Mon 24 Dec 01:10:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2a2m-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a2m-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-parrot-mrncs ############### 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 01:10:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a2m-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 4605 atoms. Observations/parameters ratio is 0.76 ------------------------------------------------------ Starting model: R = 0.3242 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3006 (Rfree = 0.000) for 4605 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 4769 seeds are put forward NCS extension: 0 residues added, 4769 seeds are put forward Round 1: 349 peptides, 52 chains. Longest chain 23 peptides. Score 0.440 Round 2: 361 peptides, 46 chains. Longest chain 20 peptides. Score 0.503 Round 3: 353 peptides, 39 chains. Longest chain 27 peptides. Score 0.539 Round 4: 367 peptides, 44 chains. Longest chain 26 peptides. Score 0.526 Round 5: 362 peptides, 43 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 3 Chains 42, Residues 314, Estimated correctness of the model 7.4 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7803 restraints for refining 3863 atoms. 6391 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2615 (Rfree = 0.000) for 3863 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 2: After refmac, R = 0.2466 (Rfree = 0.000) for 3808 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 3790 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 4: After refmac, R = 0.2313 (Rfree = 0.000) for 3782 atoms. Found 21 (28 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.2280 (Rfree = 0.000) for 3776 atoms. Found 11 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 3962 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3995 seeds are put forward Round 1: 331 peptides, 41 chains. Longest chain 38 peptides. Score 0.492 Round 2: 355 peptides, 41 chains. Longest chain 20 peptides. Score 0.529 Round 3: 348 peptides, 38 chains. Longest chain 24 peptides. Score 0.539 Round 4: 374 peptides, 40 chains. Longest chain 21 peptides. Score 0.563 Round 5: 373 peptides, 37 chains. Longest chain 23 peptides. Score 0.581 Taking the results from Round 5 Chains 43, Residues 336, Estimated correctness of the model 22.3 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7357 restraints for refining 3752 atoms. 5848 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2717 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 7: After refmac, R = 0.2523 (Rfree = 0.000) for 3724 atoms. Found 25 (28 requested) and removed 19 (14 requested) atoms. Cycle 8: After refmac, R = 0.2455 (Rfree = 0.000) for 3711 atoms. Found 16 (28 requested) and removed 19 (14 requested) atoms. Cycle 9: After refmac, R = 0.2399 (Rfree = 0.000) for 3697 atoms. Found 12 (27 requested) and removed 23 (13 requested) atoms. Cycle 10: After refmac, R = 0.2367 (Rfree = 0.000) for 3675 atoms. Found 17 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.44 Search for helices and strands: 0 residues in 0 chains, 3860 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3869 seeds are put forward Round 1: 355 peptides, 44 chains. Longest chain 25 peptides. Score 0.508 Round 2: 360 peptides, 35 chains. Longest chain 27 peptides. Score 0.576 Round 3: 355 peptides, 37 chains. Longest chain 24 peptides. Score 0.556 Round 4: 362 peptides, 35 chains. Longest chain 31 peptides. Score 0.579 Round 5: 369 peptides, 43 chains. Longest chain 23 peptides. Score 0.535 Taking the results from Round 4 Chains 39, Residues 327, Estimated correctness of the model 21.6 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7398 restraints for refining 3752 atoms. 5865 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2743 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 12: After refmac, R = 0.2592 (Rfree = 0.000) for 3720 atoms. Found 27 (28 requested) and removed 19 (14 requested) atoms. Cycle 13: After refmac, R = 0.2498 (Rfree = 0.000) for 3693 atoms. Found 17 (28 requested) and removed 23 (14 requested) atoms. Cycle 14: After refmac, R = 0.2433 (Rfree = 0.000) for 3668 atoms. Found 14 (27 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.2429 (Rfree = 0.000) for 3655 atoms. Found 8 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 3792 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3808 seeds are put forward Round 1: 346 peptides, 39 chains. Longest chain 32 peptides. Score 0.529 Round 2: 358 peptides, 36 chains. Longest chain 29 peptides. Score 0.567 Round 3: 354 peptides, 38 chains. Longest chain 25 peptides. Score 0.548 Round 4: 366 peptides, 36 chains. Longest chain 22 peptides. Score 0.578 Round 5: 353 peptides, 37 chains. Longest chain 18 peptides. Score 0.553 Taking the results from Round 4 Chains 37, Residues 330, Estimated correctness of the model 21.3 % 6 chains (78 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7158 restraints for refining 3752 atoms. 