Tue 25 Dec 19:27:55 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 2ffj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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/2ffj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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 ============================================================ Tue 25 Dec 19:28:05 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/2ffj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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 407 and 0 Target number of residues in the AU: 407 Target solvent content: 0.6717 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-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: 19 Cell parameters: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.60 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: 29.898 4.000 Wilson plot Bfac: 93.41 5972 reflections ( 98.65 % complete ) and 0 restraints for refining 5320 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3482 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3638 (Rfree = 0.000) for 5320 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.95 3.85 Search for helices and strands: 0 residues in 0 chains, 5440 seeds are put forward NCS extension: 0 residues added, 5440 seeds are put forward Round 1: 185 peptides, 38 chains. Longest chain 9 peptides. Score 0.267 Round 2: 238 peptides, 42 chains. Longest chain 11 peptides. Score 0.363 Round 3: 264 peptides, 41 chains. Longest chain 15 peptides. Score 0.436 Round 4: 264 peptides, 39 chains. Longest chain 13 peptides. Score 0.457 Round 5: 267 peptides, 34 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 5 Chains 35, Residues 233, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9802 restraints for refining 4144 atoms. 8869 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3287 (Rfree = 0.000) for 4144 atoms. Found 19 (19 requested) and removed 45 (9 requested) atoms. Cycle 2: After refmac, R = 0.3101 (Rfree = 0.000) for 4014 atoms. Found 10 (19 requested) and removed 30 (9 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.3067 (Rfree = 0.000) for 3929 atoms. Found 15 (18 requested) and removed 43 (9 requested) atoms. Cycle 4: After refmac, R = 0.2916 (Rfree = 0.000) for 3836 atoms. Found 14 (18 requested) and removed 29 (9 requested) atoms. Cycle 5: After refmac, R = 0.2557 (Rfree = 0.000) for 3765 atoms. Found 10 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3941 seeds are put forward Round 1: 213 peptides, 47 chains. Longest chain 9 peptides. Score 0.240 Round 2: 275 peptides, 48 chains. Longest chain 12 peptides. Score 0.390 Round 3: 274 peptides, 43 chains. Longest chain 18 peptides. Score 0.439 Round 4: 285 peptides, 42 chains. Longest chain 16 peptides. Score 0.474 Round 5: 299 peptides, 44 chains. Longest chain 22 peptides. Score 0.485 Taking the results from Round 5 Chains 44, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5972 reflections ( 98.65 % complete ) and 8632 restraints for refining 3804 atoms. 7656 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3073 (Rfree = 0.000) for 3804 atoms. Found 18 (18 requested) and removed 69 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2754 (Rfree = 0.000) for 3671 atoms. Found 17 (17 requested) and removed 48 (8 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2711 (Rfree = 0.000) for 3607 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2599 (Rfree = 0.000) for 3552 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2616 (Rfree = 0.000) for 3529 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 3783 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3803 seeds are put forward Round 1: 237 peptides, 41 chains. Longest chain 12 peptides. Score 0.371 Round 2: 277 peptides, 39 chains. Longest chain 18 peptides. Score 0.486 Round 3: 287 peptides, 39 chains. Longest chain 18 peptides. Score 0.507 Round 4: 288 peptides, 42 chains. Longest chain 22 peptides. Score 0.481 Round 5: 287 peptides, 37 chains. Longest chain 21 peptides. Score 0.526 Taking the results from Round 5 Chains 38, Residues 250, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8357 restraints for refining 3894 atoms. 7289 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2774 (Rfree = 0.000) for 3894 atoms. Found 17 (18 requested) and removed 53 (9 requested) atoms. Cycle 12: After refmac, R = 0.2634 (Rfree = 0.000) for 3813 atoms. Found 14 (18 requested) and removed 34 (9 requested) atoms. Cycle 13: After refmac, R = 0.2574 (Rfree = 0.000) for 3750 atoms. Found 15 (18 requested) and removed 36 (9 requested) atoms. Cycle 14: After refmac, R = 0.2537 (Rfree = 0.000) for 3689 atoms. Found 12 (17 requested) and removed 30 (8 requested) atoms. Cycle 15: After refmac, R = 0.2064 (Rfree = 0.000) for 3649 atoms. Found 1 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 3810 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3839 seeds are put forward Round 1: 229 peptides, 42 chains. Longest chain 14 peptides. Score 0.340 Round 2: 250 peptides, 36 chains. Longest chain 17 peptides. Score 0.455 Round 3: 268 peptides, 37 chains. Longest chain 17 peptides. Score 0.486 Round 4: 274 peptides, 39 chains. Longest chain 20 peptides. Score 0.479 Round 5: 271 peptides, 39 chains. Longest chain 26 peptides. Score 0.473 Taking the results from Round 3 Chains 37, Residues 231, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5972 reflections ( 98.65 % complete ) and 8311 restraints for refining 3795 atoms. 7403 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2766 (Rfree = 0.000) for 3795 atoms. Found 18 (18 requested) and removed 40 (9 requested) atoms. Cycle 17: After refmac, R = 0.2537 (Rfree = 0.000) for 3737 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 18: After refmac, R = 0.2598 (Rfree = 0.000) for 3702 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 19: After refmac, R = 0.2659 (Rfree = 0.000) for 3672 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 20: After refmac, R = 0.2466 (Rfree = 0.000) for 3642 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3900 seeds are put forward Round 1: 206 peptides, 36 chains. Longest chain 11 peptides. Score 0.348 Round 2: 225 peptides, 34 chains. Longest chain 20 peptides. Score 0.418 Round 3: 241 peptides, 36 chains. Longest chain 12 peptides. Score 0.435 Round 4: 247 peptides, 39 chains. Longest chain 18 peptides. Score 0.417 Round 5: 234 peptides, 33 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 5 Chains 34, Residues 201, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8558 restraints for refining 3845 atoms. 