Sun 23 Dec 23:46:29 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 2aml-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-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/2aml-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-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 23:46:33 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/2aml-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-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 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-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: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.6-parrot-mrncs.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 6575 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2654 (Rfree = 0.000) for 6575 atoms. Found 42 (42 requested) and removed 42 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 6732 seeds are put forward NCS extension: 0 residues added, 6732 seeds are put forward Round 1: 321 peptides, 62 chains. Longest chain 12 peptides. Score 0.354 Round 2: 396 peptides, 64 chains. Longest chain 16 peptides. Score 0.501 Round 3: 423 peptides, 54 chains. Longest chain 19 peptides. Score 0.629 Round 4: 438 peptides, 56 chains. Longest chain 24 peptides. Score 0.638 Round 5: 435 peptides, 54 chains. Longest chain 19 peptides. Score 0.648 Taking the results from Round 5 Chains 56, Residues 381, Estimated correctness of the model 32.5 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 11466 restraints for refining 5410 atoms. 9795 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2362 (Rfree = 0.000) for 5410 atoms. Found 34 (34 requested) and removed 36 (17 requested) atoms. Cycle 2: After refmac, R = 0.2011 (Rfree = 0.000) for 5340 atoms. Found 21 (34 requested) and removed 28 (17 requested) atoms. Cycle 3: After refmac, R = 0.1962 (Rfree = 0.000) for 5307 atoms. Found 20 (34 requested) and removed 25 (17 requested) atoms. Cycle 4: After refmac, R = 0.1847 (Rfree = 0.000) for 5277 atoms. Found 12 (34 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.1887 (Rfree = 0.000) for 5266 atoms. Found 23 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5454 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5473 seeds are put forward Round 1: 358 peptides, 64 chains. Longest chain 15 peptides. Score 0.420 Round 2: 384 peptides, 57 chains. Longest chain 20 peptides. Score 0.537 Round 3: 415 peptides, 60 chains. Longest chain 19 peptides. Score 0.570 Round 4: 398 peptides, 56 chains. Longest chain 21 peptides. Score 0.571 Round 5: 399 peptides, 54 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 5 Chains 58, Residues 345, Estimated correctness of the model 9.9 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12032 restraints for refining 5409 atoms. 10494 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1982 (Rfree = 0.000) for 5409 atoms. Found 20 (34 requested) and removed 29 (17 requested) atoms. Cycle 7: After refmac, R = 0.1810 (Rfree = 0.000) for 5381 atoms. Found 12 (34 requested) and removed 23 (17 requested) atoms. Cycle 8: After refmac, R = 0.1681 (Rfree = 0.000) for 5357 atoms. Found 9 (34 requested) and removed 20 (17 requested) atoms. Cycle 9: After refmac, R = 0.1684 (Rfree = 0.000) for 5339 atoms. Found 12 (34 requested) and removed 25 (17 requested) atoms. Cycle 10: After refmac, R = 0.1675 (Rfree = 0.000) for 5324 atoms. Found 18 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5529 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5544 seeds are put forward Round 1: 322 peptides, 60 chains. Longest chain 15 peptides. Score 0.377 Round 2: 397 peptides, 61 chains. Longest chain 15 peptides. Score 0.528 Round 3: 396 peptides, 56 chains. Longest chain 20 peptides. Score 0.567 Round 4: 382 peptides, 52 chains. Longest chain 18 peptides. Score 0.574 Round 5: 386 peptides, 55 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 4 Chains 54, Residues 330, Estimated correctness of the model 4.2 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12256 restraints for refining 5410 atoms. 