Mon 24 Dec 00:00:35 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 1vl0-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.2-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/1vl0-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.2-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 00:00:40 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/1vl0-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.2-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 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-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-3.2-parrot-mrncs.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 7730 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3837 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3667 (Rfree = 0.000) for 7730 atoms. Found 69 (69 requested) and removed 114 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 7714 seeds are put forward NCS extension: 0 residues added, 7714 seeds are put forward Round 1: 253 peptides, 57 chains. Longest chain 8 peptides. Score 0.217 Round 2: 298 peptides, 61 chains. Longest chain 10 peptides. Score 0.270 Round 3: 354 peptides, 69 chains. Longest chain 11 peptides. Score 0.309 Round 4: 359 peptides, 65 chains. Longest chain 13 peptides. Score 0.346 Round 5: 359 peptides, 64 chains. Longest chain 15 peptides. Score 0.353 Taking the results from Round 5 Chains 64, Residues 295, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 14029 restraints for refining 6398 atoms. 12913 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3469 (Rfree = 0.000) for 6398 atoms. Found 57 (57 requested) and removed 57 (28 requested) atoms. Cycle 2: After refmac, R = 0.3341 (Rfree = 0.000) for 6344 atoms. Found 57 (57 requested) and removed 46 (28 requested) atoms. Cycle 3: After refmac, R = 0.3403 (Rfree = 0.000) for 6326 atoms. Found 57 (57 requested) and removed 49 (28 requested) atoms. Cycle 4: After refmac, R = 0.3275 (Rfree = 0.000) for 6308 atoms. Found 56 (56 requested) and removed 40 (28 requested) atoms. Cycle 5: After refmac, R = 0.3245 (Rfree = 0.000) for 6298 atoms. Found 56 (56 requested) and removed 41 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 6443 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6457 seeds are put forward Round 1: 311 peptides, 66 chains. Longest chain 8 peptides. Score 0.256 Round 2: 389 peptides, 72 chains. Longest chain 16 peptides. Score 0.346 Round 3: 403 peptides, 74 chains. Longest chain 15 peptides. Score 0.355 Round 4: 388 peptides, 64 chains. Longest chain 16 peptides. Score 0.399 Round 5: 382 peptides, 67 chains. Longest chain 16 peptides. Score 0.369 Taking the results from Round 4 Chains 66, Residues 324, Estimated correctness of the model 0.0 % 6 chains (28 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13713 restraints for refining 6398 atoms. 12397 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3135 (Rfree = 0.000) for 6398 atoms. Found 57 (57 requested) and removed 63 (28 requested) atoms. Cycle 7: After refmac, R = 0.3002 (Rfree = 0.000) for 6341 atoms. Found 57 (57 requested) and removed 60 (28 requested) atoms. Cycle 8: After refmac, R = 0.2883 (Rfree = 0.000) for 6311 atoms. Found 56 (56 requested) and removed 40 (28 requested) atoms. Cycle 9: After refmac, R = 0.2447 (Rfree = 0.000) for 6304 atoms. Found 24 (56 requested) and removed 32 (28 requested) atoms. Cycle 10: After refmac, R = 0.2616 (Rfree = 0.000) for 6284 atoms. Found 50 (56 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.95 Search for helices and strands: 0 residues in 0 chains, 6380 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6399 seeds are put forward Round 1: 373 peptides, 78 chains. Longest chain 9 peptides. Score 0.277 Round 2: 417 peptides, 74 chains. Longest chain 14 peptides. Score 0.377 Round 3: 405 peptides, 72 chains. Longest chain 18 peptides. Score 0.371 Round 4: 425 peptides, 77 chains. Longest chain 11 peptides. Score 0.369 Round 5: 436 peptides, 74 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 5 Chains 75, Residues 362, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13501 restraints for refining 6398 atoms. 