Mon 24 Dec 00:46:25 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-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/2aml-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-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 ============================================================ Mon 24 Dec 00:46:30 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-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 444 and 0 Target number of residues in the AU: 444 Target solvent content: 0.6498 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-3.8-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: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.70 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 3.800 Wilson plot Bfac: 77.83 7174 reflections ( 99.71 % complete ) and 0 restraints for refining 6652 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3064 (Rfree = 0.000) for 6652 atoms. Found 36 (36 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 6824 seeds are put forward NCS extension: 0 residues added, 6824 seeds are put forward Round 1: 248 peptides, 54 chains. Longest chain 9 peptides. Score 0.255 Round 2: 343 peptides, 60 chains. Longest chain 13 peptides. Score 0.425 Round 3: 376 peptides, 56 chains. Longest chain 18 peptides. Score 0.530 Round 4: 383 peptides, 61 chains. Longest chain 14 peptides. Score 0.501 Round 5: 404 peptides, 59 chains. Longest chain 18 peptides. Score 0.558 Taking the results from Round 5 Chains 59, Residues 345, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12359 restraints for refining 5396 atoms. 11018 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2397 (Rfree = 0.000) for 5396 atoms. Found 29 (29 requested) and removed 46 (14 requested) atoms. Cycle 2: After refmac, R = 0.2060 (Rfree = 0.000) for 5292 atoms. Found 17 (29 requested) and removed 29 (14 requested) atoms. Cycle 3: After refmac, R = 0.2131 (Rfree = 0.000) for 5247 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 4: After refmac, R = 0.2000 (Rfree = 0.000) for 5217 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1493 (Rfree = 0.000) for 5206 atoms. Found 9 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5436 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5458 seeds are put forward Round 1: 319 peptides, 60 chains. Longest chain 12 peptides. Score 0.370 Round 2: 347 peptides, 56 chains. Longest chain 18 peptides. Score 0.471 Round 3: 370 peptides, 57 chains. Longest chain 18 peptides. Score 0.509 Round 4: 374 peptides, 53 chains. Longest chain 19 peptides. Score 0.551 Round 5: 376 peptides, 52 chains. Longest chain 18 peptides. Score 0.563 Taking the results from Round 5 Chains 52, Residues 324, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7174 reflections ( 99.71 % complete ) and 12299 restraints for refining 5310 atoms. 11055 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1907 (Rfree = 0.000) for 5310 atoms. Found 29 (29 requested) and removed 51 (14 requested) atoms. Cycle 7: After refmac, R = 0.1838 (Rfree = 0.000) for 5265 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 8: After refmac, R = 0.1883 (Rfree = 0.000) for 5250 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 9: After refmac, R = 0.1749 (Rfree = 0.000) for 5232 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 10: After refmac, R = 0.1777 (Rfree = 0.000) for 5221 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.97 Search for helices and strands: 0 residues in 0 chains, 5444 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5464 seeds are put forward Round 1: 312 peptides, 62 chains. Longest chain 11 peptides. Score 0.333 Round 2: 345 peptides, 57 chains. Longest chain 18 peptides. Score 0.457 Round 3: 355 peptides, 53 chains. Longest chain 17 peptides. Score 0.514 Round 4: 370 peptides, 50 chains. Longest chain 20 peptides. Score 0.568 Round 5: 375 peptides, 57 chains. Longest chain 14 peptides. Score 0.519 Taking the results from Round 4 Chains 51, Residues 320, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12475 restraints for refining 5398 atoms. 11214 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1914 (Rfree = 0.000) for 5398 atoms. Found 29 (29 requested) and removed 46 (14 requested) atoms. Cycle 12: After refmac, R = 0.1783 (Rfree = 0.000) for 5352 atoms. Found 26 (29 requested) and removed 23 (14 requested) atoms. Cycle 13: After refmac, R = 0.1746 (Rfree = 0.000) for 5340 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 14: After refmac, R = 0.1316 (Rfree = 0.000) for 5328 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.1727 (Rfree = 0.000) for 5315 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5500 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 5522 seeds are put forward Round 1: 327 peptides, 63 chains. Longest chain 12 peptides. Score 0.359 Round 2: 360 peptides, 58 chains. Longest chain 17 peptides. Score 0.480 Round 3: 376 peptides, 56 chains. Longest chain 15 peptides. Score 0.530 Round 4: 379 peptides, 58 chains. Longest chain 18 peptides. Score 0.518 Round 5: 385 peptides, 59 chains. Longest chain 16 peptides. Score 0.522 Taking the results from Round 3 Chains 56, Residues 320, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12288 restraints for refining 5397 atoms. 11041 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1710 (Rfree = 0.000) for 5397 atoms. Found 26 (29 requested) and removed 24 (14 requested) atoms. Cycle 17: After refmac, R = 0.1783 (Rfree = 0.000) for 5371 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 18: After refmac, R = 0.1891 (Rfree = 0.000) for 5351 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.1782 (Rfree = 0.000) for 5341 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 20: After refmac, R = 0.1801 (Rfree = 0.000) for 5326 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5574 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5590 seeds are put forward Round 1: 270 peptides, 58 chains. Longest chain 8 peptides. Score 0.269 Round 2: 303 peptides, 56 chains. Longest chain 11 peptides. Score 0.372 Round 3: 309 peptides, 49 chains. Longest chain 12 peptides. Score 0.454 Round 4: 316 peptides, 52 chains. Longest chain 14 peptides. Score 0.441 Round 5: 318 peptides, 51 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Chains 51, Residues 267, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12783 restraints for refining 5397 atoms. 