Mon 24 Dec 07:28:55 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-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 07:29:00 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 77.83 Failed to save intermediate PDB 7174 reflections ( 99.71 % complete ) and 0 restraints for refining 6569 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3452 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3211 (Rfree = 0.000) for 6569 atoms. Found 36 (36 requested) and removed 83 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 4.02 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: 221 peptides, 48 chains. Longest chain 8 peptides. Score 0.249 Round 2: 303 peptides, 58 chains. Longest chain 12 peptides. Score 0.352 Round 3: 337 peptides, 59 chains. Longest chain 19 peptides. Score 0.421 Round 4: 334 peptides, 51 chains. Longest chain 19 peptides. Score 0.489 Round 5: 371 peptides, 56 chains. Longest chain 21 peptides. Score 0.520 Taking the results from Round 5 Chains 60, Residues 315, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12283 restraints for refining 5396 atoms. 10946 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2534 (Rfree = 0.000) for 5396 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. Cycle 2: After refmac, R = 0.2514 (Rfree = 0.000) for 5295 atoms. Found 25 (29 requested) and removed 41 (14 requested) atoms. Cycle 3: After refmac, R = 0.2278 (Rfree = 0.000) for 5239 atoms. Found 28 (29 requested) and removed 39 (14 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 5204 atoms. Found 26 (28 requested) and removed 32 (14 requested) atoms. Cycle 5: After refmac, R = 0.2216 (Rfree = 0.000) for 5179 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5397 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5413 seeds are put forward Round 1: 247 peptides, 52 chains. Longest chain 9 peptides. Score 0.274 Round 2: 293 peptides, 52 chains. Longest chain 12 peptides. Score 0.389 Round 3: 319 peptides, 49 chains. Longest chain 13 peptides. Score 0.476 Round 4: 299 peptides, 48 chains. Longest chain 13 peptides. Score 0.442 Round 5: 305 peptides, 49 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 3 Chains 50, Residues 270, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12611 restraints for refining 5328 atoms. 11552 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2140 (Rfree = 0.000) for 5328 atoms. Found 29 (29 requested) and removed 48 (14 requested) atoms. Cycle 7: After refmac, R = 0.2142 (Rfree = 0.000) for 5269 atoms. Found 29 (29 requested) and removed 43 (14 requested) atoms. Cycle 8: After refmac, R = 0.2002 (Rfree = 0.000) for 5240 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 9: After refmac, R = 0.1662 (Rfree = 0.000) for 5223 atoms. Found 8 (28 requested) and removed 29 (14 requested) atoms. Cycle 10: After refmac, R = 0.1462 (Rfree = 0.000) for 5196 atoms. Found 6 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5417 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5430 seeds are put forward Round 1: 259 peptides, 56 chains. Longest chain 8 peptides. Score 0.262 Round 2: 323 peptides, 54 chains. Longest chain 20 peptides. Score 0.437 Round 3: 332 peptides, 56 chains. Longest chain 21 peptides. Score 0.438 Round 4: 331 peptides, 55 chains. Longest chain 18 peptides. Score 0.446 Round 5: 332 peptides, 53 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 56, Residues 279, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12639 restraints for refining 5398 atoms. 11518 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1997 (Rfree = 0.000) for 5398 atoms. Found 29 (29 requested) and removed 66 (14 requested) atoms. Cycle 12: After refmac, R = 0.2007 (Rfree = 0.000) for 5330 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. Cycle 13: After refmac, R = 0.1756 (Rfree = 0.000) for 5300 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 14: After refmac, R = 0.1921 (Rfree = 0.000) for 5296 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 15: After refmac, R = 0.1784 (Rfree = 0.000) for 5282 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 4.06 Search for helices and strands: 0 residues in 0 chains, 5503 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 5516 seeds are put forward Round 1: 232 peptides, 49 chains. Longest chain 9 peptides. Score 0.267 Round 2: 301 peptides, 54 chains. Longest chain 11 peptides. Score 0.387 Round 3: 311 peptides, 53 chains. Longest chain 15 peptides. Score 0.420 Round 4: 302 peptides, 52 chains. Longest chain 18 peptides. Score 0.409 Round 5: 313 peptides, 54 chains. Longest chain 13 peptides. Score 0.415 Taking the results from Round 3 Chains 54, Residues 258, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12881 restraints for refining 5398 atoms. 