null Mon 24 Dec 07:47:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2avn-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2avn-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2avn-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.4-parrot-noncs ############### 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 07:47:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-3.4-parrot-noncs/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-noncs.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-noncs.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 4637 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Starting model: R = 0.3599 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3270 (Rfree = 0.000) for 4637 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 2.46 Search for helices and strands: 0 residues in 0 chains, 4760 seeds are put forward NCS extension: 0 residues added, 4760 seeds are put forward Round 1: 361 peptides, 47 chains. Longest chain 18 peptides. Score 0.489 Round 2: 374 peptides, 40 chains. Longest chain 21 peptides. Score 0.555 Round 3: 371 peptides, 39 chains. Longest chain 20 peptides. Score 0.558 Round 4: 379 peptides, 36 chains. Longest chain 25 peptides. Score 0.588 Round 5: 383 peptides, 32 chains. Longest chain 31 peptides. Score 0.618 Taking the results from Round 5 Chains 36, Residues 351, Estimated correctness of the model 34.4 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7934 restraints for refining 4013 atoms. 6284 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 4013 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 2: After refmac, R = 0.2660 (Rfree = 0.000) for 3955 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. Cycle 3: After refmac, R = 0.2526 (Rfree = 0.000) for 3944 atoms. Found 19 (29 requested) and removed 15 (14 requested) atoms. Cycle 4: After refmac, R = 0.2469 (Rfree = 0.000) for 3938 atoms. Found 15 (29 requested) and removed 16 (14 requested) atoms. Cycle 5: After refmac, R = 0.2445 (Rfree = 0.000) for 3923 atoms. Found 22 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.45 Search for helices and strands: 0 residues in 0 chains, 4093 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 4113 seeds are put forward Round 1: 405 peptides, 42 chains. Longest chain 37 peptides. Score 0.584 Round 2: 411 peptides, 37 chains. Longest chain 26 peptides. Score 0.622 Round 3: 400 peptides, 36 chains. Longest chain 33 peptides. Score 0.615 Round 4: 402 peptides, 38 chains. Longest chain 39 peptides. Score 0.605 Round 5: 412 peptides, 36 chains. Longest chain 36 peptides. Score 0.629 Taking the results from Round 5 Chains 37, Residues 376, Estimated correctness of the model 37.9 % 4 chains (112 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7414 restraints for refining 4061 atoms. 5440 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2736 (Rfree = 0.000) for 4061 atoms. Found 30 (30 requested) and removed 19 (15 requested) atoms. Cycle 7: After refmac, R = 0.2527 (Rfree = 0.000) for 4039 atoms. Found 25 (30 requested) and removed 21 (15 requested) atoms. Cycle 8: After refmac, R = 0.2387 (Rfree = 0.000) for 4027 atoms. Found 19 (30 requested) and removed 21 (15 requested) atoms. Cycle 9: After refmac, R = 0.2294 (Rfree = 0.000) for 4020 atoms. Found 12 (30 requested) and removed 20 (15 requested) atoms. Cycle 10: After refmac, R = 0.2339 (Rfree = 0.000) for 4008 atoms. Found 18 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 2.46 Search for helices and strands: 0 residues in 0 chains, 4163 seeds are put forward NCS extension: 49 residues added (3 deleted due to clashes), 4212 seeds are put forward Round 1: 391 peptides, 35 chains. Longest chain 26 peptides. Score 0.609 Round 2: 385 peptides, 36 chains. Longest chain 27 peptides. Score 0.596 Round 3: 404 peptides, 35 chains. Longest chain 33 peptides. Score 0.625 Round 4: 409 peptides, 33 chains. Longest chain 41 peptides. Score 0.643 Round 5: 407 peptides, 34 chains. Longest chain 35 peptides. Score 0.635 Taking the results from Round 4 Chains 38, Residues 376, Estimated correctness of the model 42.1 % 6 chains (116 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7528 restraints for refining 4152 atoms. 