7754 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2867 (Rfree = 0.000) for 3845 atoms. Found 18 (18 requested) and removed 55 (9 requested) atoms. Cycle 22: After refmac, R = 0.2529 (Rfree = 0.000) for 3770 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 23: After refmac, R = 0.2678 (Rfree = 0.000) for 3729 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 24: After refmac, R = 0.2173 (Rfree = 0.000) for 3698 atoms. Found 4 (17 requested) and removed 18 (8 requested) atoms. Cycle 25: After refmac, R = 0.1974 (Rfree = 0.000) for 3671 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 3834 seeds are put forward NCS extension: 0 residues added, 3834 seeds are put forward Round 1: 220 peptides, 42 chains. Longest chain 9 peptides. Score 0.316 Round 2: 243 peptides, 37 chains. Longest chain 18 peptides. Score 0.429 Round 3: 249 peptides, 38 chains. Longest chain 12 peptides. Score 0.432 Round 4: 248 peptides, 36 chains. Longest chain 22 peptides. Score 0.451 Round 5: 261 peptides, 42 chains. Longest chain 18 peptides. Score 0.419 Taking the results from Round 4 Chains 37, Residues 212, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8412 restraints for refining 3848 atoms. 7548 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2785 (Rfree = 0.000) for 3848 atoms. Found 18 (18 requested) and removed 47 (9 requested) atoms. Cycle 27: After refmac, R = 0.2488 (Rfree = 0.000) for 3770 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 28: After refmac, R = 0.2513 (Rfree = 0.000) for 3743 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2442 (Rfree = 0.000) for 3708 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 30: After refmac, R = 0.2296 (Rfree = 0.000) for 3682 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 3858 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3875 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 8 peptides. Score 0.272 Round 2: 243 peptides, 41 chains. Longest chain 15 peptides. Score 0.386 Round 3: 245 peptides, 40 chains. Longest chain 16 peptides. Score 0.402 Round 4: 248 peptides, 41 chains. Longest chain 15 peptides. Score 0.398 Round 5: 247 peptides, 39 chains. Longest chain 18 peptides. Score 0.417 Taking the results from Round 5 Chains 39, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8567 restraints for refining 3847 atoms. 7774 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2544 (Rfree = 0.000) for 3847 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2530 (Rfree = 0.000) for 3800 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 33: After refmac, R = 0.2249 (Rfree = 0.000) for 3760 atoms. Found 14 (17 requested) and removed 20 (8 requested) atoms. Cycle 34: After refmac, R = 0.2306 (Rfree = 0.000) for 3733 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2333 (Rfree = 0.000) for 3713 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 3937 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3959 seeds are put forward Round 1: 191 peptides, 41 chains. Longest chain 7 peptides. Score 0.248 Round 2: 226 peptides, 40 chains. Longest chain 12 peptides. Score 0.354 Round 3: 232 peptides, 41 chains. Longest chain 10 peptides. Score 0.359 Round 4: 246 peptides, 41 chains. Longest chain 12 peptides. Score 0.393 Round 5: 240 peptides, 38 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 5 Chains 38, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8424 restraints for refining 3793 atoms. 7654 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2712 (Rfree = 0.000) for 3793 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2527 (Rfree = 0.000) for 3737 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 38: After refmac, R = 0.2437 (Rfree = 0.000) for 3700 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Cycle 39: After refmac, R = 0.2569 (Rfree = 0.000) for 3660 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 40: After refmac, R = 0.2306 (Rfree = 0.000) for 3642 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 3837 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3852 seeds are put forward Round 1: 182 peptides, 40 chains. Longest chain 7 peptides. Score 0.234 Round 2: 230 peptides, 43 chains. Longest chain 11 peptides. Score 0.331 Round 3: 225 peptides, 39 chains. Longest chain 14 peptides. Score 0.363 Round 4: 232 peptides, 36 chains. Longest chain 14 peptides. Score 0.413 Round 5: 224 peptides, 34 chains. Longest chain 21 peptides. Score 0.415 Taking the results from Round 5 Chains 35, Residues 190, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8178 restraints for refining 3706 atoms. 7421 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2595 (Rfree = 0.000) for 3706 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 42: After refmac, R = 0.2330 (Rfree = 0.000) for 3679 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1901 (Rfree = 0.000) for 3657 atoms. Found 4 (17 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.1827 (Rfree = 0.000) for 3637 atoms. Found 2 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1794 (Rfree = 0.000) for 3622 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 3748 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 3762 seeds are put forward Round 1: 197 peptides, 39 chains. Longest chain 12 peptides. Score 0.288 Round 2: 231 peptides, 40 chains. Longest chain 13 peptides. Score 0.367 Round 3: 241 peptides, 40 chains. Longest chain 14 peptides. Score 0.392 Round 4: 226 peptides, 36 chains. Longest chain 15 peptides. Score 0.398 Round 5: 224 peptides, 35 chains. Longest chain 17 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ffj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5972 reflections ( 98.65 % complete ) and 8722 restraints for refining 3858 atoms. 8001 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2744 (Rfree = 0.000) for 3858 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2762 (Rfree = 0.000) for 3825 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2485 (Rfree = 0.000) for 3779 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2611 (Rfree = 0.000) for 3751 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB TimeTaking 62.89