null Sun 23 Dec 22:22:56 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 1vl0-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.2-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/1vl0-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.2-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 22:23:05 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/1vl0-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.2-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 756 and 0 Target number of residues in the AU: 756 Target solvent content: 0.6110 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-3.2-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 7008 target number of atoms Had to go as low as 0.80 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: 29.987 3.200 Wilson plot Bfac: 57.18 17612 reflections ( 99.18 % complete ) and 0 restraints for refining 7733 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3838 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3727 (Rfree = 0.000) for 7733 atoms. Found 69 (69 requested) and removed 111 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 7723 seeds are put forward NCS extension: 0 residues added, 7723 seeds are put forward Round 1: 260 peptides, 55 chains. Longest chain 8 peptides. Score 0.247 Round 2: 323 peptides, 62 chains. Longest chain 14 peptides. Score 0.307 Round 3: 394 peptides, 75 chains. Longest chain 14 peptides. Score 0.333 Round 4: 391 peptides, 71 chains. Longest chain 14 peptides. Score 0.356 Round 5: 407 peptides, 72 chains. Longest chain 16 peptides. Score 0.375 Taking the results from Round 5 Chains 74, Residues 335, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13987 restraints for refining 6396 atoms. 12686 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3235 (Rfree = 0.000) for 6396 atoms. Found 34 (57 requested) and removed 77 (28 requested) atoms. Cycle 2: After refmac, R = 0.3069 (Rfree = 0.000) for 6298 atoms. Found 56 (57 requested) and removed 42 (28 requested) atoms. Cycle 3: After refmac, R = 0.3296 (Rfree = 0.000) for 6277 atoms. Found 56 (56 requested) and removed 50 (28 requested) atoms. Cycle 4: After refmac, R = 0.2904 (Rfree = 0.000) for 6245 atoms. Found 34 (56 requested) and removed 42 (28 requested) atoms. Cycle 5: After refmac, R = 0.2812 (Rfree = 0.000) for 6219 atoms. Found 26 (55 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 6330 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6349 seeds are put forward Round 1: 368 peptides, 74 chains. Longest chain 9 peptides. Score 0.297 Round 2: 406 peptides, 74 chains. Longest chain 17 peptides. Score 0.359 Round 3: 395 peptides, 70 chains. Longest chain 12 peptides. Score 0.369 Round 4: 410 peptides, 73 chains. Longest chain 16 peptides. Score 0.372 Round 5: 413 peptides, 68 chains. Longest chain 20 peptides. Score 0.411 Taking the results from Round 5 Chains 68, Residues 345, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 14017 restraints for refining 6398 atoms. 12680 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3003 (Rfree = 0.000) for 6398 atoms. Found 44 (57 requested) and removed 51 (28 requested) atoms. Cycle 7: After refmac, R = 0.2777 (Rfree = 0.000) for 6349 atoms. Found 32 (57 requested) and removed 42 (28 requested) atoms. Cycle 8: After refmac, R = 0.2627 (Rfree = 0.000) for 6320 atoms. Found 15 (56 requested) and removed 35 (28 requested) atoms. Cycle 9: After refmac, R = 0.2480 (Rfree = 0.000) for 6286 atoms. Found 9 (56 requested) and removed 33 (28 requested) atoms. Cycle 10: After refmac, R = 0.2502 (Rfree = 0.000) for 6257 atoms. Found 7 (56 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 6364 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 6394 seeds are put forward Round 1: 353 peptides, 71 chains. Longest chain 9 peptides. Score 0.293 Round 2: 406 peptides, 72 chains. Longest chain 17 peptides. Score 0.373 Round 3: 426 peptides, 71 chains. Longest chain 15 peptides. Score 0.411 Round 4: 428 peptides, 72 chains. Longest chain 12 peptides. Score 0.407 Round 5: 435 peptides, 70 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 5 Chains 70, Residues 365, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13874 restraints for refining 6397 atoms. 