Sun 23 Dec 22:23:05 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-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/2avn-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-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 ============================================================ Sun 23 Dec 22:23:15 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-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 638 and 0 Target number of residues in the AU: 638 Target solvent content: 0.6456 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-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.6-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 3.600 Wilson plot Bfac: 75.33 12083 reflections ( 99.62 % complete ) and 0 restraints for refining 4609 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3593 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3461 (Rfree = 0.000) for 4609 atoms. Found 29 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 2.61 Search for helices and strands: 0 residues in 0 chains, 4722 seeds are put forward NCS extension: 0 residues added, 4722 seeds are put forward Round 1: 305 peptides, 42 chains. Longest chain 16 peptides. Score 0.437 Round 2: 345 peptides, 35 chains. Longest chain 28 peptides. Score 0.548 Round 3: 347 peptides, 31 chains. Longest chain 40 peptides. Score 0.578 Round 4: 360 peptides, 35 chains. Longest chain 29 peptides. Score 0.569 Round 5: 364 peptides, 34 chains. Longest chain 35 peptides. Score 0.581 Taking the results from Round 5 Chains 36, Residues 330, Estimated correctness of the model 7.1 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7743 restraints for refining 3819 atoms. 6335 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2946 (Rfree = 0.000) for 3819 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 2: After refmac, R = 0.2756 (Rfree = 0.000) for 3773 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 3: After refmac, R = 0.2675 (Rfree = 0.000) for 3750 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2520 (Rfree = 0.000) for 3740 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2532 (Rfree = 0.000) for 3738 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 3911 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3934 seeds are put forward Round 1: 356 peptides, 40 chains. Longest chain 23 peptides. Score 0.530 Round 2: 361 peptides, 36 chains. Longest chain 27 peptides. Score 0.564 Round 3: 364 peptides, 37 chains. Longest chain 25 peptides. Score 0.561 Round 4: 376 peptides, 36 chains. Longest chain 46 peptides. Score 0.584 Round 5: 369 peptides, 33 chains. Longest chain 44 peptides. Score 0.594 Taking the results from Round 5 Chains 34, Residues 336, Estimated correctness of the model 12.3 % 2 chains (61 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7661 restraints for refining 3859 atoms. 6100 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2893 (Rfree = 0.000) for 3859 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 7: After refmac, R = 0.3081 (Rfree = 0.000) for 3821 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 8: After refmac, R = 0.2677 (Rfree = 0.000) for 3794 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 9: After refmac, R = 0.2657 (Rfree = 0.000) for 3783 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 10: After refmac, R = 0.2632 (Rfree = 0.000) for 3774 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 3909 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 3941 seeds are put forward Round 1: 361 peptides, 42 chains. Longest chain 28 peptides. Score 0.524 Round 2: 379 peptides, 35 chains. Longest chain 26 peptides. Score 0.594 Round 3: 387 peptides, 36 chains. Longest chain 25 peptides. Score 0.598 Round 4: 384 peptides, 37 chains. Longest chain 30 peptides. Score 0.588 Round 5: 381 peptides, 36 chains. Longest chain 29 peptides. Score 0.590 Taking the results from Round 3 Chains 38, Residues 351, Estimated correctness of the model 13.9 % 4 chains (57 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7221 restraints for refining 3780 atoms. 