Sun 23 Dec 23:48:18 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 2ajr-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-4.0-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/2ajr-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-4.0-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 ============================================================ Sun 23 Dec 23:48:22 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/2ajr-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-4.0-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 529 and 0 Target number of residues in the AU: 529 Target solvent content: 0.6574 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-4.0-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.70 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: 29.168 4.000 Wilson plot Bfac: 83.11 7545 reflections ( 99.38 % complete ) and 0 restraints for refining 5846 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3717 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3635 (Rfree = 0.000) for 5846 atoms. Found 27 (27 requested) and removed 48 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.40 Search for helices and strands: 0 residues in 0 chains, 5902 seeds are put forward NCS extension: 0 residues added, 5902 seeds are put forward Round 1: 213 peptides, 44 chains. Longest chain 10 peptides. Score 0.259 Round 2: 259 peptides, 49 chains. Longest chain 15 peptides. Score 0.314 Round 3: 291 peptides, 53 chains. Longest chain 17 peptides. Score 0.346 Round 4: 294 peptides, 49 chains. Longest chain 13 peptides. Score 0.387 Round 5: 311 peptides, 51 chains. Longest chain 19 peptides. Score 0.403 Taking the results from Round 5 Chains 53, Residues 260, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 11406 restraints for refining 4781 atoms. 10350 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3338 (Rfree = 0.000) for 4781 atoms. Found 18 (22 requested) and removed 48 (11 requested) atoms. Cycle 2: After refmac, R = 0.3067 (Rfree = 0.000) for 4661 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 3: After refmac, R = 0.2913 (Rfree = 0.000) for 4590 atoms. Found 22 (22 requested) and removed 42 (11 requested) atoms. Cycle 4: After refmac, R = 0.2852 (Rfree = 0.000) for 4534 atoms. Found 21 (21 requested) and removed 31 (10 requested) atoms. Cycle 5: After refmac, R = 0.2784 (Rfree = 0.000) for 4489 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 4637 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4651 seeds are put forward Round 1: 243 peptides, 44 chains. Longest chain 12 peptides. Score 0.327 Round 2: 293 peptides, 49 chains. Longest chain 14 peptides. Score 0.385 Round 3: 303 peptides, 49 chains. Longest chain 17 peptides. Score 0.405 Round 4: 301 peptides, 45 chains. Longest chain 14 peptides. Score 0.435 Round 5: 310 peptides, 50 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 4 Chains 45, Residues 256, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10898 restraints for refining 4681 atoms. 9851 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2956 (Rfree = 0.000) for 4681 atoms. Found 22 (22 requested) and removed 47 (11 requested) atoms. Cycle 7: After refmac, R = 0.2672 (Rfree = 0.000) for 4602 atoms. Found 22 (22 requested) and removed 46 (11 requested) atoms. Cycle 8: After refmac, R = 0.2305 (Rfree = 0.000) for 4536 atoms. Found 17 (21 requested) and removed 30 (10 requested) atoms. Cycle 9: After refmac, R = 0.2267 (Rfree = 0.000) for 4506 atoms. Found 7 (21 requested) and removed 29 (10 requested) atoms. Cycle 10: After refmac, R = 0.2244 (Rfree = 0.000) for 4477 atoms. Found 2 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.41 Search for helices and strands: 0 residues in 0 chains, 4565 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4579 seeds are put forward Round 1: 275 peptides, 53 chains. Longest chain 11 peptides. Score 0.312 Round 2: 311 peptides, 49 chains. Longest chain 16 peptides. Score 0.420 Round 3: 311 peptides, 44 chains. Longest chain 16 peptides. Score 0.462 Round 4: 298 peptides, 45 chains. Longest chain 15 peptides. Score 0.429 Round 5: 297 peptides, 45 chains. Longest chain 19 peptides. Score 0.427 Taking the results from Round 3 Chains 47, Residues 267, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10689 restraints for refining 4711 atoms. 