Sun 23 Dec 23:57:09 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 1vrb-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vrb-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.8-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/1vrb-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.8-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 23:57:14 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/1vrb-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vrb-3.8-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 874 and 0 Target number of residues in the AU: 874 Target solvent content: 0.6664 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-3.8-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.65 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: 48.979 3.800 Wilson plot Bfac: 89.57 14699 reflections ( 99.13 % complete ) and 0 restraints for refining 12046 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3494 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3372 (Rfree = 0.000) for 12046 atoms. Found 62 (66 requested) and removed 443 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 11813 seeds are put forward NCS extension: 0 residues added, 11813 seeds are put forward Round 1: 297 peptides, 66 chains. Longest chain 8 peptides. Score 0.219 Round 2: 428 peptides, 80 chains. Longest chain 14 peptides. Score 0.317 Round 3: 479 peptides, 86 chains. Longest chain 14 peptides. Score 0.348 Round 4: 507 peptides, 91 chains. Longest chain 11 peptides. Score 0.356 Round 5: 518 peptides, 90 chains. Longest chain 16 peptides. Score 0.374 Taking the results from Round 5 Chains 90, Residues 428, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 24324 restraints for refining 9896 atoms. 22664 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2919 (Rfree = 0.000) for 9896 atoms. Found 45 (54 requested) and removed 104 (27 requested) atoms. Cycle 2: After refmac, R = 0.2718 (Rfree = 0.000) for 9628 atoms. Found 47 (54 requested) and removed 72 (27 requested) atoms. Cycle 3: After refmac, R = 0.2598 (Rfree = 0.000) for 9537 atoms. Found 38 (52 requested) and removed 72 (26 requested) atoms. Cycle 4: After refmac, R = 0.2509 (Rfree = 0.000) for 9456 atoms. Found 38 (52 requested) and removed 58 (26 requested) atoms. Cycle 5: After refmac, R = 0.2478 (Rfree = 0.000) for 9404 atoms. Found 51 (51 requested) and removed 57 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 9769 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 9789 seeds are put forward Round 1: 450 peptides, 97 chains. Longest chain 9 peptides. Score 0.252 Round 2: 564 peptides, 105 chains. Longest chain 13 peptides. Score 0.353 Round 3: 552 peptides, 102 chains. Longest chain 14 peptides. Score 0.353 Round 4: 559 peptides, 98 chains. Longest chain 15 peptides. Score 0.382 Round 5: 573 peptides, 94 chains. Longest chain 16 peptides. Score 0.417 Taking the results from Round 5 Chains 95, Residues 479, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21379 restraints for refining 9245 atoms. 19461 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2450 (Rfree = 0.000) for 9245 atoms. Found 38 (50 requested) and removed 95 (25 requested) atoms. Cycle 7: After refmac, R = 0.2300 (Rfree = 0.000) for 9089 atoms. Found 38 (50 requested) and removed 67 (25 requested) atoms. Cycle 8: After refmac, R = 0.2163 (Rfree = 0.000) for 8996 atoms. Found 49 (49 requested) and removed 47 (24 requested) atoms. Cycle 9: After refmac, R = 0.1859 (Rfree = 0.000) for 8962 atoms. Found 12 (49 requested) and removed 36 (24 requested) atoms. Cycle 10: After refmac, R = 0.1767 (Rfree = 0.000) for 8906 atoms. Found 8 (49 requested) and removed 42 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 9151 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 9165 seeds are put forward Round 1: 509 peptides, 101 chains. Longest chain 14 peptides. Score 0.306 Round 2: 596 peptides, 102 chains. Longest chain 17 peptides. Score 0.404 Round 3: 627 peptides, 100 chains. Longest chain 21 peptides. Score 0.448 Round 4: 635 peptides, 92 chains. Longest chain 24 peptides. Score 0.493 Round 5: 633 peptides, 97 chains. Longest chain 25 peptides. Score 0.468 Taking the results from Round 4 Chains 97, Residues 543, Estimated correctness of the model 0.0 % 9 chains (60 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 20660 restraints for refining 9293 atoms. 