides. Score 0.501 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 274, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2avn-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8899 reflections ( 99.49 % complete ) and 8452 restraints for refining 3756 atoms. 7358 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2844 (Rfree = 0.000) for 3756 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2660 (Rfree = 0.000) for 3726 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2739 (Rfree = 0.000) for 3702 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2753 (Rfree = 0.000) for 3685 atoms. TimeTaking 72.22