5590 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2817 (Rfree = 0.000) for 3780 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 12: After refmac, R = 0.2668 (Rfree = 0.000) for 3758 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 13: After refmac, R = 0.2683 (Rfree = 0.000) for 3736 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 14: After refmac, R = 0.2542 (Rfree = 0.000) for 3724 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 15: After refmac, R = 0.2515 (Rfree = 0.000) for 3715 atoms. Found 19 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.55 Search for helices and strands: 0 residues in 0 chains, 3859 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3892 seeds are put forward Round 1: 371 peptides, 44 chains. Longest chain 26 peptides. Score 0.525 Round 2: 385 peptides, 33 chains. Longest chain 43 peptides. Score 0.614 Round 3: 362 peptides, 36 chains. Longest chain 24 peptides. Score 0.565 Round 4: 381 peptides, 33 chains. Longest chain 26 peptides. Score 0.609 Round 5: 382 peptides, 33 chains. Longest chain 31 peptides. Score 0.610 Taking the results from Round 2 Chains 34, Residues 352, Estimated correctness of the model 20.0 % 6 chains (96 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7008 restraints for refining 3835 atoms. 5181 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2710 (Rfree = 0.000) for 3835 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 17: After refmac, R = 0.2583 (Rfree = 0.000) for 3810 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2521 (Rfree = 0.000) for 3800 atoms. Found 24 (24 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2456 (Rfree = 0.000) for 3793 atoms. Found 19 (24 requested) and removed 14 (12 requested) atoms. Cycle 20: After refmac, R = 0.2395 (Rfree = 0.000) for 3786 atoms. Found 21 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 3924 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3943 seeds are put forward Round 1: 385 peptides, 40 chains. Longest chain 31 peptides. Score 0.570 Round 2: 370 peptides, 37 chains. Longest chain 26 peptides. Score 0.570 Round 3: 381 peptides, 36 chains. Longest chain 43 peptides. Score 0.590 Round 4: 390 peptides, 40 chains. Longest chain 27 peptides. Score 0.577 Round 5: 398 peptides, 35 chains. Longest chain 35 peptides. Score 0.618 Taking the results from Round 5 Chains 40, Residues 363, Estimated correctness of the model 21.6 % 6 chains (119 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7270 restraints for refining 4071 atoms. 5275 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2891 (Rfree = 0.000) for 4071 atoms. Found 26 (26 requested) and removed 42 (13 requested) atoms. Cycle 22: After refmac, R = 0.2652 (Rfree = 0.000) for 4032 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 23: After refmac, R = 0.2554 (Rfree = 0.000) for 4022 atoms. Found 10 (25 requested) and removed 19 (12 requested) atoms. Cycle 24: After refmac, R = 0.2529 (Rfree = 0.000) for 3995 atoms. Found 18 (25 requested) and removed 17 (12 requested) atoms. Cycle 25: After refmac, R = 0.2451 (Rfree = 0.000) for 3987 atoms. Found 14 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 2.60 Search for helices and strands: 0 residues in 0 chains, 4133 seeds are put forward NCS extension: 50 residues added (0 deleted due to clashes), 4183 seeds are put forward Round 1: 353 peptides, 40 chains. Longest chain 27 peptides. Score 0.526 Round 2: 378 peptides, 40 chains. Longest chain 24 peptides. Score 0.561 Round 3: 371 peptides, 39 chains. Longest chain 25 peptides. Score 0.558 Round 4: 384 peptides, 37 chains. Longest chain 27 peptides. Score 0.588 Round 5: 381 peptides, 37 chains. Longest chain 30 peptides. Score 0.584 Taking the results from Round 4 Chains 42, Residues 347, Estimated correctness of the model 9.9 % 4 chains (64 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7430 restraints for refining 3881 atoms. 5805 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2771 (Rfree = 0.000) for 3881 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.2575 (Rfree = 0.000) for 3858 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 28: After refmac, R = 0.2497 (Rfree = 0.000) for 3845 atoms. Found 18 (24 requested) and removed 14 (12 requested) atoms. Cycle 29: After refmac, R = 0.2550 (Rfree = 0.000) for 3826 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2397 (Rfree = 0.000) for 3821 atoms. Found 17 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 2.60 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3987 seeds are put forward Round 1: 342 peptides, 43 chains. Longest chain 26 peptides. Score 0.489 Round 2: 359 peptides, 38 chains. Longest chain 19 peptides. Score 0.548 Round 3: 359 peptides, 36 chains. Longest chain 24 peptides. Score 0.561 Round 4: 385 peptides, 33 chains. Longest chain 34 peptides. Score 0.614 Round 5: 386 peptides, 37 chains. Longest chain 29 peptides. Score 0.591 Taking the results from Round 4 Chains 38, Residues 352, Estimated correctness of the model 20.0 % 4 chains (76 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7651 restraints for refining 3936 atoms. 