Mon 24 Dec 07:25:52 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aml-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-parrot-noncs ############### 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 07:25:56 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/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.6-parrot-noncs/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-noncs.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-noncs.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 6569 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3339 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2931 (Rfree = 0.000) for 6569 atoms. Found 42 (42 requested) and removed 65 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 6692 seeds are put forward NCS extension: 0 residues added, 6692 seeds are put forward Round 1: 219 peptides, 50 chains. Longest chain 7 peptides. Score 0.221 Round 2: 292 peptides, 59 chains. Longest chain 13 peptides. Score 0.315 Round 3: 299 peptides, 54 chains. Longest chain 16 peptides. Score 0.383 Round 4: 332 peptides, 57 chains. Longest chain 12 peptides. Score 0.429 Round 5: 338 peptides, 53 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 5 Chains 53, Residues 285, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12504 restraints for refining 5407 atoms. 11372 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2601 (Rfree = 0.000) for 5407 atoms. Found 33 (34 requested) and removed 32 (17 requested) atoms. Cycle 2: After refmac, R = 0.2423 (Rfree = 0.000) for 5337 atoms. Found 20 (34 requested) and removed 31 (17 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2214 (Rfree = 0.000) for 5285 atoms. Found 27 (34 requested) and removed 38 (17 requested) atoms. Cycle 4: After refmac, R = 0.1996 (Rfree = 0.000) for 5248 atoms. Found 16 (33 requested) and removed 22 (16 requested) atoms. Cycle 5: After refmac, R = 0.1738 (Rfree = 0.000) for 5226 atoms. Found 10 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 5414 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5440 seeds are put forward Round 1: 323 peptides, 68 chains. Longest chain 12 peptides. Score 0.299 Round 2: 362 peptides, 62 chains. Longest chain 16 peptides. Score 0.448 Round 3: 360 peptides, 60 chains. Longest chain 15 peptides. Score 0.462 Round 4: 358 peptides, 58 chains. Longest chain 12 peptides. Score 0.476 Round 5: 381 peptides, 64 chains. Longest chain 16 peptides. Score 0.470 Taking the results from Round 4 Chains 58, Residues 300, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12372 restraints for refining 5268 atoms. 11230 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2048 (Rfree = 0.000) for 5268 atoms. Found 24 (33 requested) and removed 33 (16 requested) atoms. Cycle 7: After refmac, R = 0.1926 (Rfree = 0.000) for 5234 atoms. Found 14 (33 requested) and removed 27 (16 requested) atoms. Cycle 8: After refmac, R = 0.1951 (Rfree = 0.000) for 5208 atoms. Found 31 (33 requested) and removed 27 (16 requested) atoms. Cycle 9: After refmac, R = 0.1847 (Rfree = 0.000) for 5200 atoms. Found 20 (33 requested) and removed 31 (16 requested) atoms. Cycle 10: After refmac, R = 0.1778 (Rfree = 0.000) for 5176 atoms. Found 31 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 5433 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5447 seeds are put forward Round 1: 290 peptides, 60 chains. Longest chain 13 peptides. Score 0.299 Round 2: 352 peptides, 58 chains. Longest chain 18 peptides. Score 0.463 Round 3: 360 peptides, 59 chains. Longest chain 16 peptides. Score 0.471 Round 4: 358 peptides, 64 chains. Longest chain 15 peptides. Score 0.420 Round 5: 344 peptides, 56 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 3 Chains 60, Residues 301, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12452 restraints for refining 5374 atoms. 