null Mon 24 Dec 01:00:44 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 2avn-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-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/2avn-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-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 01:00:48 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/2avn-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-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 654 and 0 Target number of residues in the AU: 654 Target solvent content: 0.6367 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-3.4-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.15 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 3.400 Wilson plot Bfac: 70.16 14269 reflections ( 99.68 % complete ) and 0 restraints for refining 4609 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Starting model: R = 0.3539 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3240 (Rfree = 0.000) for 4609 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 2.45 Search for helices and strands: 0 residues in 0 chains, 4736 seeds are put forward NCS extension: 0 residues added, 4736 seeds are put forward Round 1: 350 peptides, 46 chains. Longest chain 24 peptides. Score 0.480 Round 2: 390 peptides, 40 chains. Longest chain 27 peptides. Score 0.577 Round 3: 386 peptides, 41 chains. Longest chain 28 peptides. Score 0.565 Round 4: 400 peptides, 36 chains. Longest chain 34 peptides. Score 0.615 Round 5: 376 peptides, 36 chains. Longest chain 31 peptides. Score 0.584 Taking the results from Round 4 Chains 37, Residues 364, Estimated correctness of the model 33.5 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7859 restraints for refining 4089 atoms. 6077 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2794 (Rfree = 0.000) for 4089 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 2: After refmac, R = 0.2608 (Rfree = 0.000) for 4012 atoms. Found 30 (30 requested) and removed 18 (15 requested) atoms. Cycle 3: After refmac, R = 0.2485 (Rfree = 0.000) for 3995 atoms. Found 20 (30 requested) and removed 17 (15 requested) atoms. Cycle 4: After refmac, R = 0.2404 (Rfree = 0.000) for 3982 atoms. Found 16 (30 requested) and removed 16 (15 requested) atoms. Cycle 5: After refmac, R = 0.2337 (Rfree = 0.000) for 3968 atoms. Found 10 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.50 Search for helices and strands: 0 residues in 0 chains, 4126 seeds are put forward NCS extension: 21 residues added (13 deleted due to clashes), 4147 seeds are put forward Round 1: 401 peptides, 38 chains. Longest chain 26 peptides. Score 0.604 Round 2: 417 peptides, 31 chains. Longest chain 50 peptides. Score 0.663 Round 3: 403 peptides, 27 chains. Longest chain 54 peptides. Score 0.670 Round 4: 404 peptides, 31 chains. Longest chain 40 peptides. Score 0.649 Round 5: 399 peptides, 32 chains. Longest chain 42 peptides. Score 0.637 Taking the results from Round 3 Chains 34, Residues 376, Estimated correctness of the model 49.8 % 9 chains (193 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6615 restraints for refining 4121 atoms. 4271 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2780 (Rfree = 0.000) for 4121 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 7: After refmac, R = 0.2607 (Rfree = 0.000) for 4076 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 8: After refmac, R = 0.2503 (Rfree = 0.000) for 4062 atoms. Found 19 (30 requested) and removed 15 (15 requested) atoms. Cycle 9: After refmac, R = 0.2464 (Rfree = 0.000) for 4058 atoms. Found 14 (30 requested) and removed 15 (15 requested) atoms. Cycle 10: After refmac, R = 0.2423 (Rfree = 0.000) for 4053 atoms. Found 17 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 2.49 Search for helices and strands: 0 residues in 0 chains, 4183 seeds are put forward NCS extension: 26 residues added (19 deleted due to clashes), 4209 seeds are put forward Round 1: 392 peptides, 37 chains. Longest chain 27 peptides. Score 0.598 Round 2: 394 peptides, 34 chains. Longest chain 28 peptides. Score 0.619 Round 3: 413 peptides, 35 chains. Longest chain 32 peptides. Score 0.636 Round 4: 415 peptides, 35 chains. Longest chain 34 peptides. Score 0.639 Round 5: 397 peptides, 38 chains. Longest chain 40 peptides. Score 0.599 Taking the results from Round 4 Chains 37, Residues 380, Estimated correctness of the model 40.9 % 5 chains (100 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7175 restraints for refining 3953 atoms. 