12048 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2956 (Rfree = 0.000) for 6398 atoms. Found 57 (57 requested) and removed 52 (28 requested) atoms. Cycle 12: After refmac, R = 0.2747 (Rfree = 0.000) for 6377 atoms. Found 52 (57 requested) and removed 39 (28 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2673 (Rfree = 0.000) for 6360 atoms. Found 44 (57 requested) and removed 35 (28 requested) atoms. Cycle 14: After refmac, R = 0.2531 (Rfree = 0.000) for 6358 atoms. Found 29 (57 requested) and removed 30 (28 requested) atoms. Cycle 15: After refmac, R = 0.2512 (Rfree = 0.000) for 6346 atoms. Found 31 (57 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 6483 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6503 seeds are put forward Round 1: 365 peptides, 73 chains. Longest chain 10 peptides. Score 0.299 Round 2: 402 peptides, 75 chains. Longest chain 12 peptides. Score 0.346 Round 3: 421 peptides, 75 chains. Longest chain 15 peptides. Score 0.376 Round 4: 431 peptides, 73 chains. Longest chain 16 peptides. Score 0.405 Round 5: 433 peptides, 72 chains. Longest chain 20 peptides. Score 0.415 Taking the results from Round 5 Chains 74, Residues 361, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13343 restraints for refining 6397 atoms. 11906 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2665 (Rfree = 0.000) for 6397 atoms. Found 47 (57 requested) and removed 36 (28 requested) atoms. Cycle 17: After refmac, R = 0.2553 (Rfree = 0.000) for 6383 atoms. Found 29 (57 requested) and removed 32 (28 requested) atoms. Cycle 18: After refmac, R = 0.2461 (Rfree = 0.000) for 6361 atoms. Found 31 (57 requested) and removed 35 (28 requested) atoms. Cycle 19: After refmac, R = 0.2443 (Rfree = 0.000) for 6346 atoms. Found 25 (57 requested) and removed 30 (28 requested) atoms. Cycle 20: After refmac, R = 0.2475 (Rfree = 0.000) for 6334 atoms. Found 32 (56 requested) and removed 38 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.96 Search for helices and strands: 0 residues in 0 chains, 6404 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6418 seeds are put forward Round 1: 401 peptides, 80 chains. Longest chain 10 peptides. Score 0.310 Round 2: 431 peptides, 81 chains. Longest chain 12 peptides. Score 0.352 Round 3: 412 peptides, 73 chains. Longest chain 16 peptides. Score 0.376 Round 4: 414 peptides, 72 chains. Longest chain 11 peptides. Score 0.385 Round 5: 435 peptides, 68 chains. Longest chain 19 peptides. Score 0.443 Taking the results from Round 5 Chains 68, Residues 367, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13558 restraints for refining 6397 atoms. 12112 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2832 (Rfree = 0.000) for 6397 atoms. Found 57 (57 requested) and removed 46 (28 requested) atoms. Cycle 22: After refmac, R = 0.2486 (Rfree = 0.000) for 6385 atoms. Found 47 (57 requested) and removed 34 (28 requested) atoms. Cycle 23: After refmac, R = 0.2323 (Rfree = 0.000) for 6378 atoms. Found 46 (57 requested) and removed 35 (28 requested) atoms. Cycle 24: After refmac, R = 0.2236 (Rfree = 0.000) for 6382 atoms. Found 17 (57 requested) and removed 34 (28 requested) atoms. Cycle 25: After refmac, R = 0.2358 (Rfree = 0.000) for 6359 atoms. Found 37 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.89 Search for helices and strands: 0 residues in 0 chains, 6483 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6508 seeds are put forward Round 1: 368 peptides, 77 chains. Longest chain 10 peptides. Score 0.275 Round 2: 397 peptides, 72 chains. Longest chain 16 peptides. Score 0.359 Round 3: 379 peptides, 63 chains. Longest chain 19 peptides. Score 0.392 Round 4: 386 peptides, 62 chains. Longest chain 17 peptides. Score 0.410 Round 5: 391 peptides, 65 chains. Longest chain 16 peptides. Score 0.397 Taking the results from Round 4 Chains 62, Residues 324, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13749 restraints for refining 6398 atoms. 12515 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2402 (Rfree = 0.000) for 6398 atoms. Found 41 (57 requested) and removed 29 (28 requested) atoms. Cycle 27: After refmac, R = 0.2356 (Rfree = 0.000) for 6392 atoms. Found 24 (57 requested) and removed 30 (28 requested) atoms. Cycle 28: After refmac, R = 0.2283 (Rfree = 0.000) for 6378 atoms. Found 19 (57 requested) and removed 31 (28 requested) atoms. Cycle 29: After refmac, R = 0.2222 (Rfree = 0.000) for 6360 atoms. Found 16 (57 requested) and removed 34 (28 requested) atoms. Cycle 30: After refmac, R = 0.2244 (Rfree = 0.000) for 6338 atoms. Found 11 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 2.90 Search for helices and strands: 0 residues in 0 chains, 6400 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 6429 seeds are put forward Round 1: 325 peptides, 64 chains. Longest chain 13 peptides. Score 0.296 Round 2: 387 peptides, 71 chains. Longest chain 15 peptides. Score 0.349 Round 3: 383 peptides, 66 chains. Longest chain 18 peptides. Score 0.378 Round 4: 386 peptides, 65 chains. Longest chain 19 peptides. Score 0.389 Round 5: 400 peptides, 64 chains. Longest chain 19 peptides. Score 0.418 Taking the results from Round 5 Chains 66, Residues 336, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13321 restraints for refining 6397 atoms. 