Tue 25 Dec 19:27:57 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 1vl0-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl0-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.4-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/1vl0-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.4-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 ============================================================ Tue 25 Dec 19:28:06 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/1vl0-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl0-3.4-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 737 and 0 Target number of residues in the AU: 737 Target solvent content: 0.6208 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: 1vl0-3.4-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: 1vl0-3.4-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 3.400 Wilson plot Bfac: 61.68 14719 reflections ( 99.09 % complete ) and 0 restraints for refining 7761 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3809 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3578 (Rfree = 0.000) for 7761 atoms. Found 58 (58 requested) and removed 81 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 7798 seeds are put forward NCS extension: 0 residues added, 7798 seeds are put forward Round 1: 201 peptides, 46 chains. Longest chain 8 peptides. Score 0.204 Round 2: 302 peptides, 62 chains. Longest chain 11 peptides. Score 0.270 Round 3: 317 peptides, 62 chains. Longest chain 9 peptides. Score 0.296 Round 4: 352 peptides, 63 chains. Longest chain 11 peptides. Score 0.348 Round 5: 363 peptides, 65 chains. Longest chain 11 peptides. Score 0.352 Taking the results from Round 5 Chains 65, Residues 298, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 14299 restraints for refining 6372 atoms. 13151 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3144 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 51 (24 requested) atoms. Cycle 2: After refmac, R = 0.2950 (Rfree = 0.000) for 6292 atoms. Found 43 (48 requested) and removed 45 (24 requested) atoms. Cycle 3: After refmac, R = 0.2896 (Rfree = 0.000) for 6242 atoms. Found 43 (47 requested) and removed 38 (23 requested) atoms. Cycle 4: After refmac, R = 0.2798 (Rfree = 0.000) for 6206 atoms. Found 38 (47 requested) and removed 33 (23 requested) atoms. Cycle 5: After refmac, R = 0.2801 (Rfree = 0.000) for 6177 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.06 Search for helices and strands: 0 residues in 0 chains, 6309 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6322 seeds are put forward Round 1: 309 peptides, 62 chains. Longest chain 12 peptides. Score 0.282 Round 2: 345 peptides, 65 chains. Longest chain 11 peptides. Score 0.322 Round 3: 373 peptides, 65 chains. Longest chain 12 peptides. Score 0.369 Round 4: 364 peptides, 64 chains. Longest chain 16 peptides. Score 0.361 Round 5: 398 peptides, 70 chains. Longest chain 13 peptides. Score 0.374 Taking the results from Round 5 Chains 70, Residues 328, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14719 reflections ( 99.09 % complete ) and 14094 restraints for refining 6348 atoms. 12806 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2811 (Rfree = 0.000) for 6348 atoms. Found 47 (47 requested) and removed 56 (23 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2660 (Rfree = 0.000) for 6275 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 8: After refmac, R = 0.2616 (Rfree = 0.000) for 6254 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2481 (Rfree = 0.000) for 6236 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 10: After refmac, R = 0.2451 (Rfree = 0.000) for 6234 atoms. Found 42 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 6337 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6353 seeds are put forward Round 1: 377 peptides, 80 chains. Longest chain 9 peptides. Score 0.269 Round 2: 428 peptides, 78 chains. Longest chain 12 peptides. Score 0.367 Round 3: 410 peptides, 74 chains. Longest chain 20 peptides. Score 0.366 Round 4: 442 peptides, 77 chains. Longest chain 13 peptides. Score 0.395 Round 5: 446 peptides, 76 chains. Longest chain 15 peptides. Score 0.408 Taking the results from Round 5 Chains 77, Residues 370, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13685 restraints for refining 6372 atoms. 