5538 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2703 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 17: After refmac, R = 0.2494 (Rfree = 0.000) for 3714 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 18: After refmac, R = 0.2400 (Rfree = 0.000) for 3696 atoms. Found 19 (28 requested) and removed 20 (14 requested) atoms. Cycle 19: After refmac, R = 0.2361 (Rfree = 0.000) for 3678 atoms. Found 19 (27 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2323 (Rfree = 0.000) for 3670 atoms. Found 17 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 2.46 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3876 seeds are put forward Round 1: 334 peptides, 43 chains. Longest chain 17 peptides. Score 0.482 Round 2: 356 peptides, 40 chains. Longest chain 20 peptides. Score 0.537 Round 3: 351 peptides, 38 chains. Longest chain 16 peptides. Score 0.543 Round 4: 341 peptides, 36 chains. Longest chain 24 peptides. Score 0.543 Round 5: 351 peptides, 36 chains. Longest chain 24 peptides. Score 0.557 Taking the results from Round 5 Chains 43, Residues 315, Estimated correctness of the model 13.9 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7539 restraints for refining 3753 atoms. 6085 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2562 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 22: After refmac, R = 0.2359 (Rfree = 0.000) for 3731 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 23: After refmac, R = 0.2293 (Rfree = 0.000) for 3721 atoms. Found 23 (28 requested) and removed 16 (14 requested) atoms. Cycle 24: After refmac, R = 0.2225 (Rfree = 0.000) for 3718 atoms. Found 17 (28 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2224 (Rfree = 0.000) for 3707 atoms. Found 17 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 2.41 Search for helices and strands: 0 residues in 0 chains, 3887 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3906 seeds are put forward Round 1: 304 peptides, 40 chains. Longest chain 22 peptides. Score 0.456 Round 2: 349 peptides, 43 chains. Longest chain 21 peptides. Score 0.506 Round 3: 374 peptides, 38 chains. Longest chain 30 peptides. Score 0.576 Round 4: 350 peptides, 40 chains. Longest chain 25 peptides. Score 0.528 Round 5: 335 peptides, 37 chains. Longest chain 29 peptides. Score 0.527 Taking the results from Round 3 Chains 41, Residues 336, Estimated correctness of the model 20.6 % 6 chains (73 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7162 restraints for refining 3753 atoms. 5573 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2616 (Rfree = 0.000) for 3753 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 27: After refmac, R = 0.2493 (Rfree = 0.000) for 3719 atoms. Found 25 (28 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.2630 (Rfree = 0.000) for 3715 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 29: After refmac, R = 0.2460 (Rfree = 0.000) for 3704 atoms. Found 16 (28 requested) and removed 24 (14 requested) atoms. Cycle 30: After refmac, R = 0.2369 (Rfree = 0.000) for 3692 atoms. Found 12 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 3871 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3894 seeds are put forward Round 1: 332 peptides, 46 chains. Longest chain 17 peptides. Score 0.457 Round 2: 350 peptides, 40 chains. Longest chain 17 peptides. Score 0.528 Round 3: 350 peptides, 42 chains. Longest chain 20 peptides. Score 0.514 Round 4: 336 peptides, 36 chains. Longest chain 23 peptides. Score 0.535 Round 5: 349 peptides, 41 chains. Longest chain 23 peptides. Score 0.520 Taking the results from Round 4 Chains 40, Residues 300, Estimated correctness of the model 6.0 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7816 restraints for refining 3752 atoms. 