9600 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2650 (Rfree = 0.000) for 4711 atoms. Found 22 (22 requested) and removed 46 (11 requested) atoms. Cycle 12: After refmac, R = 0.2667 (Rfree = 0.000) for 4631 atoms. Found 22 (22 requested) and removed 54 (11 requested) atoms. Cycle 13: After refmac, R = 0.2438 (Rfree = 0.000) for 4577 atoms. Found 21 (21 requested) and removed 39 (10 requested) atoms. Cycle 14: After refmac, R = 0.2354 (Rfree = 0.000) for 4533 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 15: After refmac, R = 0.2025 (Rfree = 0.000) for 4508 atoms. Found 16 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 4645 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4660 seeds are put forward Round 1: 275 peptides, 48 chains. Longest chain 14 peptides. Score 0.357 Round 2: 330 peptides, 49 chains. Longest chain 33 peptides. Score 0.456 Round 3: 319 peptides, 50 chains. Longest chain 15 peptides. Score 0.427 Round 4: 338 peptides, 54 chains. Longest chain 16 peptides. Score 0.430 Round 5: 319 peptides, 47 chains. Longest chain 18 peptides. Score 0.452 Taking the results from Round 2 Chains 49, Residues 281, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10294 restraints for refining 4705 atoms. 9179 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2391 (Rfree = 0.000) for 4705 atoms. Found 20 (22 requested) and removed 49 (11 requested) atoms. Cycle 17: After refmac, R = 0.2357 (Rfree = 0.000) for 4652 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 18: After refmac, R = 0.2275 (Rfree = 0.000) for 4611 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 19: After refmac, R = 0.2266 (Rfree = 0.000) for 4583 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. Cycle 20: After refmac, R = 0.2299 (Rfree = 0.000) for 4556 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 4685 seeds are put forward NCS extension: 43 residues added (4 deleted due to clashes), 4728 seeds are put forward Round 1: 267 peptides, 50 chains. Longest chain 13 peptides. Score 0.322 Round 2: 297 peptides, 49 chains. Longest chain 15 peptides. Score 0.393 Round 3: 295 peptides, 50 chains. Longest chain 14 peptides. Score 0.380 Round 4: 321 peptides, 49 chains. Longest chain 16 peptides. Score 0.439 Round 5: 326 peptides, 47 chains. Longest chain 20 peptides. Score 0.465 Taking the results from Round 5 Chains 47, Residues 279, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10754 restraints for refining 4783 atoms. 9667 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2661 (Rfree = 0.000) for 4783 atoms. Found 22 (22 requested) and removed 48 (11 requested) atoms. Cycle 22: After refmac, R = 0.2574 (Rfree = 0.000) for 4701 atoms. Found 22 (22 requested) and removed 54 (11 requested) atoms. Cycle 23: After refmac, R = 0.2115 (Rfree = 0.000) for 4645 atoms. Found 8 (22 requested) and removed 26 (11 requested) atoms. Cycle 24: After refmac, R = 0.2486 (Rfree = 0.000) for 4603 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 25: After refmac, R = 0.2473 (Rfree = 0.000) for 4571 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 4695 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4713 seeds are put forward Round 1: 275 peptides, 56 chains. Longest chain 11 peptides. Score 0.285 Round 2: 311 peptides, 55 chains. Longest chain 13 peptides. Score 0.369 Round 3: 314 peptides, 50 chains. Longest chain 13 peptides. Score 0.417 Round 4: 300 peptides, 46 chains. Longest chain 15 peptides. Score 0.424 Round 5: 330 peptides, 47 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 47, Residues 283, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10462 restraints for refining 4781 atoms. 9332 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2723 (Rfree = 0.000) for 4781 atoms. Found 22 (22 requested) and removed 40 (11 requested) atoms. Cycle 27: After refmac, R = 0.2486 (Rfree = 0.000) for 4709 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 28: After refmac, R = 0.2395 (Rfree = 0.000) for 4663 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 29: After refmac, R = 0.2131 (Rfree = 0.000) for 4622 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 30: After refmac, R = 0.2071 (Rfree = 0.000) for 4607 atoms. Found 6 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 4701 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4714 seeds are put forward Round 1: 257 peptides, 52 chains. Longest chain 10 peptides. Score 0.282 Round 2: 279 peptides, 49 chains. Longest chain 12 peptides. Score 0.357 Round 3: 273 peptides, 44 chains. Longest chain 14 peptides. Score 0.389 Round 4: 287 peptides, 45 chains. Longest chain 13 peptides. Score 0.408 Round 5: 281 peptides, 40 chains. Longest chain 20 peptides. Score 0.440 Taking the results from Round 5 Chains 42, Residues 241, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10888 restraints for refining 4783 atoms. 