12484 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2747 (Rfree = 0.000) for 6397 atoms. Found 46 (57 requested) and removed 38 (28 requested) atoms. Cycle 12: After refmac, R = 0.2601 (Rfree = 0.000) for 6382 atoms. Found 21 (57 requested) and removed 37 (28 requested) atoms. Cycle 13: After refmac, R = 0.2711 (Rfree = 0.000) for 6351 atoms. Found 26 (57 requested) and removed 35 (28 requested) atoms. Cycle 14: After refmac, R = 0.2476 (Rfree = 0.000) for 6323 atoms. Found 15 (56 requested) and removed 34 (28 requested) atoms. Cycle 15: After refmac, R = 0.2281 (Rfree = 0.000) for 6293 atoms. Found 12 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 6365 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 6380 seeds are put forward Round 1: 362 peptides, 72 chains. Longest chain 12 peptides. Score 0.301 Round 2: 400 peptides, 72 chains. Longest chain 14 peptides. Score 0.363 Round 3: 420 peptides, 66 chains. Longest chain 15 peptides. Score 0.434 Round 4: 421 peptides, 66 chains. Longest chain 16 peptides. Score 0.436 Round 5: 444 peptides, 73 chains. Longest chain 21 peptides. Score 0.425 Taking the results from Round 4 Chains 66, Residues 355, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13827 restraints for refining 6398 atoms. 12426 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2519 (Rfree = 0.000) for 6398 atoms. Found 46 (57 requested) and removed 33 (28 requested) atoms. Cycle 17: After refmac, R = 0.2366 (Rfree = 0.000) for 6387 atoms. Found 26 (57 requested) and removed 35 (28 requested) atoms. Cycle 18: After refmac, R = 0.2291 (Rfree = 0.000) for 6362 atoms. Found 21 (57 requested) and removed 33 (28 requested) atoms. Cycle 19: After refmac, R = 0.2271 (Rfree = 0.000) for 6337 atoms. Found 20 (56 requested) and removed 32 (28 requested) atoms. Cycle 20: After refmac, R = 0.2184 (Rfree = 0.000) for 6320 atoms. Found 10 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 2.90 Search for helices and strands: 0 residues in 0 chains, 6376 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6395 seeds are put forward Round 1: 365 peptides, 71 chains. Longest chain 13 peptides. Score 0.313 Round 2: 410 peptides, 68 chains. Longest chain 15 peptides. Score 0.406 Round 3: 398 peptides, 61 chains. Longest chain 16 peptides. Score 0.434 Round 4: 398 peptides, 65 chains. Longest chain 17 peptides. Score 0.408 Round 5: 411 peptides, 66 chains. Longest chain 15 peptides. Score 0.421 Taking the results from Round 3 Chains 63, Residues 337, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13783 restraints for refining 6398 atoms. 12401 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2470 (Rfree = 0.000) for 6398 atoms. Found 42 (57 requested) and removed 36 (28 requested) atoms. Cycle 22: After refmac, R = 0.2353 (Rfree = 0.000) for 6384 atoms. Found 30 (57 requested) and removed 29 (28 requested) atoms. Cycle 23: After refmac, R = 0.2272 (Rfree = 0.000) for 6382 atoms. Found 19 (57 requested) and removed 34 (28 requested) atoms. Cycle 24: After refmac, R = 0.2247 (Rfree = 0.000) for 6364 atoms. Found 8 (57 requested) and removed 28 (28 requested) atoms. Cycle 25: After refmac, R = 0.2239 (Rfree = 0.000) for 6343 atoms. Found 12 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 6403 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6423 seeds are put forward Round 1: 352 peptides, 70 chains. Longest chain 13 peptides. Score 0.298 Round 2: 405 peptides, 70 chains. Longest chain 14 peptides. Score 0.385 Round 3: 415 peptides, 69 chains. Longest chain 18 peptides. Score 0.407 Round 4: 403 peptides, 63 chains. Longest chain 13 peptides. Score 0.429 Round 5: 409 peptides, 66 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 4 Chains 63, Residues 340, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13890 restraints for refining 6397 atoms. 12579 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2547 (Rfree = 0.000) for 6397 atoms. Found 40 (57 requested) and removed 61 (28 requested) atoms. Cycle 27: After refmac, R = 0.2540 (Rfree = 0.000) for 6357 atoms. Found 43 (57 requested) and removed 30 (28 requested) atoms. Cycle 28: After refmac, R = 0.2362 (Rfree = 0.000) for 6366 atoms. Found 32 (57 requested) and removed 31 (28 requested) atoms. Cycle 29: After refmac, R = 0.2305 (Rfree = 0.000) for 6362 atoms. Found 14 (57 requested) and removed 30 (28 requested) atoms. Cycle 30: After refmac, R = 0.2292 (Rfree = 0.000) for 6337 atoms. Found 10 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 2.90 Search for helices and strands: 0 residues in 0 chains, 6404 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6416 seeds are put forward Round 1: 352 peptides, 68 chains. Longest chain 11 peptides. Score 0.313 Round 2: 381 peptides, 63 chains. Longest chain 16 peptides. Score 0.395 Round 3: 369 peptides, 65 chains. Longest chain 12 peptides. Score 0.362 Round 4: 362 peptides, 60 chains. Longest chain 13 peptides. Score 0.386 Round 5: 371 peptides, 64 chains. Longest chain 14 peptides. Score 0.372 Taking the results from Round 2 Chains 63, Residues 318, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13856 restraints for refining 6398 atoms. 