5476 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2696 (Rfree = 0.000) for 4152 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 12: After refmac, R = 0.2495 (Rfree = 0.000) for 4121 atoms. Found 29 (31 requested) and removed 19 (15 requested) atoms. Cycle 13: After refmac, R = 0.2413 (Rfree = 0.000) for 4121 atoms. Found 15 (31 requested) and removed 18 (15 requested) atoms. Cycle 14: After refmac, R = 0.2349 (Rfree = 0.000) for 4115 atoms. Found 7 (31 requested) and removed 20 (15 requested) atoms. Cycle 15: After refmac, R = 0.2296 (Rfree = 0.000) for 4100 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.49 Search for helices and strands: 0 residues in 0 chains, 4232 seeds are put forward NCS extension: 17 residues added (9 deleted due to clashes), 4249 seeds are put forward Round 1: 398 peptides, 38 chains. Longest chain 35 peptides. Score 0.600 Round 2: 411 peptides, 34 chains. Longest chain 26 peptides. Score 0.640 Round 3: 401 peptides, 29 chains. Longest chain 46 peptides. Score 0.657 Round 4: 402 peptides, 34 chains. Longest chain 54 peptides. Score 0.629 Round 5: 401 peptides, 34 chains. Longest chain 30 peptides. Score 0.628 Taking the results from Round 3 Chains 30, Residues 372, Estimated correctness of the model 46.2 % 5 chains (149 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7457 restraints for refining 4165 atoms. 5378 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2666 (Rfree = 0.000) for 4165 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 17: After refmac, R = 0.2676 (Rfree = 0.000) for 4146 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. Cycle 18: After refmac, R = 0.2546 (Rfree = 0.000) for 4136 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 19: After refmac, R = 0.2310 (Rfree = 0.000) for 4125 atoms. Found 20 (31 requested) and removed 18 (15 requested) atoms. Cycle 20: After refmac, R = 0.2277 (Rfree = 0.000) for 4119 atoms. Found 8 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.46 Search for helices and strands: 0 residues in 0 chains, 4231 seeds are put forward NCS extension: 35 residues added (5 deleted due to clashes), 4266 seeds are put forward Round 1: 386 peptides, 39 chains. Longest chain 28 peptides. Score 0.578 Round 2: 412 peptides, 36 chains. Longest chain 36 peptides. Score 0.629 Round 3: 401 peptides, 36 chains. Longest chain 28 peptides. Score 0.616 Round 4: 400 peptides, 31 chains. Longest chain 54 peptides. Score 0.644 Round 5: 407 peptides, 34 chains. Longest chain 28 peptides. Score 0.635 Taking the results from Round 4 Chains 36, Residues 369, Estimated correctness of the model 42.4 % 7 chains (176 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7261 restraints for refining 4199 atoms. 5052 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2638 (Rfree = 0.000) for 4199 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 22: After refmac, R = 0.2465 (Rfree = 0.000) for 4162 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 23: After refmac, R = 0.2319 (Rfree = 0.000) for 4154 atoms. Found 20 (31 requested) and removed 17 (15 requested) atoms. Cycle 24: After refmac, R = 0.2280 (Rfree = 0.000) for 4127 atoms. Found 16 (31 requested) and removed 20 (15 requested) atoms. Cycle 25: After refmac, R = 0.2111 (Rfree = 0.000) for 4115 atoms. Found 8 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 2.45 Search for helices and strands: 0 residues in 0 chains, 4222 seeds are put forward NCS extension: 36 residues added (15 deleted due to clashes), 4258 seeds are put forward Round 1: 408 peptides, 41 chains. Longest chain 32 peptides. Score 0.594 Round 2: 425 peptides, 34 chains. Longest chain 36 peptides. Score 0.656 Round 3: 433 peptides, 37 chains. Longest chain 33 peptides. Score 0.648 Round 4: 423 peptides, 35 chains. Longest chain 34 peptides. Score 0.648 Round 5: 420 peptides, 33 chains. Longest chain 44 peptides. Score 0.656 Taking the results from Round 5 Chains 36, Residues 387, Estimated correctness of the model 45.9 % 7 chains (173 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6986 restraints for refining 4188 atoms. 4652 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2724 (Rfree = 0.000) for 4188 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 27: After refmac, R = 0.2456 (Rfree = 0.000) for 4158 atoms. Found 25 (31 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2516 (Rfree = 0.000) for 4148 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 29: After refmac, R = 0.2239 (Rfree = 0.000) for 4138 atoms. Found 19 (31 requested) and removed 18 (15 requested) atoms. Cycle 30: After refmac, R = 0.2292 (Rfree = 0.000) for 4129 atoms. Found 18 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.48 Search for helices and strands: 0 residues in 0 chains, 4283 seeds are put forward NCS extension: 26 residues added (18 deleted due to clashes), 4309 seeds are put forward Round 1: 410 peptides, 38 chains. Longest chain 34 peptides. Score 0.615 Round 2: 425 peptides, 37 chains. Longest chain 55 peptides. Score 0.639 Round 3: 426 peptides, 36 chains. Longest chain 44 peptides. Score 0.646 Round 4: 414 peptides, 30 chains. Longest chain 51 peptides. Score 0.666 Round 5: 422 peptides, 33 chains. Longest chain 51 peptides. Score 0.658 Taking the results from Round 4 Chains 34, Residues 384, Estimated correctness of the model 48.7 % 6 chains (158 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7301 restraints for refining 4169 atoms. 