10861 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2047 (Rfree = 0.000) for 5410 atoms. Found 32 (34 requested) and removed 40 (17 requested) atoms. Cycle 12: After refmac, R = 0.1795 (Rfree = 0.000) for 5387 atoms. Found 23 (34 requested) and removed 26 (17 requested) atoms. Cycle 13: After refmac, R = 0.1738 (Rfree = 0.000) for 5374 atoms. Found 12 (34 requested) and removed 26 (17 requested) atoms. Cycle 14: After refmac, R = 0.1695 (Rfree = 0.000) for 5351 atoms. Found 23 (34 requested) and removed 19 (17 requested) atoms. Cycle 15: After refmac, R = 0.1684 (Rfree = 0.000) for 5343 atoms. Found 25 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 5515 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5538 seeds are put forward Round 1: 339 peptides, 57 chains. Longest chain 27 peptides. Score 0.444 Round 2: 359 peptides, 51 chains. Longest chain 18 peptides. Score 0.539 Round 3: 388 peptides, 53 chains. Longest chain 18 peptides. Score 0.577 Round 4: 366 peptides, 49 chains. Longest chain 19 peptides. Score 0.569 Round 5: 366 peptides, 52 chains. Longest chain 19 peptides. Score 0.544 Taking the results from Round 3 Chains 55, Residues 335, Estimated correctness of the model 5.5 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12093 restraints for refining 5409 atoms. 10687 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1830 (Rfree = 0.000) for 5409 atoms. Found 33 (34 requested) and removed 29 (17 requested) atoms. Cycle 17: After refmac, R = 0.1766 (Rfree = 0.000) for 5384 atoms. Found 27 (34 requested) and removed 20 (17 requested) atoms. Cycle 18: After refmac, R = 0.1698 (Rfree = 0.000) for 5385 atoms. Found 26 (34 requested) and removed 26 (17 requested) atoms. Cycle 19: After refmac, R = 0.1748 (Rfree = 0.000) for 5381 atoms. Found 27 (34 requested) and removed 29 (17 requested) atoms. Cycle 20: After refmac, R = 0.1662 (Rfree = 0.000) for 5374 atoms. Found 24 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 5601 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5617 seeds are put forward Round 1: 317 peptides, 57 chains. Longest chain 15 peptides. Score 0.395 Round 2: 343 peptides, 49 chains. Longest chain 18 peptides. Score 0.525 Round 3: 361 peptides, 53 chains. Longest chain 22 peptides. Score 0.526 Round 4: 356 peptides, 48 chains. Longest chain 17 peptides. Score 0.559 Round 5: 353 peptides, 47 chains. Longest chain 18 peptides. Score 0.562 Taking the results from Round 5 Chains 49, Residues 306, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12313 restraints for refining 5410 atoms. 11009 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1952 (Rfree = 0.000) for 5410 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 22: After refmac, R = 0.1795 (Rfree = 0.000) for 5401 atoms. Found 20 (34 requested) and removed 22 (17 requested) atoms. Cycle 23: After refmac, R = 0.1801 (Rfree = 0.000) for 5391 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 24: After refmac, R = 0.1713 (Rfree = 0.000) for 5390 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 25: After refmac, R = 0.1622 (Rfree = 0.000) for 5386 atoms. Found 20 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 5594 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5615 seeds are put forward Round 1: 278 peptides, 51 chains. Longest chain 13 peptides. Score 0.363 Round 2: 309 peptides, 50 chains. Longest chain 16 peptides. Score 0.445 Round 3: 319 peptides, 48 chains. Longest chain 17 peptides. Score 0.485 Round 4: 326 peptides, 48 chains. Longest chain 16 peptides. Score 0.500 Round 5: 314 peptides, 46 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 4 Chains 49, Residues 278, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12677 restraints for refining 5409 atoms. 11528 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1883 (Rfree = 0.000) for 5409 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 27: After refmac, R = 0.1741 (Rfree = 0.000) for 5403 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. Cycle 28: After refmac, R = 0.1680 (Rfree = 0.000) for 5407 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 29: After refmac, R = 0.1620 (Rfree = 0.000) for 5410 atoms. Found 33 (34 requested) and removed 23 (17 requested) atoms. Cycle 30: After refmac, R = 0.1588 (Rfree = 0.000) for 5411 atoms. Found 33 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.85 Search for helices and strands: 0 residues in 0 chains, 5633 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5650 seeds are put forward Round 1: 234 peptides, 47 chains. Longest chain 10 peptides. Score 0.295 Round 2: 286 peptides, 47 chains. Longest chain 16 peptides. Score 0.422 Round 3: 307 peptides, 47 chains. Longest chain 16 peptides. Score 0.469 Round 4: 299 peptides, 44 chains. Longest chain 17 peptides. Score 0.480 Round 5: 296 peptides, 45 chains. Longest chain 24 peptides. Score 0.464 Taking the results from Round 4 Chains 44, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12861 restraints for refining 5409 atoms. 