5244 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2751 (Rfree = 0.000) for 3953 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 12: After refmac, R = 0.2559 (Rfree = 0.000) for 3921 atoms. Found 25 (29 requested) and removed 14 (14 requested) atoms. Cycle 13: After refmac, R = 0.2491 (Rfree = 0.000) for 3914 atoms. Found 24 (29 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.2389 (Rfree = 0.000) for 3915 atoms. Found 12 (29 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2356 (Rfree = 0.000) for 3903 atoms. Found 14 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 2.46 Search for helices and strands: 0 residues in 0 chains, 4025 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 4059 seeds are put forward Round 1: 401 peptides, 44 chains. Longest chain 25 peptides. Score 0.567 Round 2: 400 peptides, 37 chains. Longest chain 28 peptides. Score 0.608 Round 3: 412 peptides, 35 chains. Longest chain 39 peptides. Score 0.635 Round 4: 400 peptides, 33 chains. Longest chain 43 peptides. Score 0.632 Round 5: 418 peptides, 39 chains. Longest chain 40 peptides. Score 0.619 Taking the results from Round 3 Chains 35, Residues 377, Estimated correctness of the model 39.7 % 6 chains (137 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6922 restraints for refining 3979 atoms. 4855 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2731 (Rfree = 0.000) for 3979 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 17: After refmac, R = 0.2621 (Rfree = 0.000) for 3952 atoms. Found 29 (30 requested) and removed 19 (15 requested) atoms. Cycle 18: After refmac, R = 0.2609 (Rfree = 0.000) for 3944 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 19: After refmac, R = 0.2466 (Rfree = 0.000) for 3947 atoms. Found 9 (29 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.2424 (Rfree = 0.000) for 3932 atoms. Found 16 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 2.48 Search for helices and strands: 0 residues in 0 chains, 4084 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 4104 seeds are put forward Round 1: 399 peptides, 44 chains. Longest chain 38 peptides. Score 0.564 Round 2: 413 peptides, 38 chains. Longest chain 36 peptides. Score 0.619 Round 3: 400 peptides, 36 chains. Longest chain 48 peptides. Score 0.615 Round 4: 421 peptides, 36 chains. Longest chain 40 peptides. Score 0.640 Round 5: 420 peptides, 41 chains. Longest chain 38 peptides. Score 0.609 Taking the results from Round 4 Chains 37, Residues 385, Estimated correctness of the model 41.2 % 4 chains (125 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7144 restraints for refining 3972 atoms. 5064 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2739 (Rfree = 0.000) for 3972 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 22: After refmac, R = 0.2559 (Rfree = 0.000) for 3961 atoms. Found 27 (30 requested) and removed 18 (15 requested) atoms. Cycle 23: After refmac, R = 0.2433 (Rfree = 0.000) for 3964 atoms. Found 12 (29 requested) and removed 17 (14 requested) atoms. Cycle 24: After refmac, R = 0.2406 (Rfree = 0.000) for 3950 atoms. Found 5 (29 requested) and removed 16 (14 requested) atoms. Cycle 25: After refmac, R = 0.2359 (Rfree = 0.000) for 3935 atoms. Found 11 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.47 Search for helices and strands: 0 residues in 0 chains, 4045 seeds are put forward NCS extension: 29 residues added (15 deleted due to clashes), 4074 seeds are put forward Round 1: 405 peptides, 42 chains. Longest chain 34 peptides. Score 0.584 Round 2: 413 peptides, 36 chains. Longest chain 29 peptides. Score 0.630 Round 3: 419 peptides, 35 chains. Longest chain 44 peptides. Score 0.643 Round 4: 407 peptides, 36 chains. Longest chain 34 peptides. Score 0.623 Round 5: 412 peptides, 38 chains. Longest chain 44 peptides. Score 0.617 Taking the results from Round 3 Chains 36, Residues 384, Estimated correctness of the model 42.1 % 4 chains (96 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7409 restraints for refining 3976 atoms. 5461 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2599 (Rfree = 0.000) for 3976 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. Cycle 27: After refmac, R = 0.2460 (Rfree = 0.000) for 3967 atoms. Found 22 (30 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2331 (Rfree = 0.000) for 3950 atoms. Found 27 (29 requested) and removed 18 (14 requested) atoms. Cycle 29: After refmac, R = 0.2225 (Rfree = 0.000) for 3952 atoms. Found 19 (29 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2163 (Rfree = 0.000) for 3947 atoms. Found 19 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 2.47 Search for helices and strands: 0 residues in 0 chains, 4079 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 4096 seeds are put forward Round 1: 377 peptides, 37 chains. Longest chain 51 peptides. Score 0.579 Round 2: 406 peptides, 32 chains. Longest chain 34 peptides. Score 0.645 Round 3: 413 peptides, 35 chains. Longest chain 43 peptides. Score 0.636 Round 4: 409 peptides, 36 chains. Longest chain 32 peptides. Score 0.626 Round 5: 418 peptides, 34 chains. Longest chain 38 peptides. Score 0.648 Taking the results from Round 5 Chains 39, Residues 384, Estimated correctness of the model 43.6 % 6 chains (138 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7178 restraints for refining 4097 atoms. 