5110 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2752 (Rfree = 0.000) for 4169 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 32: After refmac, R = 0.2537 (Rfree = 0.000) for 4147 atoms. Found 26 (31 requested) and removed 20 (15 requested) atoms. Cycle 33: After refmac, R = 0.2438 (Rfree = 0.000) for 4135 atoms. Found 24 (31 requested) and removed 17 (15 requested) atoms. Cycle 34: After refmac, R = 0.2310 (Rfree = 0.000) for 4133 atoms. Found 17 (31 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.2226 (Rfree = 0.000) for 4125 atoms. Found 15 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 2.47 Search for helices and strands: 0 residues in 0 chains, 4245 seeds are put forward NCS extension: 58 residues added (17 deleted due to clashes), 4303 seeds are put forward Round 1: 406 peptides, 41 chains. Longest chain 26 peptides. Score 0.592 Round 2: 415 peptides, 32 chains. Longest chain 51 peptides. Score 0.656 Round 3: 400 peptides, 35 chains. Longest chain 32 peptides. Score 0.621 Round 4: 414 peptides, 31 chains. Longest chain 46 peptides. Score 0.660 Round 5: 390 peptides, 36 chains. Longest chain 27 peptides. Score 0.602 Taking the results from Round 4 Chains 35, Residues 383, Estimated correctness of the model 47.0 % 8 chains (179 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7098 restraints for refining 4200 atoms. 4809 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2593 (Rfree = 0.000) for 4200 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 37: After refmac, R = 0.2381 (Rfree = 0.000) for 4180 atoms. Found 18 (31 requested) and removed 16 (15 requested) atoms. Cycle 38: After refmac, R = 0.2277 (Rfree = 0.000) for 4171 atoms. Found 13 (31 requested) and removed 17 (15 requested) atoms. Cycle 39: After refmac, R = 0.2423 (Rfree = 0.000) for 4160 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 40: After refmac, R = 0.2219 (Rfree = 0.000) for 4163 atoms. Found 15 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.49 Search for helices and strands: 0 residues in 0 chains, 4283 seeds are put forward NCS extension: 28 residues added (23 deleted due to clashes), 4311 seeds are put forward Round 1: 380 peptides, 43 chains. Longest chain 23 peptides. Score 0.544 Round 2: 403 peptides, 32 chains. Longest chain 46 peptides. Score 0.642 Round 3: 405 peptides, 35 chains. Longest chain 31 peptides. Score 0.627 Round 4: 403 peptides, 31 chains. Longest chain 35 peptides. Score 0.648 Round 5: 412 peptides, 34 chains. Longest chain 27 peptides. Score 0.641 Taking the results from Round 4 Chains 35, Residues 372, Estimated correctness of the model 43.6 % 6 chains (133 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7301 restraints for refining 4037 atoms. 5297 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2642 (Rfree = 0.000) for 4037 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 42: After refmac, R = 0.2421 (Rfree = 0.000) for 4031 atoms. Found 17 (30 requested) and removed 21 (15 requested) atoms. Cycle 43: After refmac, R = 0.2581 (Rfree = 0.000) for 4018 atoms. Found 23 (30 requested) and removed 17 (15 requested) atoms. Cycle 44: After refmac, R = 0.2498 (Rfree = 0.000) for 4014 atoms. Found 30 (30 requested) and removed 16 (15 requested) atoms. Cycle 45: After refmac, R = 0.2296 (Rfree = 0.000) for 4019 atoms. Found 12 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.50 Search for helices and strands: 0 residues in 0 chains, 4156 seeds are put forward NCS extension: 37 residues added (12 deleted due to clashes), 4193 seeds are put forward Round 1: 389 peptides, 41 chains. Longest chain 27 peptides. Score 0.569 Round 2: 409 peptides, 33 chains. Longest chain 38 peptides. Score 0.643 Round 3: 408 peptides, 30 chains. Longest chain 45 peptides. Score 0.659 Round 4: 419 peptides, 33 chains. Longest chain 27 peptides. Score 0.654 Round 5: 384 peptides, 35 chains. Longest chain 26 peptides. Score 0.601 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 378, Estimated correctness of the model 46.7 % 6 chains (146 residues) have been docked in sequence Sequence coverage is 38 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 41 A and 47 A 31 chains (383 residues) following loop building 5 chains (151 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14269 reflections ( 99.68 % complete ) and 7028 restraints for refining 4009 atoms. 4908 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2512 (Rfree = 0.000) for 4009 atoms. Found 0 (30 requested) and removed 11 (15 requested) atoms. Cycle 47: After refmac, R = 0.2416 (Rfree = 0.000) for 3979 atoms. Found 0 (30 requested) and removed 7 (15 requested) atoms. Cycle 48: After refmac, R = 0.2536 (Rfree = 0.000) for 3968 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2326 (Rfree = 0.000) for 3952 atoms. Found 0 (29 requested) and removed 10 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:57:04 GMT 2018 Job finished. TimeTaking 69.18 Used memory is bytes: 17662848