Sun 23 Dec 23:46:59 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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 23:47:03 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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 474 and 0 Target number of residues in the AU: 474 Target solvent content: 0.6261 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 64.20 9931 reflections ( 99.79 % complete ) and 0 restraints for refining 6657 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3093 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3071 (Rfree = 0.000) for 6657 atoms. Found 50 (50 requested) and removed 67 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 6807 seeds are put forward NCS extension: 0 residues added, 6807 seeds are put forward Round 1: 280 peptides, 55 chains. Longest chain 10 peptides. Score 0.326 Round 2: 350 peptides, 60 chains. Longest chain 19 peptides. Score 0.440 Round 3: 363 peptides, 54 chains. Longest chain 20 peptides. Score 0.521 Round 4: 393 peptides, 62 chains. Longest chain 15 peptides. Score 0.512 Round 5: 397 peptides, 54 chains. Longest chain 16 peptides. Score 0.585 Taking the results from Round 5 Chains 56, Residues 343, Estimated correctness of the model 23.7 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11948 restraints for refining 5425 atoms. 10498 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2522 (Rfree = 0.000) for 5425 atoms. Found 39 (40 requested) and removed 38 (20 requested) atoms. Cycle 2: After refmac, R = 0.2348 (Rfree = 0.000) for 5365 atoms. Found 30 (40 requested) and removed 33 (20 requested) atoms. Cycle 3: After refmac, R = 0.2196 (Rfree = 0.000) for 5329 atoms. Found 30 (40 requested) and removed 29 (20 requested) atoms. Cycle 4: After refmac, R = 0.1857 (Rfree = 0.000) for 5317 atoms. Found 11 (40 requested) and removed 25 (20 requested) atoms. Cycle 5: After refmac, R = 0.1901 (Rfree = 0.000) for 5295 atoms. Found 22 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 5517 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5528 seeds are put forward Round 1: 355 peptides, 65 chains. Longest chain 14 peptides. Score 0.404 Round 2: 393 peptides, 59 chains. Longest chain 20 peptides. Score 0.537 Round 3: 383 peptides, 61 chains. Longest chain 18 peptides. Score 0.501 Round 4: 398 peptides, 55 chains. Longest chain 21 peptides. Score 0.579 Round 5: 402 peptides, 61 chains. Longest chain 16 peptides. Score 0.538 Taking the results from Round 4 Chains 56, Residues 343, Estimated correctness of the model 21.7 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12131 restraints for refining 5427 atoms. 10690 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2287 (Rfree = 0.000) for 5427 atoms. Found 38 (40 requested) and removed 42 (20 requested) atoms. Cycle 7: After refmac, R = 0.2266 (Rfree = 0.000) for 5405 atoms. Found 40 (40 requested) and removed 26 (20 requested) atoms. Cycle 8: After refmac, R = 0.2157 (Rfree = 0.000) for 5399 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 9: After refmac, R = 0.1774 (Rfree = 0.000) for 5391 atoms. Found 12 (40 requested) and removed 21 (20 requested) atoms. Cycle 10: After refmac, R = 0.1695 (Rfree = 0.000) for 5373 atoms. Found 10 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.71 Search for helices and strands: 0 residues in 0 chains, 5573 seeds are put forward NCS extension: 32 residues added (4 deleted due to clashes), 5605 seeds are put forward Round 1: 362 peptides, 62 chains. Longest chain 16 peptides. Score 0.448 Round 2: 382 peptides, 53 chains. Longest chain 20 peptides. Score 0.566 Round 3: 387 peptides, 56 chains. Longest chain 15 peptides. Score 0.551 Round 4: 408 peptides, 52 chains. Longest chain 29 peptides. Score 0.619 Round 5: 400 peptides, 56 chains. Longest chain 16 peptides. Score 0.575 Taking the results from Round 4 Chains 56, Residues 356, Estimated correctness of the model 34.8 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11682 restraints for refining 5427 atoms. 