18385 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2347 (Rfree = 0.000) for 9293 atoms. Found 37 (51 requested) and removed 102 (25 requested) atoms. Cycle 12: After refmac, R = 0.2194 (Rfree = 0.000) for 9169 atoms. Found 39 (50 requested) and removed 50 (25 requested) atoms. Cycle 13: After refmac, R = 0.2168 (Rfree = 0.000) for 9115 atoms. Found 40 (50 requested) and removed 58 (25 requested) atoms. Cycle 14: After refmac, R = 0.1885 (Rfree = 0.000) for 9064 atoms. Found 12 (50 requested) and removed 35 (25 requested) atoms. Cycle 15: After refmac, R = 0.1845 (Rfree = 0.000) for 9018 atoms. Found 15 (49 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 9308 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 9347 seeds are put forward Round 1: 526 peptides, 106 chains. Longest chain 11 peptides. Score 0.301 Round 2: 594 peptides, 100 chains. Longest chain 17 peptides. Score 0.412 Round 3: 621 peptides, 98 chains. Longest chain 19 peptides. Score 0.451 Round 4: 607 peptides, 98 chains. Longest chain 18 peptides. Score 0.436 Round 5: 616 peptides, 102 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 3 Chains 98, Residues 523, Estimated correctness of the model 0.0 % 8 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21116 restraints for refining 9330 atoms. 19051 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2201 (Rfree = 0.000) for 9330 atoms. Found 44 (51 requested) and removed 84 (25 requested) atoms. Cycle 17: After refmac, R = 0.2100 (Rfree = 0.000) for 9236 atoms. Found 20 (51 requested) and removed 60 (25 requested) atoms. Cycle 18: After refmac, R = 0.2119 (Rfree = 0.000) for 9176 atoms. Found 37 (50 requested) and removed 45 (25 requested) atoms. Cycle 19: After refmac, R = 0.2055 (Rfree = 0.000) for 9153 atoms. Found 32 (50 requested) and removed 46 (25 requested) atoms. Cycle 20: After refmac, R = 0.2055 (Rfree = 0.000) for 9121 atoms. Found 47 (50 requested) and removed 49 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 9425 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 9453 seeds are put forward Round 1: 493 peptides, 96 chains. Longest chain 14 peptides. Score 0.313 Round 2: 559 peptides, 96 chains. Longest chain 16 peptides. Score 0.392 Round 3: 562 peptides, 95 chains. Longest chain 14 peptides. Score 0.400 Round 4: 602 peptides, 94 chains. Longest chain 16 peptides. Score 0.449 Round 5: 579 peptides, 92 chains. Longest chain 17 peptides. Score 0.434 Taking the results from Round 4 Chains 94, Residues 508, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22277 restraints for refining 9613 atoms. 20318 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2281 (Rfree = 0.000) for 9613 atoms. Found 52 (52 requested) and removed 88 (26 requested) atoms. Cycle 22: After refmac, R = 0.2279 (Rfree = 0.000) for 9522 atoms. Found 52 (52 requested) and removed 66 (26 requested) atoms. Cycle 23: After refmac, R = 0.2174 (Rfree = 0.000) for 9461 atoms. Found 52 (52 requested) and removed 61 (26 requested) atoms. Cycle 24: After refmac, R = 0.2083 (Rfree = 0.000) for 9416 atoms. Found 51 (51 requested) and removed 71 (25 requested) atoms. Cycle 25: After refmac, R = 0.2094 (Rfree = 0.000) for 9373 atoms. Found 51 (51 requested) and removed 50 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 9696 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 9717 seeds are put forward Round 1: 442 peptides, 96 chains. Longest chain 9 peptides. Score 0.247 Round 2: 527 peptides, 100 chains. Longest chain 15 peptides. Score 0.334 Round 3: 553 peptides, 92 chains. Longest chain 13 peptides. Score 0.405 Round 4: 560 peptides, 99 chains. Longest chain 15 peptides. Score 0.378 Round 5: 594 peptides, 95 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 5 Chains 95, Residues 499, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22438 restraints for refining 9662 atoms. 20498 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 9662 atoms. Found 53 (53 requested) and removed 90 (26 requested) atoms. Cycle 27: After refmac, R = 0.2265 (Rfree = 0.000) for 9550 atoms. Found 52 (52 requested) and removed 57 (26 requested) atoms. Cycle 28: After refmac, R = 0.2262 (Rfree = 0.000) for 9495 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 29: After refmac, R = 0.2196 (Rfree = 0.000) for 9456 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 9413 atoms. Found 52 (52 requested) and removed 50 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 9778 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 9791 seeds are put forward Round 1: 445 peptides, 99 chains. Longest chain 9 peptides. Score 0.235 Round 2: 522 peptides, 95 chains. Longest chain 18 peptides. Score 0.353 Round 3: 521 peptides, 99 chains. Longest chain 15 peptides. Score 0.332 Round 4: 529 peptides, 91 chains. Longest chain 18 peptides. Score 0.382 Round 5: 511 peptides, 94 chains. Longest chain 13 peptides. Score 0.345 Taking the results from Round 4 Chains 91, Residues 438, Estimated correctness of the model 0.0 % 6 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21692 restraints for refining 9395 atoms. 