5967 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2708 (Rfree = 0.000) for 3936 atoms. Found 25 (25 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.2549 (Rfree = 0.000) for 3915 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2482 (Rfree = 0.000) for 3900 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2410 (Rfree = 0.000) for 3897 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2401 (Rfree = 0.000) for 3874 atoms. Found 15 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 2.58 Search for helices and strands: 0 residues in 0 chains, 4020 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 4034 seeds are put forward Round 1: 334 peptides, 40 chains. Longest chain 19 peptides. Score 0.498 Round 2: 364 peptides, 46 chains. Longest chain 29 peptides. Score 0.501 Round 3: 364 peptides, 42 chains. Longest chain 27 peptides. Score 0.528 Round 4: 373 peptides, 42 chains. Longest chain 21 peptides. Score 0.541 Round 5: 364 peptides, 37 chains. Longest chain 30 peptides. Score 0.561 Taking the results from Round 5 Chains 39, Residues 327, Estimated correctness of the model 0.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 8052 restraints for refining 3892 atoms. 6617 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2748 (Rfree = 0.000) for 3892 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 37: After refmac, R = 0.2536 (Rfree = 0.000) for 3881 atoms. Found 14 (25 requested) and removed 17 (12 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2478 (Rfree = 0.000) for 3864 atoms. Found 15 (24 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 3862 atoms. Found 12 (24 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2361 (Rfree = 0.000) for 3855 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.58 Search for helices and strands: 0 residues in 0 chains, 3996 seeds are put forward NCS extension: 45 residues added (3 deleted due to clashes), 4041 seeds are put forward Round 1: 334 peptides, 38 chains. Longest chain 23 peptides. Score 0.512 Round 2: 378 peptides, 39 chains. Longest chain 22 peptides. Score 0.567 Round 3: 389 peptides, 37 chains. Longest chain 31 peptides. Score 0.595 Round 4: 367 peptides, 38 chains. Longest chain 33 peptides. Score 0.559 Round 5: 375 peptides, 35 chains. Longest chain 29 peptides. Score 0.589 Taking the results from Round 3 Chains 42, Residues 352, Estimated correctness of the model 12.7 % 5 chains (91 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.62 % complete ) and 7404 restraints for refining 3898 atoms. 5635 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2628 (Rfree = 0.000) for 3898 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 42: After refmac, R = 0.2461 (Rfree = 0.000) for 3884 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 43: After refmac, R = 0.2341 (Rfree = 0.000) for 3886 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.2325 (Rfree = 0.000) for 3875 atoms. Found 7 (24 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2295 (Rfree = 0.000) for 3870 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 2.61 Search for helices and strands: 0 residues in 0 chains, 4022 seeds are put forward NCS extension: 28 residues added (7 deleted due to clashes), 4050 seeds are put forward Round 1: 352 peptides, 42 chains. Longest chain 19 peptides. Score 0.511 Round 2: 376 peptides, 35 chains. Longest chain 25 peptides. Score 0.590 Round 3: 381 peptides, 36 chains. Longest chain 38 peptides. Score 0.590 Round 4: 382 peptides, 34 chains. Longest chain 36 peptides. Score 0.604 Round 5: 370 peptides, 36 chains. Longest chain 29 peptides. Score 0.576 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 348, Estimated correctness of the model 16.2 % 4 chains (61 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 42 A and 49 A 37 chains (352 residues) following loop building 3 chains (67 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12083 reflections ( 99.62 % complete ) and 7450 restraints for refining 3814 atoms. 5821 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2639 (Rfree = 0.000) for 3814 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2407 (Rfree = 0.000) for 3780 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2331 (Rfree = 0.000) for 3754 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2252 (Rfree = 0.000) for 3732 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 76.17