10084 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2161 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 34 (20 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 5401 atoms. Found 36 (41 requested) and removed 26 (20 requested) atoms. Cycle 13: After refmac, R = 0.1970 (Rfree = 0.000) for 5393 atoms. Found 33 (40 requested) and removed 22 (20 requested) atoms. Cycle 14: After refmac, R = 0.1855 (Rfree = 0.000) for 5385 atoms. Found 31 (40 requested) and removed 26 (20 requested) atoms. Cycle 15: After refmac, R = 0.1665 (Rfree = 0.000) for 5385 atoms. Found 9 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 5556 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5578 seeds are put forward Round 1: 311 peptides, 60 chains. Longest chain 14 peptides. Score 0.351 Round 2: 348 peptides, 54 chains. Longest chain 16 peptides. Score 0.491 Round 3: 376 peptides, 59 chains. Longest chain 18 peptides. Score 0.504 Round 4: 369 peptides, 55 chains. Longest chain 19 peptides. Score 0.525 Round 5: 376 peptides, 54 chains. Longest chain 22 peptides. Score 0.546 Taking the results from Round 5 Chains 57, Residues 322, Estimated correctness of the model 10.1 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12242 restraints for refining 5427 atoms. 10809 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2330 (Rfree = 0.000) for 5427 atoms. Found 32 (40 requested) and removed 45 (20 requested) atoms. Cycle 17: After refmac, R = 0.2206 (Rfree = 0.000) for 5396 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 18: After refmac, R = 0.2146 (Rfree = 0.000) for 5392 atoms. Found 35 (40 requested) and removed 34 (20 requested) atoms. Cycle 19: After refmac, R = 0.2004 (Rfree = 0.000) for 5388 atoms. Found 30 (40 requested) and removed 23 (20 requested) atoms. Cycle 20: After refmac, R = 0.1868 (Rfree = 0.000) for 5392 atoms. Found 25 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 5572 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 5598 seeds are put forward Round 1: 285 peptides, 49 chains. Longest chain 18 peptides. Score 0.400 Round 2: 342 peptides, 53 chains. Longest chain 21 peptides. Score 0.488 Round 3: 363 peptides, 53 chains. Longest chain 24 peptides. Score 0.530 Round 4: 372 peptides, 56 chains. Longest chain 14 peptides. Score 0.522 Round 5: 376 peptides, 56 chains. Longest chain 21 peptides. Score 0.530 Taking the results from Round 5 Chains 60, Residues 320, Estimated correctness of the model 4.2 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12155 restraints for refining 5427 atoms. 10787 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2152 (Rfree = 0.000) for 5427 atoms. Found 27 (40 requested) and removed 38 (20 requested) atoms. Cycle 22: After refmac, R = 0.2042 (Rfree = 0.000) for 5390 atoms. Found 28 (40 requested) and removed 29 (20 requested) atoms. Cycle 23: After refmac, R = 0.2052 (Rfree = 0.000) for 5374 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 24: After refmac, R = 0.1914 (Rfree = 0.000) for 5366 atoms. Found 27 (40 requested) and removed 24 (20 requested) atoms. Cycle 25: After refmac, R = 0.1875 (Rfree = 0.000) for 5357 atoms. Found 25 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 5544 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5563 seeds are put forward Round 1: 308 peptides, 58 chains. Longest chain 13 peptides. Score 0.364 Round 2: 356 peptides, 55 chains. Longest chain 16 peptides. Score 0.499 Round 3: 353 peptides, 53 chains. Longest chain 16 peptides. Score 0.510 Round 4: 378 peptides, 57 chains. Longest chain 18 peptides. Score 0.525 Round 5: 365 peptides, 51 chains. Longest chain 19 peptides. Score 0.551 Taking the results from Round 5 Chains 51, Residues 314, Estimated correctness of the model 11.9 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12406 restraints for refining 5427 atoms. 11158 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2158 (Rfree = 0.000) for 5427 atoms. Found 27 (40 requested) and removed 26 (20 requested) atoms. Cycle 27: After refmac, R = 0.1969 (Rfree = 0.000) for 5395 atoms. Found 34 (40 requested) and removed 22 (20 requested) atoms. Cycle 28: After refmac, R = 0.1969 (Rfree = 0.000) for 5394 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. Cycle 29: After refmac, R = 0.1563 (Rfree = 0.000) for 5399 atoms. Found 12 (40 requested) and removed 22 (20 requested) atoms. Cycle 30: After refmac, R = 0.1441 (Rfree = 0.000) for 5380 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 5595 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5620 seeds are put forward Round 1: 262 peptides, 51 chains. Longest chain 13 peptides. Score 0.323 Round 2: 320 peptides, 56 chains. Longest chain 16 peptides. Score 0.411 Round 3: 348 peptides, 58 chains. Longest chain 16 peptides. Score 0.454 Round 4: 327 peptides, 52 chains. Longest chain 16 peptides. Score 0.465 Round 5: 311 peptides, 52 chains. Longest chain 21 peptides. Score 0.430 Taking the results from Round 4 Chains 52, Residues 275, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12866 restraints for refining 5427 atoms. 