11960 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2426 (Rfree = 0.000) for 6397 atoms. Found 40 (57 requested) and removed 41 (28 requested) atoms. Cycle 32: After refmac, R = 0.2321 (Rfree = 0.000) for 6383 atoms. Found 24 (57 requested) and removed 33 (28 requested) atoms. Cycle 33: After refmac, R = 0.2304 (Rfree = 0.000) for 6366 atoms. Found 20 (57 requested) and removed 31 (28 requested) atoms. Cycle 34: After refmac, R = 0.2188 (Rfree = 0.000) for 6348 atoms. Found 7 (56 requested) and removed 29 (28 requested) atoms. Cycle 35: After refmac, R = 0.2220 (Rfree = 0.000) for 6316 atoms. Found 16 (56 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 2.93 Search for helices and strands: 0 residues in 0 chains, 6347 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 6378 seeds are put forward Round 1: 312 peptides, 66 chains. Longest chain 8 peptides. Score 0.258 Round 2: 369 peptides, 67 chains. Longest chain 11 peptides. Score 0.348 Round 3: 387 peptides, 64 chains. Longest chain 14 peptides. Score 0.398 Round 4: 410 peptides, 69 chains. Longest chain 13 peptides. Score 0.399 Round 5: 395 peptides, 70 chains. Longest chain 14 peptides. Score 0.369 Taking the results from Round 4 Chains 69, Residues 341, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13570 restraints for refining 6398 atoms. 12275 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2371 (Rfree = 0.000) for 6398 atoms. Found 29 (57 requested) and removed 32 (28 requested) atoms. Cycle 37: After refmac, R = 0.2249 (Rfree = 0.000) for 6381 atoms. Found 26 (57 requested) and removed 31 (28 requested) atoms. Cycle 38: After refmac, R = 0.2208 (Rfree = 0.000) for 6372 atoms. Found 12 (57 requested) and removed 28 (28 requested) atoms. Cycle 39: After refmac, R = 0.2184 (Rfree = 0.000) for 6353 atoms. Found 10 (57 requested) and removed 28 (28 requested) atoms. Cycle 40: After refmac, R = 0.2154 (Rfree = 0.000) for 6333 atoms. Found 9 (56 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 6384 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6400 seeds are put forward Round 1: 306 peptides, 65 chains. Longest chain 10 peptides. Score 0.254 Round 2: 357 peptides, 62 chains. Longest chain 16 peptides. Score 0.364 Round 3: 359 peptides, 64 chains. Longest chain 13 peptides. Score 0.353 Round 4: 362 peptides, 66 chains. Longest chain 16 peptides. Score 0.344 Round 5: 352 peptides, 61 chains. Longest chain 16 peptides. Score 0.363 Taking the results from Round 2 Chains 63, Residues 295, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 17612 reflections ( 99.18 % complete ) and 13723 restraints for refining 6398 atoms. 12562 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2282 (Rfree = 0.000) for 6398 atoms. Found 39 (57 requested) and removed 29 (28 requested) atoms. Cycle 42: After refmac, R = 0.2240 (Rfree = 0.000) for 6398 atoms. Found 16 (57 requested) and removed 29 (28 requested) atoms. Cycle 43: After refmac, R = 0.2214 (Rfree = 0.000) for 6383 atoms. Found 21 (57 requested) and removed 28 (28 requested) atoms. Cycle 44: After refmac, R = 0.2230 (Rfree = 0.000) for 6375 atoms. Found 13 (57 requested) and removed 29 (28 requested) atoms. Cycle 45: After refmac, R = 0.2174 (Rfree = 0.000) for 6357 atoms. Found 14 (57 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.91 Search for helices and strands: 0 residues in 0 chains, 6386 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6406 seeds are put forward Round 1: 311 peptides, 67 chains. Longest chain 8 peptides. Score 0.248 Round 2: 343 peptides, 65 chains. Longest chain 10 peptides. Score 0.319 Round 3: 352 peptides, 66 chains. Longest chain 10 peptides. Score 0.327 Round 4: 327 peptides, 61 chains. Longest chain 10 peptides. Score 0.321 Round 5: 331 peptides, 62 chains. Longest chain 16 peptides. Score 0.321 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 286, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (286 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17612 reflections ( 99.18 % complete ) and 13842 restraints for refining 6398 atoms. 12738 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2269 (Rfree = 0.000) for 6398 atoms. Found 0 (57 requested) and removed 25 (28 requested) atoms. Cycle 47: After refmac, R = 0.2213 (Rfree = 0.000) for 6357 atoms. Found 0 (57 requested) and removed 9 (28 requested) atoms. Cycle 48: After refmac, R = 0.2163 (Rfree = 0.000) for 6347 atoms. Found 0 (56 requested) and removed 11 (28 requested) atoms. Cycle 49: After refmac, R = 0.2154 (Rfree = 0.000) for 6335 atoms. Found 0 (56 requested) and removed 3 (28 requested) atoms. Writing output files ... TimeTaking 60.13