null Tue 25 Dec 19:27:55 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 1vrb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-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/1vrb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-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 19:28:05 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/1vrb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-3.6-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 896 and 0 Target number of residues in the AU: 896 Target solvent content: 0.6580 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-3.6-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.60 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 3.600 Wilson plot Bfac: 83.52 17139 reflections ( 98.80 % complete ) and 0 restraints for refining 12084 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3472 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3236 (Rfree = 0.000) for 12084 atoms. Found 77 (77 requested) and removed 168 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 12248 seeds are put forward NCS extension: 0 residues added, 12248 seeds are put forward Round 1: 471 peptides, 99 chains. Longest chain 11 peptides. Score 0.269 Round 2: 611 peptides, 103 chains. Longest chain 20 peptides. Score 0.416 Round 3: 650 peptides, 103 chains. Longest chain 18 peptides. Score 0.458 Round 4: 649 peptides, 97 chains. Longest chain 15 peptides. Score 0.485 Round 5: 664 peptides, 99 chains. Longest chain 21 peptides. Score 0.491 Taking the results from Round 5 Chains 99, Residues 565, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 23223 restraints for refining 9912 atoms. 20936 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2732 (Rfree = 0.000) for 9912 atoms. Found 51 (63 requested) and removed 96 (31 requested) atoms. Cycle 2: After refmac, R = 0.2515 (Rfree = 0.000) for 9716 atoms. Found 40 (63 requested) and removed 72 (31 requested) atoms. Cycle 3: After refmac, R = 0.2463 (Rfree = 0.000) for 9604 atoms. Found 32 (62 requested) and removed 70 (31 requested) atoms. Cycle 4: After refmac, R = 0.2409 (Rfree = 0.000) for 9505 atoms. Found 46 (61 requested) and removed 61 (30 requested) atoms. Cycle 5: After refmac, R = 0.2380 (Rfree = 0.000) for 9449 atoms. Found 32 (60 requested) and removed 49 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 9750 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 9782 seeds are put forward Round 1: 525 peptides, 98 chains. Longest chain 18 peptides. Score 0.342 Round 2: 630 peptides, 103 chains. Longest chain 22 peptides. Score 0.437 Round 3: 617 peptides, 95 chains. Longest chain 19 peptides. Score 0.460 Round 4: 634 peptides, 94 chains. Longest chain 23 peptides. Score 0.483 Round 5: 637 peptides, 100 chains. Longest chain 20 peptides. Score 0.458 Taking the results from Round 4 Chains 100, Residues 540, Estimated correctness of the model 0.0 % 9 chains (70 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21946 restraints for refining 9654 atoms. 19642 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2469 (Rfree = 0.000) for 9654 atoms. Found 45 (61 requested) and removed 96 (30 requested) atoms. Cycle 7: After refmac, R = 0.2385 (Rfree = 0.000) for 9530 atoms. Found 52 (61 requested) and removed 67 (30 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 9467 atoms. Found 45 (61 requested) and removed 64 (30 requested) atoms. Cycle 9: After refmac, R = 0.2337 (Rfree = 0.000) for 9406 atoms. Found 54 (60 requested) and removed 54 (30 requested) atoms. Cycle 10: After refmac, R = 0.2283 (Rfree = 0.000) for 9356 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 9697 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 9709 seeds are put forward Round 1: 492 peptides, 99 chains. Longest chain 14 peptides. Score 0.296 Round 2: 562 peptides, 96 chains. Longest chain 15 peptides. Score 0.395 Round 3: 571 peptides, 96 chains. Longest chain 15 peptides. Score 0.405 Round 4: 571 peptides, 92 chains. Longest chain 16 peptides. Score 0.425 Round 5: 573 peptides, 95 chains. Longest chain 20 peptides. Score 0.413 Taking the results from Round 4 Chains 92, Residues 479, Estimated correctness of the model 0.0 % 6 chains (25 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22491 restraints for refining 9596 atoms. 