null Tue 25 Dec 19:27:57 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 2a2m-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.6-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/2a2m-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.6-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 19:28:06 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/2a2m-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.6-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 617 and 0 Target number of residues in the AU: 617 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 258 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 516 Adjusted target solvent content: 0.71 Input MTZ file: 2a2m-3.6-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: 209 Cell parameters: 283.292 283.292 283.292 90.000 90.000 90.000 Input sequence file: 2a2m-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4128 target number of atoms Had to go as low as 0.95 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: 163.559 3.600 Wilson plot Bfac: 76.60 11808 reflections ( 99.75 % complete ) and 0 restraints for refining 4568 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3426 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3134 (Rfree = 0.000) for 4568 atoms. Found 29 (29 requested) and removed 195 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 4530 seeds are put forward NCS extension: 0 residues added, 4530 seeds are put forward Round 1: 309 peptides, 47 chains. Longest chain 15 peptides. Score 0.411 Round 2: 351 peptides, 50 chains. Longest chain 16 peptides. Score 0.458 Round 3: 344 peptides, 43 chains. Longest chain 23 peptides. Score 0.498 Round 4: 344 peptides, 46 chains. Longest chain 18 peptides. Score 0.476 Round 5: 360 peptides, 46 chains. Longest chain 18 peptides. Score 0.501 Taking the results from Round 5 Chains 48, Residues 314, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7591 restraints for refining 3742 atoms. 6208 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2869 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 32 (12 requested) atoms. Cycle 2: After refmac, R = 0.2659 (Rfree = 0.000) for 3667 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 3: After refmac, R = 0.2554 (Rfree = 0.000) for 3630 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 4: After refmac, R = 0.2523 (Rfree = 0.000) for 3614 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.2519 (Rfree = 0.000) for 3602 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 2.52 Search for helices and strands: 0 residues in 0 chains, 3845 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3862 seeds are put forward Round 1: 342 peptides, 42 chains. Longest chain 23 peptides. Score 0.502 Round 2: 337 peptides, 36 chains. Longest chain 39 peptides. Score 0.537 Round 3: 335 peptides, 34 chains. Longest chain 26 peptides. Score 0.548 Round 4: 334 peptides, 37 chains. Longest chain 20 peptides. Score 0.525 Round 5: 350 peptides, 37 chains. Longest chain 25 peptides. Score 0.549 Taking the results from Round 5 Chains 41, Residues 313, Estimated correctness of the model 0.0 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7501 restraints for refining 3739 atoms. 6060 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2718 (Rfree = 0.000) for 3739 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 7: After refmac, R = 0.2475 (Rfree = 0.000) for 3688 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 8: After refmac, R = 0.2357 (Rfree = 0.000) for 3659 atoms. Found 15 (23 requested) and removed 14 (11 requested) atoms. Cycle 9: After refmac, R = 0.2295 (Rfree = 0.000) for 3644 atoms. Found 14 (23 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2262 (Rfree = 0.000) for 3631 atoms. Found 12 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3789 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3809 seeds are put forward Round 1: 330 peptides, 39 chains. Longest chain 23 peptides. Score 0.505 Round 2: 344 peptides, 36 chains. Longest chain 28 peptides. Score 0.547 Round 3: 325 peptides, 35 chains. Longest chain 29 peptides. Score 0.526 Round 4: 338 peptides, 31 chains. Longest chain 25 peptides. Score 0.573 Round 5: 337 peptides, 28 chains. Longest chain 36 peptides. Score 0.592 Taking the results from Round 5 Chains 33, Residues 309, Estimated correctness of the model 11.5 % 6 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7321 restraints for refining 3741 atoms. 