null Sun 23 Dec 22:23:10 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a2m-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-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 22:23:19 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-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 641 and 0 Target number of residues in the AU: 641 Target solvent content: 0.6338 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 68.57 13912 reflections ( 99.78 % complete ) and 0 restraints for refining 4575 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Starting model: R = 0.3279 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2982 (Rfree = 0.000) for 4575 atoms. Found 34 (34 requested) and removed 69 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 4667 seeds are put forward NCS extension: 0 residues added, 4667 seeds are put forward Round 1: 316 peptides, 48 chains. Longest chain 30 peptides. Score 0.415 Round 2: 348 peptides, 43 chains. Longest chain 23 peptides. Score 0.504 Round 3: 359 peptides, 47 chains. Longest chain 17 peptides. Score 0.493 Round 4: 359 peptides, 40 chains. Longest chain 28 peptides. Score 0.541 Round 5: 349 peptides, 46 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 43, Residues 319, Estimated correctness of the model 8.2 % 7 chains (60 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7322 restraints for refining 3752 atoms. 5911 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2744 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. Cycle 2: After refmac, R = 0.2610 (Rfree = 0.000) for 3711 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 3: After refmac, R = 0.2510 (Rfree = 0.000) for 3698 atoms. Found 23 (28 requested) and removed 15 (14 requested) atoms. Cycle 4: After refmac, R = 0.2476 (Rfree = 0.000) for 3695 atoms. Found 16 (27 requested) and removed 13 (13 requested) atoms. Cycle 5: After refmac, R = 0.2455 (Rfree = 0.000) for 3692 atoms. Found 10 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 2.43 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3891 seeds are put forward Round 1: 336 peptides, 45 chains. Longest chain 17 peptides. Score 0.471 Round 2: 349 peptides, 43 chains. Longest chain 26 peptides. Score 0.506 Round 3: 368 peptides, 43 chains. Longest chain 27 peptides. Score 0.534 Round 4: 372 peptides, 40 chains. Longest chain 42 peptides. Score 0.560 Round 5: 355 peptides, 39 chains. Longest chain 33 peptides. Score 0.542 Taking the results from Round 4 Chains 41, Residues 332, Estimated correctness of the model 15.0 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7447 restraints for refining 3753 atoms. 5928 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2819 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 7: After refmac, R = 0.2601 (Rfree = 0.000) for 3722 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.2503 (Rfree = 0.000) for 3708 atoms. Found 23 (28 requested) and removed 24 (14 requested) atoms. Cycle 9: After refmac, R = 0.2394 (Rfree = 0.000) for 3691 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 3668 atoms. Found 20 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 2.43 Search for helices and strands: 0 residues in 0 chains, 3860 seeds are put forward NCS extension: 75 residues added (1 deleted due to clashes), 3935 seeds are put forward Round 1: 350 peptides, 39 chains. Longest chain 20 peptides. Score 0.535 Round 2: 351 peptides, 38 chains. Longest chain 21 peptides. Score 0.543 Round 3: 351 peptides, 35 chains. Longest chain 37 peptides. Score 0.564 Round 4: 363 peptides, 37 chains. Longest chain 35 peptides. Score 0.567 Round 5: 372 peptides, 37 chains. Longest chain 35 peptides. Score 0.580 Taking the results from Round 5 Chains 42, Residues 335, Estimated correctness of the model 21.9 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7428 restraints for refining 3753 atoms. 5945 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2708 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 12: After refmac, R = 0.2474 (Rfree = 0.000) for 3727 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 13: After refmac, R = 0.2381 (Rfree = 0.000) for 3706 atoms. Found 25 (28 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.2342 (Rfree = 0.000) for 3689 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. Cycle 15: After refmac, R = 0.2291 (Rfree = 0.000) for 3680 atoms. Found 17 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.44 Search for helices and strands: 0 residues in 0 chains, 3858 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 3870 seeds are put forward Round 1: 337 peptides, 45 chains. Longest chain 31 peptides. Score 0.472 Round 2: 351 peptides, 38 chains. Longest chain 22 peptides. Score 0.543 Round 3: 345 peptides, 36 chains. Longest chain 43 peptides. Score 0.548 Round 4: 366 peptides, 38 chains. Longest chain 28 peptides. Score 0.565 Round 5: 357 peptides, 39 chains. Longest chain 26 peptides. Score 0.545 Taking the results from Round 4 Chains 43, Residues 328, Estimated correctness of the model 16.8 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7547 restraints for refining 3753 atoms. 