11274 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1938 (Rfree = 0.000) for 5374 atoms. Found 27 (34 requested) and removed 49 (17 requested) atoms. Cycle 12: After refmac, R = 0.1860 (Rfree = 0.000) for 5325 atoms. Found 29 (34 requested) and removed 30 (17 requested) atoms. Cycle 13: After refmac, R = 0.1562 (Rfree = 0.000) for 5315 atoms. Found 10 (34 requested) and removed 25 (17 requested) atoms. Cycle 14: After refmac, R = 0.1768 (Rfree = 0.000) for 5290 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 15: After refmac, R = 0.1741 (Rfree = 0.000) for 5284 atoms. Found 31 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 5515 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5535 seeds are put forward Round 1: 285 peptides, 59 chains. Longest chain 9 peptides. Score 0.297 Round 2: 351 peptides, 63 chains. Longest chain 13 peptides. Score 0.414 Round 3: 345 peptides, 58 chains. Longest chain 17 peptides. Score 0.448 Round 4: 337 peptides, 57 chains. Longest chain 15 peptides. Score 0.440 Round 5: 354 peptides, 59 chains. Longest chain 17 peptides. Score 0.458 Taking the results from Round 5 Chains 59, Residues 295, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12656 restraints for refining 5409 atoms. 11535 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1939 (Rfree = 0.000) for 5409 atoms. Found 31 (34 requested) and removed 37 (17 requested) atoms. Cycle 17: After refmac, R = 0.1855 (Rfree = 0.000) for 5362 atoms. Found 29 (34 requested) and removed 29 (17 requested) atoms. Cycle 18: After refmac, R = 0.2046 (Rfree = 0.000) for 5350 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 19: After refmac, R = 0.2177 (Rfree = 0.000) for 5341 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 20: After refmac, R = 0.1658 (Rfree = 0.000) for 5337 atoms. Found 24 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 5571 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5593 seeds are put forward Round 1: 255 peptides, 53 chains. Longest chain 9 peptides. Score 0.284 Round 2: 298 peptides, 51 chains. Longest chain 11 peptides. Score 0.410 Round 3: 311 peptides, 55 chains. Longest chain 12 peptides. Score 0.401 Round 4: 313 peptides, 52 chains. Longest chain 13 peptides. Score 0.434 Round 5: 323 peptides, 50 chains. Longest chain 12 peptides. Score 0.475 Taking the results from Round 5 Chains 50, Residues 273, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12768 restraints for refining 5409 atoms. 11708 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1991 (Rfree = 0.000) for 5409 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 22: After refmac, R = 0.1913 (Rfree = 0.000) for 5390 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 23: After refmac, R = 0.1785 (Rfree = 0.000) for 5380 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 24: After refmac, R = 0.1377 (Rfree = 0.000) for 5379 atoms. Found 8 (34 requested) and removed 20 (17 requested) atoms. Cycle 25: After refmac, R = 0.1301 (Rfree = 0.000) for 5366 atoms. Found 6 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 5531 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5547 seeds are put forward Round 1: 266 peptides, 54 chains. Longest chain 9 peptides. Score 0.302 Round 2: 306 peptides, 55 chains. Longest chain 16 peptides. Score 0.389 Round 3: 312 peptides, 53 chains. Longest chain 12 peptides. Score 0.423 Round 4: 313 peptides, 52 chains. Longest chain 17 peptides. Score 0.434 Round 5: 323 peptides, 54 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 5 Chains 56, Residues 269, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12883 restraints for refining 5409 atoms. 11808 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1889 (Rfree = 0.000) for 5409 atoms. Found 34 (34 requested) and removed 34 (17 requested) atoms. Cycle 27: After refmac, R = 0.1780 (Rfree = 0.000) for 5395 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 28: After refmac, R = 0.1782 (Rfree = 0.000) for 5400 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 29: After refmac, R = 0.1618 (Rfree = 0.000) for 5399 atoms. Found 25 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.1346 (Rfree = 0.000) for 5398 atoms. Found 5 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 5586 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5602 seeds are put forward Round 1: 259 peptides, 50 chains. Longest chain 10 peptides. Score 0.327 Round 2: 274 peptides, 51 chains. Longest chain 14 peptides. Score 0.353 Round 3: 295 peptides, 51 chains. Longest chain 12 peptides. Score 0.403 Round 4: 305 peptides, 49 chains. Longest chain 15 peptides. Score 0.446 Round 5: 274 peptides, 46 chains. Longest chain 12 peptides. Score 0.405 Taking the results from Round 4 Chains 49, Residues 256, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 12538 restraints for refining 5408 atoms. 