20608 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2430 (Rfree = 0.000) for 9596 atoms. Found 61 (61 requested) and removed 88 (30 requested) atoms. Cycle 12: After refmac, R = 0.2399 (Rfree = 0.000) for 9503 atoms. Found 61 (61 requested) and removed 59 (30 requested) atoms. Cycle 13: After refmac, R = 0.2324 (Rfree = 0.000) for 9464 atoms. Found 60 (60 requested) and removed 60 (30 requested) atoms. Cycle 14: After refmac, R = 0.2251 (Rfree = 0.000) for 9428 atoms. Found 60 (60 requested) and removed 62 (30 requested) atoms. Cycle 15: After refmac, R = 0.1955 (Rfree = 0.000) for 9391 atoms. Found 21 (60 requested) and removed 42 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 9701 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 9722 seeds are put forward Round 1: 450 peptides, 93 chains. Longest chain 12 peptides. Score 0.274 Round 2: 542 peptides, 93 chains. Longest chain 11 peptides. Score 0.387 Round 3: 554 peptides, 87 chains. Longest chain 14 peptides. Score 0.430 Round 4: 532 peptides, 87 chains. Longest chain 14 peptides. Score 0.406 Round 5: 576 peptides, 91 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 5 Chains 93, Residues 485, Estimated correctness of the model 0.0 % 9 chains (46 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21872 restraints for refining 9587 atoms. 19921 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2395 (Rfree = 0.000) for 9587 atoms. Found 61 (61 requested) and removed 83 (30 requested) atoms. Cycle 17: After refmac, R = 0.2328 (Rfree = 0.000) for 9522 atoms. Found 61 (61 requested) and removed 57 (30 requested) atoms. Cycle 18: After refmac, R = 0.2259 (Rfree = 0.000) for 9501 atoms. Found 61 (61 requested) and removed 50 (30 requested) atoms. Cycle 19: After refmac, R = 0.2198 (Rfree = 0.000) for 9471 atoms. Found 61 (61 requested) and removed 42 (30 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 9461 atoms. Found 22 (60 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 9721 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 9741 seeds are put forward Round 1: 468 peptides, 97 chains. Longest chain 9 peptides. Score 0.276 Round 2: 543 peptides, 95 chains. Longest chain 18 peptides. Score 0.378 Round 3: 556 peptides, 96 chains. Longest chain 16 peptides. Score 0.388 Round 4: 551 peptides, 87 chains. Longest chain 19 peptides. Score 0.427 Round 5: 559 peptides, 93 chains. Longest chain 18 peptides. Score 0.407 Taking the results from Round 4 Chains 87, Residues 464, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21898 restraints for refining 9550 atoms. 20051 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2316 (Rfree = 0.000) for 9550 atoms. Found 51 (61 requested) and removed 75 (30 requested) atoms. Cycle 22: After refmac, R = 0.2293 (Rfree = 0.000) for 9492 atoms. Found 61 (61 requested) and removed 54 (30 requested) atoms. Cycle 23: After refmac, R = 0.2299 (Rfree = 0.000) for 9461 atoms. Found 60 (60 requested) and removed 51 (30 requested) atoms. Cycle 24: After refmac, R = 0.2221 (Rfree = 0.000) for 9430 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 25: After refmac, R = 0.1952 (Rfree = 0.000) for 9423 atoms. Found 18 (60 requested) and removed 42 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 9704 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 9717 seeds are put forward Round 1: 442 peptides, 90 chains. Longest chain 12 peptides. Score 0.280 Round 2: 494 peptides, 86 chains. Longest chain 14 peptides. Score 0.366 Round 3: 491 peptides, 86 chains. Longest chain 13 peptides. Score 0.363 Round 4: 487 peptides, 79 chains. Longest chain 16 peptides. Score 0.394 Round 5: 482 peptides, 86 chains. Longest chain 13 peptides. Score 0.352 Taking the results from Round 4 Chains 80, Residues 408, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22134 restraints for refining 9643 atoms. 20460 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2262 (Rfree = 0.000) for 9643 atoms. Found 52 (61 requested) and removed 75 (30 requested) atoms. Cycle 27: After refmac, R = 0.2254 (Rfree = 0.000) for 9578 atoms. Found 61 (61 requested) and removed 62 (30 requested) atoms. Cycle 28: After refmac, R = 0.2251 (Rfree = 0.000) for 9548 atoms. Found 61 (61 requested) and removed 82 (30 requested) atoms. Cycle 29: After refmac, R = 0.2029 (Rfree = 0.000) for 9503 atoms. Found 20 (61 requested) and removed 38 (30 requested) atoms. Cycle 30: After refmac, R = 0.1967 (Rfree = 0.000) for 9465 atoms. Found 14 (60 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 9705 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 9721 seeds are put forward Round 1: 363 peptides, 79 chains. Longest chain 7 peptides. Score 0.236 Round 2: 444 peptides, 86 chains. Longest chain 11 peptides. Score 0.305 Round 3: 433 peptides, 79 chains. Longest chain 10 peptides. Score 0.329 Round 4: 461 peptides, 87 chains. Longest chain 10 peptides. Score 0.321 Round 5: 455 peptides, 80 chains. Longest chain 15 peptides. Score 0.351 Taking the results from Round 5 Chains 82, Residues 375, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 22348 restraints for refining 9593 atoms. 