12234 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2608 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 42 (24 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2413 (Rfree = 0.000) for 6337 atoms. Found 46 (48 requested) and removed 39 (24 requested) atoms. Cycle 13: After refmac, R = 0.2279 (Rfree = 0.000) for 6323 atoms. Found 33 (47 requested) and removed 36 (23 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2258 (Rfree = 0.000) for 6304 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 15: After refmac, R = 0.2215 (Rfree = 0.000) for 6300 atoms. Found 33 (47 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.10 Search for helices and strands: 0 residues in 0 chains, 6364 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6384 seeds are put forward Round 1: 372 peptides, 75 chains. Longest chain 10 peptides. Score 0.296 Round 2: 419 peptides, 71 chains. Longest chain 16 peptides. Score 0.400 Round 3: 427 peptides, 67 chains. Longest chain 22 peptides. Score 0.438 Round 4: 440 peptides, 73 chains. Longest chain 21 peptides. Score 0.419 Round 5: 421 peptides, 71 chains. Longest chain 16 peptides. Score 0.403 Taking the results from Round 3 Chains 67, Residues 360, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 14157 restraints for refining 6372 atoms. 12764 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2532 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 17: After refmac, R = 0.2464 (Rfree = 0.000) for 6350 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2345 (Rfree = 0.000) for 6336 atoms. Found 44 (47 requested) and removed 31 (23 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2016 (Rfree = 0.000) for 6336 atoms. Found 19 (47 requested) and removed 27 (23 requested) atoms. Cycle 20: After refmac, R = 0.1959 (Rfree = 0.000) for 6318 atoms. Found 14 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 6377 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 6413 seeds are put forward Round 1: 375 peptides, 76 chains. Longest chain 12 peptides. Score 0.294 Round 2: 406 peptides, 72 chains. Longest chain 12 peptides. Score 0.373 Round 3: 421 peptides, 75 chains. Longest chain 12 peptides. Score 0.376 Round 4: 422 peptides, 72 chains. Longest chain 15 peptides. Score 0.398 Round 5: 424 peptides, 68 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 5 Chains 68, Residues 356, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14719 reflections ( 99.09 % complete ) and 13838 restraints for refining 6372 atoms. 12461 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2485 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 33 (24 requested) atoms. Cycle 22: After refmac, R = 0.2413 (Rfree = 0.000) for 6357 atoms. Found 48 (48 requested) and removed 34 (24 requested) atoms. Cycle 23: After refmac, R = 0.2417 (Rfree = 0.000) for 6350 atoms. Found 48 (48 requested) and removed 32 (24 requested) atoms. Cycle 24: After refmac, R = 0.2312 (Rfree = 0.000) for 6354 atoms. Found 48 (48 requested) and removed 28 (24 requested) atoms. Cycle 25: After refmac, R = 0.2266 (Rfree = 0.000) for 6363 atoms. Found 43 (48 requested) and removed 33 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.07 Search for helices and strands: 0 residues in 0 chains, 6447 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6473 seeds are put forward Round 1: 336 peptides, 70 chains. Longest chain 14 peptides. Score 0.270 Round 2: 365 peptides, 64 chains. Longest chain 17 peptides. Score 0.363 Round 3: 376 peptides, 68 chains. Longest chain 10 peptides. Score 0.352 Round 4: 384 peptides, 67 chains. Longest chain 15 peptides. Score 0.372 Round 5: 385 peptides, 66 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 5 Chains 67, Residues 319, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13719 restraints for refining 6372 atoms. 12417 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2493 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 40 (24 requested) atoms. Cycle 27: After refmac, R = 0.2321 (Rfree = 0.000) for 6339 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2018 (Rfree = 0.000) for 6319 atoms. Found 22 (47 requested) and removed 26 (23 requested) atoms. Cycle 29: After refmac, R = 0.1950 (Rfree = 0.000) for 6296 atoms. Found 16 (47 requested) and removed 25 (23 requested) atoms. Cycle 30: After refmac, R = 0.2162 (Rfree = 0.000) for 6280 atoms. Found 35 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 6340 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6355 seeds are put forward Round 1: 329 peptides, 67 chains. Longest chain 10 peptides. Score 0.280 Round 2: 381 peptides, 65 chains. Longest chain 17 peptides. Score 0.381 Round 3: 359 peptides, 66 chains. Longest chain 11 peptides. Score 0.339 Round 4: 382 peptides, 68 chains. Longest chain 12 peptides. Score 0.362 Round 5: 366 peptides, 62 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 2 Chains 66, Residues 316, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13791 restraints for refining 6372 atoms. 