11478 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1961 (Rfree = 0.000) for 5408 atoms. Found 22 (34 requested) and removed 25 (17 requested) atoms. Cycle 32: After refmac, R = 0.1980 (Rfree = 0.000) for 5396 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 33: After refmac, R = 0.2154 (Rfree = 0.000) for 5396 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 34: After refmac, R = 0.1642 (Rfree = 0.000) for 5393 atoms. Found 13 (34 requested) and removed 20 (17 requested) atoms. Cycle 35: After refmac, R = 0.1599 (Rfree = 0.000) for 5383 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 5526 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5541 seeds are put forward Round 1: 228 peptides, 48 chains. Longest chain 10 peptides. Score 0.268 Round 2: 255 peptides, 49 chains. Longest chain 12 peptides. Score 0.327 Round 3: 271 peptides, 49 chains. Longest chain 10 peptides. Score 0.367 Round 4: 276 peptides, 47 chains. Longest chain 12 peptides. Score 0.399 Round 5: 261 peptides, 49 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 4 Chains 47, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 13107 restraints for refining 5409 atoms. 12238 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1910 (Rfree = 0.000) for 5409 atoms. Found 33 (34 requested) and removed 24 (17 requested) atoms. Cycle 37: After refmac, R = 0.1880 (Rfree = 0.000) for 5403 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 38: After refmac, R = 0.1887 (Rfree = 0.000) for 5408 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 39: After refmac, R = 0.1809 (Rfree = 0.000) for 5411 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. Cycle 40: After refmac, R = 0.1407 (Rfree = 0.000) for 5408 atoms. Found 7 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 5557 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5569 seeds are put forward Round 1: 192 peptides, 41 chains. Longest chain 8 peptides. Score 0.249 Round 2: 241 peptides, 49 chains. Longest chain 9 peptides. Score 0.291 Round 3: 259 peptides, 50 chains. Longest chain 10 peptides. Score 0.327 Round 4: 256 peptides, 50 chains. Longest chain 8 peptides. Score 0.319 Round 5: 264 peptides, 51 chains. Longest chain 10 peptides. Score 0.328 Taking the results from Round 5 Chains 51, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8411 reflections ( 99.75 % complete ) and 13022 restraints for refining 5409 atoms. 12221 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1880 (Rfree = 0.000) for 5409 atoms. Found 34 (34 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.2029 (Rfree = 0.000) for 5406 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 43: After refmac, R = 0.1881 (Rfree = 0.000) for 5405 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 44: After refmac, R = 0.1528 (Rfree = 0.000) for 5401 atoms. Found 15 (34 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.1472 (Rfree = 0.000) for 5388 atoms. Found 13 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 5563 seeds are put forward NCS extension: 0 residues added, 5563 seeds are put forward Round 1: 166 peptides, 37 chains. Longest chain 8 peptides. Score 0.222 Round 2: 197 peptides, 38 chains. Longest chain 11 peptides. Score 0.298 Round 3: 205 peptides, 38 chains. Longest chain 14 peptides. Score 0.319 Round 4: 194 peptides, 36 chains. Longest chain 12 peptides. Score 0.313 Round 5: 187 peptides, 36 chains. Longest chain 12 peptides. Score 0.294 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 167, 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 12982 restraints for refining 5315 atoms. 12352 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1873 (Rfree = 0.000) for 5315 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1909 (Rfree = 0.000) for 5285 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1822 (Rfree = 0.000) for 5259 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1952 (Rfree = 0.000) for 5230 atoms. TimeTaking 56.83