5046 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2678 (Rfree = 0.000) for 4097 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 32: After refmac, R = 0.2377 (Rfree = 0.000) for 4078 atoms. Found 18 (30 requested) and removed 17 (15 requested) atoms. Cycle 33: After refmac, R = 0.2303 (Rfree = 0.000) for 4064 atoms. Found 20 (30 requested) and removed 17 (15 requested) atoms. Cycle 34: After refmac, R = 0.2209 (Rfree = 0.000) for 4056 atoms. Found 10 (30 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.2170 (Rfree = 0.000) for 4043 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.50 Search for helices and strands: 0 residues in 0 chains, 4155 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 4175 seeds are put forward Round 1: 381 peptides, 33 chains. Longest chain 26 peptides. Score 0.609 Round 2: 409 peptides, 32 chains. Longest chain 51 peptides. Score 0.649 Round 3: 396 peptides, 38 chains. Longest chain 27 peptides. Score 0.597 Round 4: 391 peptides, 38 chains. Longest chain 33 peptides. Score 0.591 Round 5: 398 peptides, 37 chains. Longest chain 36 peptides. Score 0.606 Taking the results from Round 2 Chains 32, Residues 377, Estimated correctness of the model 43.8 % 8 chains (201 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6933 restraints for refining 4179 atoms. 4520 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2911 (Rfree = 0.000) for 4179 atoms. Found 31 (31 requested) and removed 42 (15 requested) atoms. Cycle 37: After refmac, R = 0.2391 (Rfree = 0.000) for 4139 atoms. Found 29 (31 requested) and removed 22 (15 requested) atoms. Cycle 38: After refmac, R = 0.2220 (Rfree = 0.000) for 4127 atoms. Found 17 (31 requested) and removed 19 (15 requested) atoms. Cycle 39: After refmac, R = 0.2156 (Rfree = 0.000) for 4107 atoms. Found 18 (31 requested) and removed 18 (15 requested) atoms. Cycle 40: After refmac, R = 0.2110 (Rfree = 0.000) for 4100 atoms. Found 12 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 2.48 Search for helices and strands: 0 residues in 0 chains, 4228 seeds are put forward NCS extension: 16 residues added (15 deleted due to clashes), 4244 seeds are put forward Round 1: 392 peptides, 42 chains. Longest chain 34 peptides. Score 0.567 Round 2: 410 peptides, 32 chains. Longest chain 33 peptides. Score 0.650 Round 3: 411 peptides, 32 chains. Longest chain 54 peptides. Score 0.651 Round 4: 421 peptides, 30 chains. Longest chain 44 peptides. Score 0.673 Round 5: 412 peptides, 32 chains. Longest chain 41 peptides. Score 0.652 Taking the results from Round 4 Chains 34, Residues 391, Estimated correctness of the model 50.7 % 7 chains (173 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6938 restraints for refining 4070 atoms. 4642 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2933 (Rfree = 0.000) for 4070 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Cycle 42: After refmac, R = 0.2536 (Rfree = 0.000) for 4053 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 43: After refmac, R = 0.2472 (Rfree = 0.000) for 4045 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Cycle 44: After refmac, R = 0.2256 (Rfree = 0.000) for 4042 atoms. Found 19 (30 requested) and removed 17 (15 requested) atoms. Cycle 45: After refmac, R = 0.2216 (Rfree = 0.000) for 4038 atoms. Found 10 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.49 Search for helices and strands: 0 residues in 0 chains, 4145 seeds are put forward NCS extension: 17 residues added (32 deleted due to clashes), 4162 seeds are put forward Round 1: 406 peptides, 38 chains. Longest chain 34 peptides. Score 0.610 Round 2: 433 peptides, 39 chains. Longest chain 34 peptides. Score 0.637 Round 3: 410 peptides, 34 chains. Longest chain 44 peptides. Score 0.638 Round 4: 413 peptides, 33 chains. Longest chain 44 peptides. Score 0.648 Round 5: 411 peptides, 34 chains. Longest chain 36 peptides. Score 0.640 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 380, Estimated correctness of the model 43.6 % 6 chains (150 residues) have been docked in sequence Sequence coverage is 39 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 85 A and 90 A Built loop between residues 132 A and 145 A Built loop between residues 160 A and 172 A 29 chains (403 residues) following loop building 3 chains (177 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14269 reflections ( 99.68 % complete ) and 6995 restraints for refining 4146 atoms. 4648 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2675 (Rfree = 0.000) for 4146 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2548 (Rfree = 0.000) for 4102 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2759 (Rfree = 0.000) for 4073 atoms. Found 0 (30 requested) and removed 14 (15 requested) atoms. Cycle 49: After refmac, R = 0.2524 (Rfree = 0.000) for 4042 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:56:15 GMT 2018 Job finished. TimeTaking 55.52 Used memory is bytes: 5355424