Sun 23 Dec 22:22:46 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 2aml-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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/2aml-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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 ============================================================ Sun 23 Dec 22:22:55 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/2aml-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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 460 and 0 Target number of residues in the AU: 460 Target solvent content: 0.6371 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-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: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5968 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: 77.491 3.600 Wilson plot Bfac: 70.35 8411 reflections ( 99.75 % complete ) and 0 restraints for refining 6648 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3144 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2718 (Rfree = 0.000) for 6648 atoms. Found 42 (42 requested) and removed 46 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 6813 seeds are put forward NCS extension: 0 residues added, 6813 seeds are put forward Round 1: 288 peptides, 59 chains. Longest chain 10 peptides. Score 0.304 Round 2: 357 peptides, 56 chains. Longest chain 14 peptides. Score 0.492 Round 3: 390 peptides, 57 chains. Longest chain 17 peptides. Score 0.548 Round 4: 408 peptides, 58 chains. Longest chain 14 peptides. Score 0.573 Round 5: 422 peptides, 54 chains. Longest chain 23 peptides. Score 0.627 Taking the results from Round 5 Chains 60, Residues 368, Estimated correctness of the model 24.9 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 11835 restraints for refining 5407 atoms. 10267 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2277 (Rfree = 0.000) for 5407 atoms. Found 32 (34 requested) and removed 37 (17 requested) atoms. Cycle 2: After refmac, R = 0.2064 (Rfree = 0.000) for 5345 atoms. Found 18 (34 requested) and removed 25 (17 requested) atoms. Cycle 3: After refmac, R = 0.1999 (Rfree = 0.000) for 5303 atoms. Found 10 (34 requested) and removed 25 (17 requested) atoms. Cycle 4: After refmac, R = 0.1976 (Rfree = 0.000) for 5256 atoms. Found 15 (33 requested) and removed 24 (16 requested) atoms. Cycle 5: After refmac, R = 0.1899 (Rfree = 0.000) for 5237 atoms. Found 12 (33 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 5461 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5483 seeds are put forward Round 1: 347 peptides, 65 chains. Longest chain 19 peptides. Score 0.386 Round 2: 422 peptides, 59 chains. Longest chain 20 peptides. Score 0.590 Round 3: 405 peptides, 54 chains. Longest chain 25 peptides. Score 0.599 Round 4: 414 peptides, 55 chains. Longest chain 28 peptides. Score 0.607 Round 5: 406 peptides, 53 chains. Longest chain 28 peptides. Score 0.608 Taking the results from Round 5 Chains 56, Residues 353, Estimated correctness of the model 17.8 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12222 restraints for refining 5392 atoms. 10783 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2174 (Rfree = 0.000) for 5392 atoms. Found 28 (34 requested) and removed 32 (17 requested) atoms. Cycle 7: After refmac, R = 0.1994 (Rfree = 0.000) for 5355 atoms. Found 18 (34 requested) and removed 27 (17 requested) atoms. Cycle 8: After refmac, R = 0.1862 (Rfree = 0.000) for 5327 atoms. Found 25 (34 requested) and removed 20 (17 requested) atoms. Cycle 9: After refmac, R = 0.1561 (Rfree = 0.000) for 5313 atoms. Found 9 (34 requested) and removed 21 (17 requested) atoms. Cycle 10: After refmac, R = 0.1644 (Rfree = 0.000) for 5294 atoms. Found 18 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 5513 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 5535 seeds are put forward Round 1: 360 peptides, 63 chains. Longest chain 14 peptides. Score 0.434 Round 2: 400 peptides, 59 chains. Longest chain 20 peptides. Score 0.550 Round 3: 415 peptides, 57 chains. Longest chain 20 peptides. Score 0.593 Round 4: 406 peptides, 57 chains. Longest chain 20 peptides. Score 0.577 Round 5: 408 peptides, 55 chains. Longest chain 26 peptides. Score 0.596 Taking the results from Round 5 Chains 58, Residues 353, Estimated correctness of the model 13.1 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12185 restraints for refining 5410 atoms. 