12548 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2453 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 33 (24 requested) atoms. Cycle 32: After refmac, R = 0.2426 (Rfree = 0.000) for 6356 atoms. Found 48 (48 requested) and removed 34 (24 requested) atoms. Cycle 33: After refmac, R = 0.2427 (Rfree = 0.000) for 6349 atoms. Found 43 (48 requested) and removed 31 (24 requested) atoms. Cycle 34: After refmac, R = 0.2427 (Rfree = 0.000) for 6346 atoms. Found 47 (47 requested) and removed 31 (23 requested) atoms. Cycle 35: After refmac, R = 0.2355 (Rfree = 0.000) for 6348 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.07 Search for helices and strands: 0 residues in 0 chains, 6420 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6435 seeds are put forward Round 1: 331 peptides, 68 chains. Longest chain 14 peptides. Score 0.276 Round 2: 361 peptides, 68 chains. Longest chain 13 peptides. Score 0.328 Round 3: 356 peptides, 63 chains. Longest chain 17 peptides. Score 0.355 Round 4: 375 peptides, 69 chains. Longest chain 14 peptides. Score 0.344 Round 5: 370 peptides, 65 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Chains 65, Residues 305, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 14029 restraints for refining 6370 atoms. 12845 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2531 (Rfree = 0.000) for 6370 atoms. Found 48 (48 requested) and removed 38 (24 requested) atoms. Cycle 37: After refmac, R = 0.2411 (Rfree = 0.000) for 6345 atoms. Found 48 (48 requested) and removed 33 (24 requested) atoms. Cycle 38: After refmac, R = 0.2302 (Rfree = 0.000) for 6342 atoms. Found 48 (48 requested) and removed 34 (24 requested) atoms. Cycle 39: After refmac, R = 0.2506 (Rfree = 0.000) for 6345 atoms. Found 47 (47 requested) and removed 26 (23 requested) atoms. Cycle 40: After refmac, R = 0.2258 (Rfree = 0.000) for 6349 atoms. Found 48 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 6440 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6456 seeds are put forward Round 1: 318 peptides, 68 chains. Longest chain 11 peptides. Score 0.253 Round 2: 358 peptides, 66 chains. Longest chain 15 peptides. Score 0.337 Round 3: 357 peptides, 66 chains. Longest chain 12 peptides. Score 0.335 Round 4: 351 peptides, 61 chains. Longest chain 16 peptides. Score 0.361 Round 5: 351 peptides, 64 chains. Longest chain 10 peptides. Score 0.340 Taking the results from Round 4 Chains 61, Residues 290, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13955 restraints for refining 6372 atoms. 12820 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2545 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 33 (24 requested) atoms. Cycle 42: After refmac, R = 0.2533 (Rfree = 0.000) for 6354 atoms. Found 48 (48 requested) and removed 33 (24 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2379 (Rfree = 0.000) for 6350 atoms. Found 48 (48 requested) and removed 36 (24 requested) atoms. Cycle 44: After refmac, R = 0.2328 (Rfree = 0.000) for 6343 atoms. Found 48 (48 requested) and removed 28 (24 requested) atoms. Cycle 45: After refmac, R = 0.2351 (Rfree = 0.000) for 6356 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.05 Search for helices and strands: 0 residues in 0 chains, 6432 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 6449 seeds are put forward Round 1: 269 peptides, 58 chains. Longest chain 13 peptides. Score 0.240 Round 2: 299 peptides, 56 chains. Longest chain 17 peptides. Score 0.310 Round 3: 306 peptides, 55 chains. Longest chain 15 peptides. Score 0.330 Round 4: 337 peptides, 58 chains. Longest chain 12 peptides. Score 0.360 Round 5: 326 peptides, 58 chains. Longest chain 11 peptides. Score 0.341 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 279, 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. 14719 reflections ( 99.09 % complete ) and 14049 restraints for refining 6370 atoms. 12977 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2367 (Rfree = 0.000) for 6370 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2317 (Rfree = 0.000) for 6319 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1967 (Rfree = 0.000) for 6283 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1950 (Rfree = 0.000) for 6248 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:01:25 GMT 2018 Job finished. TimeTaking 93.47