11766 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1880 (Rfree = 0.000) for 5397 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 22: After refmac, R = 0.1673 (Rfree = 0.000) for 5369 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. Cycle 23: After refmac, R = 0.1801 (Rfree = 0.000) for 5364 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 24: After refmac, R = 0.1515 (Rfree = 0.000) for 5350 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 25: After refmac, R = 0.1742 (Rfree = 0.000) for 5349 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 5585 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5608 seeds are put forward Round 1: 238 peptides, 48 chains. Longest chain 10 peptides. Score 0.294 Round 2: 281 peptides, 54 chains. Longest chain 13 peptides. Score 0.339 Round 3: 276 peptides, 49 chains. Longest chain 11 peptides. Score 0.379 Round 4: 279 peptides, 46 chains. Longest chain 12 peptides. Score 0.416 Round 5: 298 peptides, 50 chains. Longest chain 15 peptides. Score 0.420 Taking the results from Round 5 Chains 50, Residues 248, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 13040 restraints for refining 5398 atoms. 12098 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1794 (Rfree = 0.000) for 5398 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 27: After refmac, R = 0.1820 (Rfree = 0.000) for 5382 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 28: After refmac, R = 0.1841 (Rfree = 0.000) for 5383 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 29: After refmac, R = 0.1691 (Rfree = 0.000) for 5372 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 30: After refmac, R = 0.1163 (Rfree = 0.000) for 5368 atoms. Found 14 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 5561 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5578 seeds are put forward Round 1: 225 peptides, 46 chains. Longest chain 12 peptides. Score 0.282 Round 2: 248 peptides, 45 chains. Longest chain 14 peptides. Score 0.352 Round 3: 247 peptides, 40 chains. Longest chain 15 peptides. Score 0.403 Round 4: 247 peptides, 42 chains. Longest chain 12 peptides. Score 0.382 Round 5: 249 peptides, 41 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 3 Chains 40, Residues 207, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12949 restraints for refining 5397 atoms. 12143 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1739 (Rfree = 0.000) for 5397 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 32: After refmac, R = 0.1795 (Rfree = 0.000) for 5391 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 33: After refmac, R = 0.1722 (Rfree = 0.000) for 5374 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 34: After refmac, R = 0.1214 (Rfree = 0.000) for 5366 atoms. Found 11 (29 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.1412 (Rfree = 0.000) for 5347 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 5559 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5576 seeds are put forward Round 1: 191 peptides, 40 chains. Longest chain 7 peptides. Score 0.258 Round 2: 213 peptides, 39 chains. Longest chain 14 peptides. Score 0.329 Round 3: 229 peptides, 42 chains. Longest chain 10 peptides. Score 0.337 Round 4: 239 peptides, 41 chains. Longest chain 13 peptides. Score 0.373 Round 5: 251 peptides, 42 chains. Longest chain 12 peptides. Score 0.391 Taking the results from Round 5 Chains 42, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12910 restraints for refining 5381 atoms. 12116 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1904 (Rfree = 0.000) for 5381 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 37: After refmac, R = 0.1767 (Rfree = 0.000) for 5346 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 38: After refmac, R = 0.1832 (Rfree = 0.000) for 5339 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 39: After refmac, R = 0.1738 (Rfree = 0.000) for 5322 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. Cycle 40: After refmac, R = 0.1734 (Rfree = 0.000) for 5323 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 5506 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5519 seeds are put forward Round 1: 179 peptides, 39 chains. Longest chain 6 peptides. Score 0.236 Round 2: 228 peptides, 44 chains. Longest chain 10 peptides. Score 0.312 Round 3: 239 peptides, 42 chains. Longest chain 11 peptides. Score 0.362 Round 4: 238 peptides, 39 chains. Longest chain 12 peptides. Score 0.392 Round 5: 240 peptides, 40 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 4 Chains 40, Residues 199, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12736 restraints for refining 5327 atoms. 11950 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1778 (Rfree = 0.000) for 5327 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 42: After refmac, R = 0.1831 (Rfree = 0.000) for 5317 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 43: After refmac, R = 0.1749 (Rfree = 0.000) for 5306 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 44: After refmac, R = 0.1623 (Rfree = 0.000) for 5293 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 45: After refmac, R = 0.1804 (Rfree = 0.000) for 5294 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5480 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5495 seeds are put forward Round 1: 171 peptides, 39 chains. Longest chain 8 peptides. Score 0.213 Round 2: 208 peptides, 41 chains. Longest chain 12 peptides. Score 0.293 Round 3: 226 peptides, 44 chains. Longest chain 8 peptides. Score 0.307 Round 4: 209 peptides, 40 chains. Longest chain 10 peptides. Score 0.307 Round 5: 212 peptides, 41 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 169, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7174 reflections ( 99.71 % complete ) and 12811 restraints for refining 5250 atoms. 12147 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1500 (Rfree = 0.000) for 5250 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1647 (Rfree = 0.000) for 5228 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1587 (Rfree = 0.000) for 5202 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1590 (Rfree = 0.000) for 5179 atoms. TimeTaking 63.4