10724 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2080 (Rfree = 0.000) for 5410 atoms. Found 31 (34 requested) and removed 38 (17 requested) atoms. Cycle 12: After refmac, R = 0.1878 (Rfree = 0.000) for 5382 atoms. Found 20 (34 requested) and removed 32 (17 requested) atoms. Cycle 13: After refmac, R = 0.1754 (Rfree = 0.000) for 5354 atoms. Found 23 (34 requested) and removed 22 (17 requested) atoms. Cycle 14: After refmac, R = 0.1697 (Rfree = 0.000) for 5343 atoms. Found 19 (34 requested) and removed 27 (17 requested) atoms. Cycle 15: After refmac, R = 0.1638 (Rfree = 0.000) for 5330 atoms. Found 17 (34 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5520 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 5559 seeds are put forward Round 1: 317 peptides, 55 chains. Longest chain 15 peptides. Score 0.414 Round 2: 359 peptides, 52 chains. Longest chain 16 peptides. Score 0.531 Round 3: 367 peptides, 55 chains. Longest chain 17 peptides. Score 0.521 Round 4: 365 peptides, 55 chains. Longest chain 15 peptides. Score 0.517 Round 5: 387 peptides, 54 chains. Longest chain 21 peptides. Score 0.567 Taking the results from Round 5 Chains 60, Residues 333, Estimated correctness of the model 1.3 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12100 restraints for refining 5407 atoms. 10665 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2057 (Rfree = 0.000) for 5407 atoms. Found 23 (34 requested) and removed 27 (17 requested) atoms. Cycle 17: After refmac, R = 0.1749 (Rfree = 0.000) for 5385 atoms. Found 11 (34 requested) and removed 24 (17 requested) atoms. Cycle 18: After refmac, R = 0.1722 (Rfree = 0.000) for 5358 atoms. Found 18 (34 requested) and removed 24 (17 requested) atoms. Cycle 19: After refmac, R = 0.1685 (Rfree = 0.000) for 5345 atoms. Found 26 (34 requested) and removed 23 (17 requested) atoms. Cycle 20: After refmac, R = 0.1674 (Rfree = 0.000) for 5339 atoms. Found 23 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 5519 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 5535 seeds are put forward Round 1: 300 peptides, 54 chains. Longest chain 15 peptides. Score 0.385 Round 2: 356 peptides, 58 chains. Longest chain 17 peptides. Score 0.472 Round 3: 354 peptides, 55 chains. Longest chain 19 peptides. Score 0.494 Round 4: 345 peptides, 55 chains. Longest chain 22 peptides. Score 0.476 Round 5: 346 peptides, 54 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 3 Chains 56, Residues 299, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12559 restraints for refining 5410 atoms. 11360 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1816 (Rfree = 0.000) for 5410 atoms. Found 25 (34 requested) and removed 22 (17 requested) atoms. Cycle 22: After refmac, R = 0.1848 (Rfree = 0.000) for 5396 atoms. Found 32 (34 requested) and removed 25 (17 requested) atoms. Cycle 23: After refmac, R = 0.1745 (Rfree = 0.000) for 5394 atoms. Found 27 (34 requested) and removed 20 (17 requested) atoms. Cycle 24: After refmac, R = 0.1347 (Rfree = 0.000) for 5393 atoms. Found 6 (34 requested) and removed 19 (17 requested) atoms. Cycle 25: After refmac, R = 0.1261 (Rfree = 0.000) for 5372 atoms. Found 4 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 5551 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 5582 seeds are put forward Round 1: 305 peptides, 57 chains. Longest chain 9 peptides. Score 0.367 Round 2: 340 peptides, 56 chains. Longest chain 14 peptides. Score 0.456 Round 3: 368 peptides, 53 chains. Longest chain 19 peptides. Score 0.540 Round 4: 365 peptides, 56 chains. Longest chain 14 peptides. Score 0.508 Round 5: 375 peptides, 56 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 3 Chains 54, Residues 315, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12045 restraints for refining 5410 atoms. 10740 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1910 (Rfree = 0.000) for 5410 atoms. Found 28 (34 requested) and removed 26 (17 requested) atoms. Cycle 27: After refmac, R = 0.1621 (Rfree = 0.000) for 5389 atoms. Found 21 (34 requested) and removed 19 (17 requested) atoms. Cycle 28: After refmac, R = 0.1629 (Rfree = 0.000) for 5382 atoms. Found 23 (34 requested) and removed 27 (17 requested) atoms. Cycle 29: After refmac, R = 0.1577 (Rfree = 0.000) for 5371 atoms. Found 27 (34 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.1521 (Rfree = 0.000) for 5377 atoms. Found 16 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 5583 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5601 seeds are put forward Round 1: 282 peptides, 55 chains. Longest chain 12 peptides. Score 0.331 Round 2: 304 peptides, 49 chains. Longest chain 20 peptides. Score 0.443 Round 3: 314 peptides, 50 chains. Longest chain 21 peptides. Score 0.456 Round 4: 294 peptides, 46 chains. Longest chain 20 peptides. Score 0.450 Round 5: 304 peptides, 47 chains. Longest chain 21 peptides. Score 0.463 Taking the results from Round 5 Chains 48, Residues 257, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12593 restraints for refining 5410 atoms. 