6111 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2712 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 17: After refmac, R = 0.2468 (Rfree = 0.000) for 3734 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 18: After refmac, R = 0.2409 (Rfree = 0.000) for 3716 atoms. Found 24 (28 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.2351 (Rfree = 0.000) for 3704 atoms. Found 11 (28 requested) and removed 18 (14 requested) atoms. Cycle 20: After refmac, R = 0.2331 (Rfree = 0.000) for 3682 atoms. Found 21 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 2.42 Search for helices and strands: 0 residues in 0 chains, 3845 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3867 seeds are put forward Round 1: 328 peptides, 41 chains. Longest chain 20 peptides. Score 0.487 Round 2: 355 peptides, 35 chains. Longest chain 43 peptides. Score 0.569 Round 3: 353 peptides, 37 chains. Longest chain 22 peptides. Score 0.553 Round 4: 351 peptides, 42 chains. Longest chain 26 peptides. Score 0.516 Round 5: 319 peptides, 39 chains. Longest chain 23 peptides. Score 0.488 Taking the results from Round 2 Chains 37, Residues 320, Estimated correctness of the model 18.2 % 3 chains (78 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7144 restraints for refining 3753 atoms. 5556 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2663 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 22: After refmac, R = 0.2587 (Rfree = 0.000) for 3740 atoms. Found 23 (28 requested) and removed 27 (14 requested) atoms. Cycle 23: After refmac, R = 0.2615 (Rfree = 0.000) for 3725 atoms. Found 23 (28 requested) and removed 26 (14 requested) atoms. Cycle 24: After refmac, R = 0.2564 (Rfree = 0.000) for 3704 atoms. Found 25 (28 requested) and removed 22 (14 requested) atoms. Cycle 25: After refmac, R = 0.2457 (Rfree = 0.000) for 3696 atoms. Found 13 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 3852 seeds are put forward NCS extension: 33 residues added (8 deleted due to clashes), 3885 seeds are put forward Round 1: 344 peptides, 42 chains. Longest chain 21 peptides. Score 0.505 Round 2: 367 peptides, 39 chains. Longest chain 27 peptides. Score 0.559 Round 3: 355 peptides, 37 chains. Longest chain 25 peptides. Score 0.556 Round 4: 356 peptides, 34 chains. Longest chain 29 peptides. Score 0.577 Round 5: 349 peptides, 41 chains. Longest chain 18 peptides. Score 0.520 Taking the results from Round 4 Chains 35, Residues 322, Estimated correctness of the model 20.9 % 6 chains (90 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7246 restraints for refining 3752 atoms. 5657 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2665 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 27: After refmac, R = 0.2584 (Rfree = 0.000) for 3727 atoms. Found 24 (28 requested) and removed 23 (14 requested) atoms. Cycle 28: After refmac, R = 0.2605 (Rfree = 0.000) for 3720 atoms. Found 26 (28 requested) and removed 27 (14 requested) atoms. Cycle 29: After refmac, R = 0.2533 (Rfree = 0.000) for 3715 atoms. Found 16 (28 requested) and removed 22 (14 requested) atoms. Cycle 30: After refmac, R = 0.2515 (Rfree = 0.000) for 3708 atoms. Found 17 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.45 Search for helices and strands: 0 residues in 0 chains, 3888 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3903 seeds are put forward Round 1: 339 peptides, 42 chains. Longest chain 30 peptides. Score 0.497 Round 2: 340 peptides, 38 chains. Longest chain 22 peptides. Score 0.527 Round 3: 363 peptides, 40 chains. Longest chain 20 peptides. Score 0.547 Round 4: 349 peptides, 36 chains. Longest chain 33 peptides. Score 0.554 Round 5: 354 peptides, 33 chains. Longest chain 25 peptides. Score 0.581 Taking the results from Round 5 Chains 41, Residues 321, Estimated correctness of the model 22.3 % 7 chains (92 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7239 restraints for refining 3753 atoms. 