19989 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2279 (Rfree = 0.000) for 9395 atoms. Found 51 (51 requested) and removed 62 (25 requested) atoms. Cycle 32: After refmac, R = 0.2256 (Rfree = 0.000) for 9347 atoms. Found 51 (51 requested) and removed 47 (25 requested) atoms. Cycle 33: After refmac, R = 0.2208 (Rfree = 0.000) for 9315 atoms. Found 51 (51 requested) and removed 51 (25 requested) atoms. Cycle 34: After refmac, R = 0.2128 (Rfree = 0.000) for 9292 atoms. Found 51 (51 requested) and removed 42 (25 requested) atoms. Cycle 35: After refmac, R = 0.2194 (Rfree = 0.000) for 9278 atoms. Found 51 (51 requested) and removed 45 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 9537 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 9557 seeds are put forward Round 1: 444 peptides, 97 chains. Longest chain 11 peptides. Score 0.244 Round 2: 497 peptides, 92 chains. Longest chain 12 peptides. Score 0.339 Round 3: 520 peptides, 89 chains. Longest chain 13 peptides. Score 0.382 Round 4: 507 peptides, 88 chains. Longest chain 13 peptides. Score 0.371 Round 5: 516 peptides, 91 chains. Longest chain 14 peptides. Score 0.367 Taking the results from Round 3 Chains 89, Residues 431, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21823 restraints for refining 9447 atoms. 20159 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2193 (Rfree = 0.000) for 9447 atoms. Found 51 (51 requested) and removed 88 (25 requested) atoms. Cycle 37: After refmac, R = 0.2200 (Rfree = 0.000) for 9371 atoms. Found 51 (51 requested) and removed 76 (25 requested) atoms. Cycle 38: After refmac, R = 0.2208 (Rfree = 0.000) for 9317 atoms. Found 51 (51 requested) and removed 96 (25 requested) atoms. Cycle 39: After refmac, R = 0.2185 (Rfree = 0.000) for 9246 atoms. Found 50 (50 requested) and removed 38 (25 requested) atoms. Cycle 40: After refmac, R = 0.1876 (Rfree = 0.000) for 9233 atoms. Found 21 (50 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 9466 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 9482 seeds are put forward Round 1: 390 peptides, 83 chains. Longest chain 12 peptides. Score 0.250 Round 2: 465 peptides, 89 chains. Longest chain 13 peptides. Score 0.315 Round 3: 461 peptides, 84 chains. Longest chain 19 peptides. Score 0.337 Round 4: 480 peptides, 88 chains. Longest chain 12 peptides. Score 0.339 Round 5: 480 peptides, 87 chains. Longest chain 13 peptides. Score 0.344 Taking the results from Round 5 Chains 87, Residues 393, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22210 restraints for refining 9499 atoms. 20695 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2255 (Rfree = 0.000) for 9499 atoms. Found 52 (52 requested) and removed 58 (26 requested) atoms. Cycle 42: After refmac, R = 0.2293 (Rfree = 0.000) for 9447 atoms. Found 52 (52 requested) and removed 69 (26 requested) atoms. Cycle 43: After refmac, R = 0.2222 (Rfree = 0.000) for 9402 atoms. Found 51 (51 requested) and removed 41 (25 requested) atoms. Cycle 44: After refmac, R = 0.2279 (Rfree = 0.000) for 9382 atoms. Found 51 (51 requested) and removed 42 (25 requested) atoms. Cycle 45: After refmac, R = 0.2255 (Rfree = 0.000) for 9364 atoms. Found 51 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 9670 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 9686 seeds are put forward Round 1: 378 peptides, 83 chains. Longest chain 9 peptides. Score 0.233 Round 2: 446 peptides, 89 chains. Longest chain 14 peptides. Score 0.291 Round 3: 454 peptides, 85 chains. Longest chain 14 peptides. Score 0.323 Round 4: 462 peptides, 86 chains. Longest chain 14 peptides. Score 0.327 Round 5: 462 peptides, 89 chains. Longest chain 12 peptides. Score 0.311 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 87, Residues 376, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 87 chains (376 residues) following loop building 5 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14699 reflections ( 99.13 % complete ) and 22053 restraints for refining 9460 atoms. 20571 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2344 (Rfree = 0.000) for 9460 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2315 (Rfree = 0.000) for 9408 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2263 (Rfree = 0.000) for 9363 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2268 (Rfree = 0.000) for 9311 atoms. TimeTaking 88.47