5821 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2692 (Rfree = 0.000) for 3741 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 12: After refmac, R = 0.2504 (Rfree = 0.000) for 3685 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 13: After refmac, R = 0.2416 (Rfree = 0.000) for 3654 atoms. Found 19 (23 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2400 (Rfree = 0.000) for 3638 atoms. Found 21 (23 requested) and removed 21 (11 requested) atoms. Cycle 15: After refmac, R = 0.2344 (Rfree = 0.000) for 3627 atoms. Found 11 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.56 Search for helices and strands: 0 residues in 0 chains, 3798 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3810 seeds are put forward Round 1: 316 peptides, 37 chains. Longest chain 22 peptides. Score 0.498 Round 2: 339 peptides, 33 chains. Longest chain 26 peptides. Score 0.560 Round 3: 334 peptides, 37 chains. Longest chain 21 peptides. Score 0.525 Round 4: 334 peptides, 32 chains. Longest chain 24 peptides. Score 0.560 Round 5: 340 peptides, 35 chains. Longest chain 27 peptides. Score 0.548 Taking the results from Round 4 Chains 34, Residues 302, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7968 restraints for refining 3742 atoms. 6686 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2691 (Rfree = 0.000) for 3742 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 17: After refmac, R = 0.2530 (Rfree = 0.000) for 3685 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2429 (Rfree = 0.000) for 3668 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 19: After refmac, R = 0.2382 (Rfree = 0.000) for 3647 atoms. Found 22 (23 requested) and removed 17 (11 requested) atoms. Cycle 20: After refmac, R = 0.2333 (Rfree = 0.000) for 3640 atoms. Found 21 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 2.63 Search for helices and strands: 0 residues in 0 chains, 3795 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3814 seeds are put forward Round 1: 328 peptides, 39 chains. Longest chain 16 peptides. Score 0.502 Round 2: 337 peptides, 37 chains. Longest chain 25 peptides. Score 0.530 Round 3: 327 peptides, 32 chains. Longest chain 28 peptides. Score 0.550 Round 4: 318 peptides, 33 chains. Longest chain 30 peptides. Score 0.530 Round 5: 306 peptides, 29 chains. Longest chain 29 peptides. Score 0.541 Taking the results from Round 3 Chains 34, Residues 295, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7870 restraints for refining 3740 atoms. 6611 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2651 (Rfree = 0.000) for 3740 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 22: After refmac, R = 0.2373 (Rfree = 0.000) for 3723 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 23: After refmac, R = 0.2284 (Rfree = 0.000) for 3704 atoms. Found 17 (23 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.2238 (Rfree = 0.000) for 3688 atoms. Found 13 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.2194 (Rfree = 0.000) for 3676 atoms. Found 8 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3900 seeds are put forward Round 1: 304 peptides, 40 chains. Longest chain 14 peptides. Score 0.456 Round 2: 315 peptides, 33 chains. Longest chain 24 peptides. Score 0.526 Round 3: 321 peptides, 37 chains. Longest chain 22 peptides. Score 0.506 Round 4: 337 peptides, 40 chains. Longest chain 20 peptides. Score 0.509 Round 5: 340 peptides, 36 chains. Longest chain 25 peptides. Score 0.541 Taking the results from Round 5 Chains 37, Residues 304, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7917 restraints for refining 3740 atoms. 6689 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2658 (Rfree = 0.000) for 3740 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.2436 (Rfree = 0.000) for 3709 atoms. Found 15 (24 requested) and removed 18 (12 requested) atoms. Cycle 28: After refmac, R = 0.2422 (Rfree = 0.000) for 3682 atoms. Found 21 (23 requested) and removed 15 (11 requested) atoms. Cycle 29: After refmac, R = 0.2340 (Rfree = 0.000) for 3672 atoms. Found 13 (23 requested) and removed 18 (11 requested) atoms. Cycle 30: After refmac, R = 0.2343 (Rfree = 0.000) for 3649 atoms. Found 12 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 2.56 Search for helices and strands: 0 residues in 0 chains, 3828 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3854 seeds are put forward Round 1: 300 peptides, 43 chains. Longest chain 15 peptides. Score 0.426 Round 2: 320 peptides, 36 chains. Longest chain 21 peptides. Score 0.511 Round 3: 326 peptides, 36 chains. Longest chain 25 peptides. Score 0.521 Round 4: 334 peptides, 35 chains. Longest chain 28 peptides. Score 0.539 Round 5: 315 peptides, 38 chains. Longest chain 18 peptides. Score 0.489 Taking the results from Round 4 Chains 39, Residues 299, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7813 restraints for refining 3741 atoms. 