5631 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2735 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 32: After refmac, R = 0.2564 (Rfree = 0.000) for 3743 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 33: After refmac, R = 0.2487 (Rfree = 0.000) for 3739 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 34: After refmac, R = 0.2409 (Rfree = 0.000) for 3737 atoms. Found 14 (28 requested) and removed 20 (14 requested) atoms. Cycle 35: After refmac, R = 0.2389 (Rfree = 0.000) for 3726 atoms. Found 27 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 2.44 Search for helices and strands: 0 residues in 0 chains, 3910 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3928 seeds are put forward Round 1: 327 peptides, 43 chains. Longest chain 28 peptides. Score 0.471 Round 2: 339 peptides, 40 chains. Longest chain 20 peptides. Score 0.512 Round 3: 340 peptides, 40 chains. Longest chain 23 peptides. Score 0.513 Round 4: 343 peptides, 40 chains. Longest chain 21 peptides. Score 0.518 Round 5: 333 peptides, 41 chains. Longest chain 25 peptides. Score 0.495 Taking the results from Round 4 Chains 42, Residues 303, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7906 restraints for refining 3753 atoms. 6607 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2637 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 37: After refmac, R = 0.2471 (Rfree = 0.000) for 3727 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 38: After refmac, R = 0.2416 (Rfree = 0.000) for 3723 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. Cycle 39: After refmac, R = 0.2368 (Rfree = 0.000) for 3710 atoms. Found 14 (28 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2355 (Rfree = 0.000) for 3707 atoms. Found 18 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 3885 seeds are put forward NCS extension: 12 residues added (15 deleted due to clashes), 3897 seeds are put forward Round 1: 311 peptides, 44 chains. Longest chain 17 peptides. Score 0.437 Round 2: 332 peptides, 39 chains. Longest chain 27 peptides. Score 0.508 Round 3: 334 peptides, 39 chains. Longest chain 27 peptides. Score 0.511 Round 4: 333 peptides, 38 chains. Longest chain 23 peptides. Score 0.517 Round 5: 314 peptides, 39 chains. Longest chain 16 peptides. Score 0.480 Taking the results from Round 4 Chains 41, Residues 295, Estimated correctness of the model 0.0 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7689 restraints for refining 3753 atoms. 6368 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2694 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 42: After refmac, R = 0.2539 (Rfree = 0.000) for 3740 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. Cycle 43: After refmac, R = 0.2561 (Rfree = 0.000) for 3725 atoms. Found 20 (28 requested) and removed 17 (14 requested) atoms. Cycle 44: After refmac, R = 0.2486 (Rfree = 0.000) for 3724 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 45: After refmac, R = 0.2509 (Rfree = 0.000) for 3728 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 3918 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3944 seeds are put forward Round 1: 320 peptides, 48 chains. Longest chain 19 peptides. Score 0.422 Round 2: 322 peptides, 40 chains. Longest chain 29 peptides. Score 0.485 Round 3: 327 peptides, 36 chains. Longest chain 29 peptides. Score 0.522 Round 4: 327 peptides, 43 chains. Longest chain 28 peptides. Score 0.471 Round 5: 319 peptides, 38 chains. Longest chain 19 peptides. Score 0.495 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 291, Estimated correctness of the model 1.1 % 5 chains (78 residues) have been docked in sequence Sequence coverage is 26 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 176 B and 189 B 37 chains (299 residues) following loop building 4 chains (90 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13912 reflections ( 99.78 % complete ) and 7251 restraints for refining 3752 atoms. 5720 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2710 (Rfree = 0.000) for 3752 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2595 (Rfree = 0.000) for 3706 atoms. Found 0 (28 requested) and removed 10 (14 requested) atoms. Cycle 48: After refmac, R = 0.2584 (Rfree = 0.000) for 3687 atoms. Found 0 (27 requested) and removed 9 (13 requested) atoms. Cycle 49: After refmac, R = 0.2713 (Rfree = 0.000) for 3667 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:27:45 GMT 2018 Job finished. TimeTaking 304.59 Used memory is bytes: 11125880