11885 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1932 (Rfree = 0.000) for 5409 atoms. Found 34 (34 requested) and removed 18 (17 requested) atoms. Cycle 32: After refmac, R = 0.1874 (Rfree = 0.000) for 5414 atoms. Found 34 (34 requested) and removed 19 (17 requested) atoms. Cycle 33: After refmac, R = 0.1750 (Rfree = 0.000) for 5418 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. Cycle 34: After refmac, R = 0.1294 (Rfree = 0.000) for 5421 atoms. Found 13 (34 requested) and removed 18 (17 requested) atoms. Cycle 35: After refmac, R = 0.1205 (Rfree = 0.000) for 5414 atoms. Found 3 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 5582 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5600 seeds are put forward Round 1: 226 peptides, 43 chains. Longest chain 13 peptides. Score 0.318 Round 2: 262 peptides, 46 chains. Longest chain 19 peptides. Score 0.376 Round 3: 274 peptides, 47 chains. Longest chain 14 peptides. Score 0.394 Round 4: 291 peptides, 48 chains. Longest chain 15 peptides. Score 0.424 Round 5: 291 peptides, 50 chains. Longest chain 14 peptides. Score 0.404 Taking the results from Round 4 Chains 48, Residues 243, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 13040 restraints for refining 5410 atoms. 12094 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1762 (Rfree = 0.000) for 5410 atoms. Found 30 (34 requested) and removed 22 (17 requested) atoms. Cycle 37: After refmac, R = 0.1709 (Rfree = 0.000) for 5408 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 38: After refmac, R = 0.1742 (Rfree = 0.000) for 5405 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 39: After refmac, R = 0.1288 (Rfree = 0.000) for 5410 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. Cycle 40: After refmac, R = 0.1342 (Rfree = 0.000) for 5395 atoms. Found 9 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5580 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5601 seeds are put forward Round 1: 242 peptides, 49 chains. Longest chain 11 peptides. Score 0.294 Round 2: 269 peptides, 46 chains. Longest chain 13 peptides. Score 0.393 Round 3: 275 peptides, 43 chains. Longest chain 14 peptides. Score 0.437 Round 4: 271 peptides, 43 chains. Longest chain 11 peptides. Score 0.428 Round 5: 274 peptides, 45 chains. Longest chain 17 peptides. Score 0.415 Taking the results from Round 3 Chains 44, Residues 232, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12858 restraints for refining 5410 atoms. 11939 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1690 (Rfree = 0.000) for 5410 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 42: After refmac, R = 0.1593 (Rfree = 0.000) for 5403 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 43: After refmac, R = 0.1696 (Rfree = 0.000) for 5412 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. Cycle 44: After refmac, R = 0.1705 (Rfree = 0.000) for 5411 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 45: After refmac, R = 0.1686 (Rfree = 0.000) for 5413 atoms. Found 34 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5604 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5618 seeds are put forward Round 1: 229 peptides, 50 chains. Longest chain 10 peptides. Score 0.248 Round 2: 265 peptides, 49 chains. Longest chain 11 peptides. Score 0.352 Round 3: 234 peptides, 43 chains. Longest chain 11 peptides. Score 0.339 Round 4: 233 peptides, 40 chains. Longest chain 12 peptides. Score 0.369 Round 5: 247 peptides, 41 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 41, 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 13033 restraints for refining 5379 atoms. 12250 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1715 (Rfree = 0.000) for 5379 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1715 (Rfree = 0.000) for 5343 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1728 (Rfree = 0.000) for 5315 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1703 (Rfree = 0.000) for 5295 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 50.02