11818 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2263 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 32: After refmac, R = 0.2021 (Rfree = 0.000) for 5421 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 33: After refmac, R = 0.1961 (Rfree = 0.000) for 5433 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 34: After refmac, R = 0.1967 (Rfree = 0.000) for 5446 atoms. Found 41 (41 requested) and removed 24 (20 requested) atoms. Cycle 35: After refmac, R = 0.1547 (Rfree = 0.000) for 5461 atoms. Found 16 (41 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 5655 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5676 seeds are put forward Round 1: 226 peptides, 44 chains. Longest chain 14 peptides. Score 0.307 Round 2: 281 peptides, 45 chains. Longest chain 15 peptides. Score 0.431 Round 3: 279 peptides, 44 chains. Longest chain 16 peptides. Score 0.436 Round 4: 279 peptides, 49 chains. Longest chain 15 peptides. Score 0.386 Round 5: 268 peptides, 41 chains. Longest chain 19 peptides. Score 0.441 Taking the results from Round 5 Chains 43, Residues 227, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12800 restraints for refining 5427 atoms. 11863 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2071 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. Cycle 37: After refmac, R = 0.2036 (Rfree = 0.000) for 5415 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 38: After refmac, R = 0.2071 (Rfree = 0.000) for 5404 atoms. Found 40 (40 requested) and removed 26 (20 requested) atoms. Cycle 39: After refmac, R = 0.1497 (Rfree = 0.000) for 5410 atoms. Found 15 (40 requested) and removed 22 (20 requested) atoms. Cycle 40: After refmac, R = 0.1358 (Rfree = 0.000) for 5398 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 5575 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5589 seeds are put forward Round 1: 203 peptides, 39 chains. Longest chain 10 peptides. Score 0.303 Round 2: 234 peptides, 38 chains. Longest chain 14 peptides. Score 0.393 Round 3: 229 peptides, 35 chains. Longest chain 15 peptides. Score 0.413 Round 4: 234 peptides, 41 chains. Longest chain 13 peptides. Score 0.361 Round 5: 237 peptides, 39 chains. Longest chain 19 peptides. Score 0.389 Taking the results from Round 3 Chains 37, Residues 194, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12801 restraints for refining 5426 atoms. 11961 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2100 (Rfree = 0.000) for 5426 atoms. Found 40 (40 requested) and removed 24 (20 requested) atoms. Cycle 42: After refmac, R = 0.2157 (Rfree = 0.000) for 5426 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 43: After refmac, R = 0.1829 (Rfree = 0.000) for 5428 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 44: After refmac, R = 0.1855 (Rfree = 0.000) for 5438 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 45: After refmac, R = 0.1882 (Rfree = 0.000) for 5451 atoms. Found 41 (41 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 5669 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5684 seeds are put forward Round 1: 221 peptides, 45 chains. Longest chain 15 peptides. Score 0.283 Round 2: 250 peptides, 43 chains. Longest chain 18 peptides. Score 0.379 Round 3: 242 peptides, 42 chains. Longest chain 13 peptides. Score 0.370 Round 4: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.401 Round 5: 221 peptides, 40 chains. Longest chain 13 peptides. Score 0.339 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 196, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9931 reflections ( 99.79 % complete ) and 12843 restraints for refining 5427 atoms. 12035 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2003 (Rfree = 0.000) for 5427 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2504 (Rfree = 0.000) for 5395 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2067 (Rfree = 0.000) for 5362 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1874 (Rfree = 0.000) for 5332 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... TimeTaking 54.55