20861 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2311 (Rfree = 0.000) for 9593 atoms. Found 54 (61 requested) and removed 65 (30 requested) atoms. Cycle 32: After refmac, R = 0.2314 (Rfree = 0.000) for 9546 atoms. Found 61 (61 requested) and removed 57 (30 requested) atoms. Cycle 33: After refmac, R = 0.2424 (Rfree = 0.000) for 9507 atoms. Found 61 (61 requested) and removed 58 (30 requested) atoms. Cycle 34: After refmac, R = 0.2466 (Rfree = 0.000) for 9475 atoms. Found 61 (61 requested) and removed 54 (30 requested) atoms. Cycle 35: After refmac, R = 0.2492 (Rfree = 0.000) for 9437 atoms. Found 60 (60 requested) and removed 50 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 9709 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 9722 seeds are put forward Round 1: 308 peptides, 71 chains. Longest chain 7 peptides. Score 0.204 Round 2: 369 peptides, 74 chains. Longest chain 11 peptides. Score 0.273 Round 3: 380 peptides, 72 chains. Longest chain 12 peptides. Score 0.299 Round 4: 391 peptides, 76 chains. Longest chain 11 peptides. Score 0.291 Round 5: 402 peptides, 72 chains. Longest chain 17 peptides. Score 0.328 Taking the results from Round 5 Chains 72, Residues 330, Estimated correctness of the model 0.0 % 8 chains (26 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21879 restraints for refining 9397 atoms. 20579 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2444 (Rfree = 0.000) for 9397 atoms. Found 60 (60 requested) and removed 52 (30 requested) atoms. Cycle 37: After refmac, R = 0.2416 (Rfree = 0.000) for 9355 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 38: After refmac, R = 0.2379 (Rfree = 0.000) for 9336 atoms. Found 60 (60 requested) and removed 51 (30 requested) atoms. Cycle 39: After refmac, R = 0.2149 (Rfree = 0.000) for 9326 atoms. Found 14 (59 requested) and removed 38 (29 requested) atoms. Cycle 40: After refmac, R = 0.2119 (Rfree = 0.000) for 9291 atoms. Found 13 (59 requested) and removed 35 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 9513 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 9546 seeds are put forward Round 1: 293 peptides, 65 chains. Longest chain 9 peptides. Score 0.219 Round 2: 329 peptides, 67 chains. Longest chain 10 peptides. Score 0.259 Round 3: 353 peptides, 68 chains. Longest chain 11 peptides. Score 0.286 Round 4: 338 peptides, 64 chains. Longest chain 11 peptides. Score 0.290 Round 5: 362 peptides, 66 chains. Longest chain 11 peptides. Score 0.310 Taking the results from Round 5 Chains 66, Residues 296, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17139 reflections ( 98.80 % complete ) and 21769 restraints for refining 9282 atoms. 20640 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2474 (Rfree = 0.000) for 9282 atoms. Found 59 (59 requested) and removed 55 (29 requested) atoms. Cycle 42: After refmac, R = 0.2565 (Rfree = 0.000) for 9258 atoms. Found 59 (59 requested) and removed 65 (29 requested) atoms. Cycle 43: After refmac, R = 0.2576 (Rfree = 0.000) for 9225 atoms. Found 59 (59 requested) and removed 57 (29 requested) atoms. Cycle 44: After refmac, R = 0.2553 (Rfree = 0.000) for 9209 atoms. Found 59 (59 requested) and removed 54 (29 requested) atoms. Cycle 45: After refmac, R = 0.2271 (Rfree = 0.000) for 9204 atoms. Found 32 (59 requested) and removed 36 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 9463 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 9476 seeds are put forward Round 1: 254 peptides, 56 chains. Longest chain 10 peptides. Score 0.217 Round 2: 271 peptides, 53 chains. Longest chain 10 peptides. Score 0.262 Round 3: 270 peptides, 52 chains. Longest chain 10 peptides. Score 0.267 Round 4: 263 peptides, 51 chains. Longest chain 12 peptides. Score 0.264 Round 5: 259 peptides, 49 chains. Longest chain 9 peptides. Score 0.271 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 210, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (210 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17139 reflections ( 98.80 % complete ) and 21440 restraints for refining 9171 atoms. 20629 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2409 (Rfree = 0.000) for 9171 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2608 (Rfree = 0.000) for 9122 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2437 (Rfree = 0.000) for 9074 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.2492 (Rfree = 0.000) for 9024 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:34:55 GMT 2018 Job finished. TimeTaking 127 Used memory is bytes: 24011256