6454 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2627 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 32: After refmac, R = 0.2480 (Rfree = 0.000) for 3745 atoms. Found 15 (28 requested) and removed 20 (14 requested) atoms. Cycle 33: After refmac, R = 0.2566 (Rfree = 0.000) for 3728 atoms. Found 17 (28 requested) and removed 27 (14 requested) atoms. Cycle 34: After refmac, R = 0.2430 (Rfree = 0.000) for 3713 atoms. Found 19 (28 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.2469 (Rfree = 0.000) for 3709 atoms. Found 22 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.43 Search for helices and strands: 0 residues in 0 chains, 3870 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3887 seeds are put forward Round 1: 327 peptides, 41 chains. Longest chain 22 peptides. Score 0.486 Round 2: 339 peptides, 43 chains. Longest chain 28 peptides. Score 0.490 Round 3: 349 peptides, 38 chains. Longest chain 24 peptides. Score 0.540 Round 4: 354 peptides, 41 chains. Longest chain 19 peptides. Score 0.527 Round 5: 340 peptides, 41 chains. Longest chain 18 peptides. Score 0.506 Taking the results from Round 3 Chains 42, Residues 311, Estimated correctness of the model 7.8 % 6 chains (67 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7572 restraints for refining 3752 atoms. 6125 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2548 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 37: After refmac, R = 0.2420 (Rfree = 0.000) for 3735 atoms. Found 15 (28 requested) and removed 20 (14 requested) atoms. Cycle 38: After refmac, R = 0.2322 (Rfree = 0.000) for 3726 atoms. Found 13 (28 requested) and removed 21 (14 requested) atoms. Cycle 39: After refmac, R = 0.2400 (Rfree = 0.000) for 3705 atoms. Found 25 (28 requested) and removed 16 (14 requested) atoms. Cycle 40: After refmac, R = 0.2310 (Rfree = 0.000) for 3707 atoms. Found 14 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 2.44 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 3898 seeds are put forward Round 1: 348 peptides, 40 chains. Longest chain 24 peptides. Score 0.525 Round 2: 362 peptides, 41 chains. Longest chain 25 peptides. Score 0.539 Round 3: 335 peptides, 35 chains. Longest chain 31 peptides. Score 0.541 Round 4: 345 peptides, 41 chains. Longest chain 19 peptides. Score 0.514 Round 5: 342 peptides, 37 chains. Longest chain 24 peptides. Score 0.537 Taking the results from Round 3 Chains 36, Residues 300, Estimated correctness of the model 8.2 % 6 chains (90 residues) have been docked in sequence ------------------------------------------------------ 13912 reflections ( 99.78 % complete ) and 7355 restraints for refining 3752 atoms. 5807 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2645 (Rfree = 0.000) for 3752 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 42: After refmac, R = 0.2486 (Rfree = 0.000) for 3722 atoms. Found 27 (28 requested) and removed 20 (14 requested) atoms. Cycle 43: After refmac, R = 0.2422 (Rfree = 0.000) for 3716 atoms. Found 21 (28 requested) and removed 22 (14 requested) atoms. Cycle 44: After refmac, R = 0.2394 (Rfree = 0.000) for 3705 atoms. Found 14 (28 requested) and removed 19 (14 requested) atoms. Cycle 45: After refmac, R = 0.2361 (Rfree = 0.000) for 3690 atoms. Found 12 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.43 Search for helices and strands: 0 residues in 0 chains, 3840 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3867 seeds are put forward Round 1: 321 peptides, 43 chains. Longest chain 14 peptides. Score 0.461 Round 2: 342 peptides, 39 chains. Longest chain 29 peptides. Score 0.523 Round 3: 335 peptides, 40 chains. Longest chain 23 peptides. Score 0.505 Round 4: 343 peptides, 40 chains. Longest chain 30 peptides. Score 0.518 Round 5: 333 peptides, 39 chains. Longest chain 23 peptides. Score 0.510 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 303, Estimated correctness of the model 1.5 % 7 chains (95 residues) have been docked in sequence Sequence coverage is 31 % Consider running further cycles of model building using 2a2m-3_warpNtrace.pdb as input Building loops using Loopy2018 39 chains (303 residues) following loop building 7 chains (95 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13912 reflections ( 99.78 % complete ) and 7363 restraints for refining 3753 atoms. 5804 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2611 (Rfree = 0.000) for 3753 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2528 (Rfree = 0.000) for 3716 atoms. Found 0 (28 requested) and removed 12 (14 requested) atoms. Cycle 48: After refmac, R = 0.2545 (Rfree = 0.000) for 3695 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2516 (Rfree = 0.000) for 3677 atoms. Found 0 (27 requested) and removed 4 (13 requested) atoms. TimeTaking 328.08