12605 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2419 (Rfree = 0.000) for 6398 atoms. Found 20 (57 requested) and removed 34 (28 requested) atoms. Cycle 32: After refmac, R = 0.2379 (Rfree = 0.000) for 6378 atoms. Found 28 (57 requested) and removed 28 (28 requested) atoms. Cycle 33: After refmac, R = 0.2343 (Rfree = 0.000) for 6371 atoms. Found 33 (57 requested) and removed 28 (28 requested) atoms. Cycle 34: After refmac, R = 0.2297 (Rfree = 0.000) for 6373 atoms. Found 18 (57 requested) and removed 29 (28 requested) atoms. Cycle 35: After refmac, R = 0.2326 (Rfree = 0.000) for 6361 atoms. Found 14 (57 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 2.88 Search for helices and strands: 0 residues in 0 chains, 6421 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 6446 seeds are put forward Round 1: 331 peptides, 65 chains. Longest chain 9 peptides. Score 0.299 Round 2: 365 peptides, 68 chains. Longest chain 15 peptides. Score 0.334 Round 3: 368 peptides, 62 chains. Longest chain 13 peptides. Score 0.381 Round 4: 391 peptides, 66 chains. Longest chain 13 peptides. Score 0.390 Round 5: 399 peptides, 69 chains. Longest chain 13 peptides. Score 0.382 Taking the results from Round 4 Chains 66, Residues 325, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13862 restraints for refining 6398 atoms. 12592 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2325 (Rfree = 0.000) for 6398 atoms. Found 33 (57 requested) and removed 35 (28 requested) atoms. Cycle 37: After refmac, R = 0.2284 (Rfree = 0.000) for 6387 atoms. Found 35 (57 requested) and removed 30 (28 requested) atoms. Cycle 38: After refmac, R = 0.2229 (Rfree = 0.000) for 6387 atoms. Found 20 (57 requested) and removed 30 (28 requested) atoms. Cycle 39: After refmac, R = 0.2221 (Rfree = 0.000) for 6375 atoms. Found 19 (57 requested) and removed 29 (28 requested) atoms. Cycle 40: After refmac, R = 0.2176 (Rfree = 0.000) for 6364 atoms. Found 13 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 6402 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6419 seeds are put forward Round 1: 328 peptides, 69 chains. Longest chain 8 peptides. Score 0.264 Round 2: 361 peptides, 65 chains. Longest chain 14 peptides. Score 0.349 Round 3: 368 peptides, 63 chains. Longest chain 11 peptides. Score 0.374 Round 4: 377 peptides, 66 chains. Longest chain 10 peptides. Score 0.368 Round 5: 359 peptides, 60 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 60, Residues 299, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13985 restraints for refining 6396 atoms. 12824 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2335 (Rfree = 0.000) for 6396 atoms. Found 35 (57 requested) and removed 58 (28 requested) atoms. Cycle 42: After refmac, R = 0.2246 (Rfree = 0.000) for 6360 atoms. Found 32 (57 requested) and removed 32 (28 requested) atoms. Cycle 43: After refmac, R = 0.2192 (Rfree = 0.000) for 6357 atoms. Found 23 (57 requested) and removed 28 (28 requested) atoms. Cycle 44: After refmac, R = 0.2178 (Rfree = 0.000) for 6350 atoms. Found 20 (56 requested) and removed 29 (28 requested) atoms. Cycle 45: After refmac, R = 0.2173 (Rfree = 0.000) for 6337 atoms. Found 15 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 6382 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 6400 seeds are put forward Round 1: 301 peptides, 63 chains. Longest chain 9 peptides. Score 0.260 Round 2: 336 peptides, 59 chains. Longest chain 12 peptides. Score 0.351 Round 3: 331 peptides, 56 chains. Longest chain 13 peptides. Score 0.364 Round 4: 320 peptides, 57 chains. Longest chain 10 peptides. Score 0.339 Round 5: 320 peptides, 55 chains. Longest chain 13 peptides. Score 0.353 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 275, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17612 reflections ( 99.18 % complete ) and 14153 restraints for refining 6398 atoms. 13092 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2310 (Rfree = 0.000) for 6398 atoms. Found 0 (57 requested) and removed 21 (28 requested) atoms. Cycle 47: After refmac, R = 0.2206 (Rfree = 0.000) for 6364 atoms. Found 0 (57 requested) and removed 9 (28 requested) atoms. Cycle 48: After refmac, R = 0.2235 (Rfree = 0.000) for 6354 atoms. Found 0 (57 requested) and removed 10 (28 requested) atoms. Cycle 49: After refmac, R = 0.2171 (Rfree = 0.000) for 6339 atoms. Found 0 (56 requested) and removed 15 (28 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:47:42 GMT 2018 Job finished. TimeTaking 84.77 Used memory is bytes: 21067864