9915 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2695 (Rfree = 0.000) for 4783 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 32: After refmac, R = 0.2607 (Rfree = 0.000) for 4722 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 33: After refmac, R = 0.2421 (Rfree = 0.000) for 4688 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 34: After refmac, R = 0.2518 (Rfree = 0.000) for 4667 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 35: After refmac, R = 0.2281 (Rfree = 0.000) for 4641 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 4773 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4786 seeds are put forward Round 1: 233 peptides, 48 chains. Longest chain 10 peptides. Score 0.266 Round 2: 263 peptides, 47 chains. Longest chain 12 peptides. Score 0.341 Round 3: 271 peptides, 43 chains. Longest chain 21 peptides. Score 0.394 Round 4: 261 peptides, 42 chains. Longest chain 13 peptides. Score 0.383 Round 5: 260 peptides, 41 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 3 Chains 43, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10935 restraints for refining 4740 atoms. 10066 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2390 (Rfree = 0.000) for 4740 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 37: After refmac, R = 0.2413 (Rfree = 0.000) for 4695 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 38: After refmac, R = 0.2248 (Rfree = 0.000) for 4656 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 4634 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 40: After refmac, R = 0.2257 (Rfree = 0.000) for 4622 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 4740 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 4768 seeds are put forward Round 1: 223 peptides, 48 chains. Longest chain 8 peptides. Score 0.243 Round 2: 247 peptides, 43 chains. Longest chain 11 peptides. Score 0.344 Round 3: 251 peptides, 42 chains. Longest chain 12 peptides. Score 0.362 Round 4: 235 peptides, 42 chains. Longest chain 14 peptides. Score 0.328 Round 5: 229 peptides, 38 chains. Longest chain 14 peptides. Score 0.353 Taking the results from Round 3 Chains 42, Residues 209, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7545 reflections ( 99.38 % complete ) and 10964 restraints for refining 4728 atoms. 10146 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2382 (Rfree = 0.000) for 4728 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 42: After refmac, R = 0.2389 (Rfree = 0.000) for 4676 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 43: After refmac, R = 0.2315 (Rfree = 0.000) for 4634 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 44: After refmac, R = 0.2352 (Rfree = 0.000) for 4617 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 45: After refmac, R = 0.1886 (Rfree = 0.000) for 4592 atoms. Found 4 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 4693 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4705 seeds are put forward Round 1: 199 peptides, 43 chains. Longest chain 8 peptides. Score 0.236 Round 2: 230 peptides, 44 chains. Longest chain 9 peptides. Score 0.298 Round 3: 235 peptides, 42 chains. Longest chain 10 peptides. Score 0.328 Round 4: 247 peptides, 40 chains. Longest chain 14 peptides. Score 0.372 Round 5: 254 peptides, 44 chains. Longest chain 12 peptides. Score 0.350 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 207, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ajr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7545 reflections ( 99.38 % complete ) and 10674 restraints for refining 4667 atoms. 9864 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2268 (Rfree = 0.000) for 4667 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2319 (Rfree = 0.000) for 4634 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2267 (Rfree = 0.000) for 4602 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2239 (Rfree = 0.000) for 4577 atoms. TimeTaking 55.85