11555 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1719 (Rfree = 0.000) for 5410 atoms. Found 27 (34 requested) and removed 21 (17 requested) atoms. Cycle 32: After refmac, R = 0.1617 (Rfree = 0.000) for 5400 atoms. Found 26 (34 requested) and removed 22 (17 requested) atoms. Cycle 33: After refmac, R = 0.1663 (Rfree = 0.000) for 5397 atoms. Found 27 (34 requested) and removed 19 (17 requested) atoms. Cycle 34: After refmac, R = 0.1674 (Rfree = 0.000) for 5400 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 35: After refmac, R = 0.1619 (Rfree = 0.000) for 5402 atoms. Found 24 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 5594 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5613 seeds are put forward Round 1: 227 peptides, 47 chains. Longest chain 9 peptides. Score 0.276 Round 2: 264 peptides, 48 chains. Longest chain 14 peptides. Score 0.360 Round 3: 278 peptides, 49 chains. Longest chain 14 peptides. Score 0.384 Round 4: 279 peptides, 46 chains. Longest chain 14 peptides. Score 0.416 Round 5: 286 peptides, 46 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 5 Chains 46, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12900 restraints for refining 5410 atoms. 11986 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1649 (Rfree = 0.000) for 5410 atoms. Found 22 (34 requested) and removed 27 (17 requested) atoms. Cycle 37: After refmac, R = 0.1622 (Rfree = 0.000) for 5385 atoms. Found 34 (34 requested) and removed 19 (17 requested) atoms. Cycle 38: After refmac, R = 0.1588 (Rfree = 0.000) for 5396 atoms. Found 27 (34 requested) and removed 22 (17 requested) atoms. Cycle 39: After refmac, R = 0.1481 (Rfree = 0.000) for 5393 atoms. Found 33 (34 requested) and removed 22 (17 requested) atoms. Cycle 40: After refmac, R = 0.1452 (Rfree = 0.000) for 5399 atoms. Found 34 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 5595 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5617 seeds are put forward Round 1: 218 peptides, 44 chains. Longest chain 9 peptides. Score 0.286 Round 2: 250 peptides, 45 chains. Longest chain 11 peptides. Score 0.357 Round 3: 264 peptides, 43 chains. Longest chain 14 peptides. Score 0.412 Round 4: 256 peptides, 42 chains. Longest chain 14 peptides. Score 0.403 Round 5: 252 peptides, 42 chains. Longest chain 25 peptides. Score 0.394 Taking the results from Round 3 Chains 43, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12976 restraints for refining 5409 atoms. 12135 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1633 (Rfree = 0.000) for 5409 atoms. Found 13 (34 requested) and removed 21 (17 requested) atoms. Cycle 42: After refmac, R = 0.1676 (Rfree = 0.000) for 5392 atoms. Found 26 (34 requested) and removed 19 (17 requested) atoms. Cycle 43: After refmac, R = 0.1634 (Rfree = 0.000) for 5391 atoms. Found 29 (34 requested) and removed 19 (17 requested) atoms. Cycle 44: After refmac, R = 0.1524 (Rfree = 0.000) for 5394 atoms. Found 21 (34 requested) and removed 19 (17 requested) atoms. Cycle 45: After refmac, R = 0.1539 (Rfree = 0.000) for 5388 atoms. Found 28 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5565 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 5582 seeds are put forward Round 1: 224 peptides, 49 chains. Longest chain 8 peptides. Score 0.246 Round 2: 245 peptides, 47 chains. Longest chain 10 peptides. Score 0.323 Round 3: 252 peptides, 47 chains. Longest chain 10 peptides. Score 0.341 Round 4: 251 peptides, 45 chains. Longest chain 11 peptides. Score 0.360 Round 5: 266 peptides, 49 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8411 reflections ( 99.75 % complete ) and 13140 restraints for refining 5410 atoms. 12361 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1650 (Rfree = 0.000) for 5410 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1576 (Rfree = 0.000) for 5387 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1618 (Rfree = 0.000) for 5364 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1571 (Rfree = 0.000) for 5343 atoms. TimeTaking 72.8