6486 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2596 (Rfree = 0.000) for 3741 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 32: After refmac, R = 0.2439 (Rfree = 0.000) for 3712 atoms. Found 18 (23 requested) and removed 16 (11 requested) atoms. Cycle 33: After refmac, R = 0.2363 (Rfree = 0.000) for 3682 atoms. Found 14 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.2318 (Rfree = 0.000) for 3668 atoms. Found 11 (23 requested) and removed 15 (11 requested) atoms. Cycle 35: After refmac, R = 0.2275 (Rfree = 0.000) for 3653 atoms. Found 13 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 3826 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3840 seeds are put forward Round 1: 314 peptides, 39 chains. Longest chain 32 peptides. Score 0.480 Round 2: 320 peptides, 35 chains. Longest chain 22 peptides. Score 0.519 Round 3: 325 peptides, 35 chains. Longest chain 28 peptides. Score 0.526 Round 4: 325 peptides, 29 chains. Longest chain 30 peptides. Score 0.568 Round 5: 309 peptides, 34 chains. Longest chain 28 peptides. Score 0.509 Taking the results from Round 4 Chains 31, Residues 296, Estimated correctness of the model 1.7 % 5 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7590 restraints for refining 3740 atoms. 6178 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2678 (Rfree = 0.000) for 3740 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 37: After refmac, R = 0.2532 (Rfree = 0.000) for 3709 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 38: After refmac, R = 0.2405 (Rfree = 0.000) for 3699 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 39: After refmac, R = 0.2348 (Rfree = 0.000) for 3685 atoms. Found 21 (23 requested) and removed 16 (11 requested) atoms. Cycle 40: After refmac, R = 0.2287 (Rfree = 0.000) for 3674 atoms. Found 19 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 2.57 Search for helices and strands: 0 residues in 0 chains, 3808 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 3845 seeds are put forward Round 1: 308 peptides, 41 chains. Longest chain 22 peptides. Score 0.455 Round 2: 335 peptides, 36 chains. Longest chain 24 peptides. Score 0.534 Round 3: 333 peptides, 38 chains. Longest chain 25 peptides. Score 0.517 Round 4: 327 peptides, 35 chains. Longest chain 26 peptides. Score 0.529 Round 5: 318 peptides, 37 chains. Longest chain 25 peptides. Score 0.501 Taking the results from Round 2 Chains 40, Residues 299, Estimated correctness of the model 0.0 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 11808 reflections ( 99.75 % complete ) and 7525 restraints for refining 3740 atoms. 6129 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2582 (Rfree = 0.000) for 3740 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 42: After refmac, R = 0.2423 (Rfree = 0.000) for 3702 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 43: After refmac, R = 0.2362 (Rfree = 0.000) for 3692 atoms. Found 14 (23 requested) and removed 16 (11 requested) atoms. Cycle 44: After refmac, R = 0.2333 (Rfree = 0.000) for 3668 atoms. Found 18 (23 requested) and removed 19 (11 requested) atoms. Cycle 45: After refmac, R = 0.2296 (Rfree = 0.000) for 3653 atoms. Found 17 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3796 seeds are put forward Round 1: 294 peptides, 39 chains. Longest chain 20 peptides. Score 0.447 Round 2: 319 peptides, 36 chains. Longest chain 26 peptides. Score 0.510 Round 3: 323 peptides, 34 chains. Longest chain 21 peptides. Score 0.530 Round 4: 319 peptides, 36 chains. Longest chain 21 peptides. Score 0.510 Round 5: 327 peptides, 34 chains. Longest chain 22 peptides. Score 0.536 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 293, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 36 chains (293 residues) following loop building 4 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11808 reflections ( 99.75 % complete ) and 7799 restraints for refining 3742 atoms. 6511 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2678 (Rfree = 0.000) for 3742 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2511 (Rfree = 0.000) for 3701 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2496 (Rfree = 0.000) for 3682 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2467 (Rfree = 0.000) for 3661 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Wed 26 Dec 01:05:10 GMT 2018 Job finished. TimeTaking 337.22 Used memory is bytes: 21417680