11879 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1946 (Rfree = 0.000) for 5398 atoms. Found 29 (29 requested) and removed 49 (14 requested) atoms. Cycle 17: After refmac, R = 0.1915 (Rfree = 0.000) for 5338 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. Cycle 18: After refmac, R = 0.1834 (Rfree = 0.000) for 5313 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 19: After refmac, R = 0.1935 (Rfree = 0.000) for 5297 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 20: After refmac, R = 0.1424 (Rfree = 0.000) for 5286 atoms. Found 10 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5467 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5487 seeds are put forward Round 1: 228 peptides, 48 chains. Longest chain 8 peptides. Score 0.268 Round 2: 270 peptides, 50 chains. Longest chain 10 peptides. Score 0.354 Round 3: 274 peptides, 49 chains. Longest chain 11 peptides. Score 0.374 Round 4: 285 peptides, 48 chains. Longest chain 13 peptides. Score 0.410 Round 5: 276 peptides, 43 chains. Longest chain 16 peptides. Score 0.439 Taking the results from Round 5 Chains 43, Residues 233, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12558 restraints for refining 5288 atoms. 11623 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1977 (Rfree = 0.000) for 5288 atoms. Found 29 (29 requested) and removed 39 (14 requested) atoms. Cycle 22: After refmac, R = 0.1992 (Rfree = 0.000) for 5248 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 23: After refmac, R = 0.2013 (Rfree = 0.000) for 5237 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 24: After refmac, R = 0.2052 (Rfree = 0.000) for 5216 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 25: After refmac, R = 0.1534 (Rfree = 0.000) for 5209 atoms. Found 10 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5372 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5392 seeds are put forward Round 1: 192 peptides, 41 chains. Longest chain 8 peptides. Score 0.249 Round 2: 238 peptides, 43 chains. Longest chain 12 peptides. Score 0.349 Round 3: 248 peptides, 46 chains. Longest chain 11 peptides. Score 0.342 Round 4: 273 peptides, 46 chains. Longest chain 13 peptides. Score 0.402 Round 5: 245 peptides, 40 chains. Longest chain 14 peptides. Score 0.398 Taking the results from Round 4 Chains 47, Residues 227, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12313 restraints for refining 5268 atoms. 11406 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1981 (Rfree = 0.000) for 5268 atoms. Found 28 (28 requested) and removed 56 (14 requested) atoms. Cycle 27: After refmac, R = 0.1980 (Rfree = 0.000) for 5208 atoms. Found 28 (28 requested) and removed 66 (14 requested) atoms. Cycle 28: After refmac, R = 0.1907 (Rfree = 0.000) for 5148 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 29: After refmac, R = 0.1440 (Rfree = 0.000) for 5129 atoms. Found 6 (28 requested) and removed 30 (14 requested) atoms. Cycle 30: After refmac, R = 0.1338 (Rfree = 0.000) for 5098 atoms. Found 3 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5278 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5291 seeds are put forward Round 1: 190 peptides, 43 chains. Longest chain 8 peptides. Score 0.220 Round 2: 245 peptides, 49 chains. Longest chain 12 peptides. Score 0.302 Round 3: 231 peptides, 44 chains. Longest chain 13 peptides. Score 0.320 Round 4: 244 peptides, 44 chains. Longest chain 14 peptides. Score 0.353 Round 5: 258 peptides, 46 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 5 Chains 46, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12156 restraints for refining 5155 atoms. 11354 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1954 (Rfree = 0.000) for 5155 atoms. Found 28 (28 requested) and removed 37 (14 requested) atoms. Cycle 32: After refmac, R = 0.2031 (Rfree = 0.000) for 5120 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 33: After refmac, R = 0.1839 (Rfree = 0.000) for 5095 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 34: After refmac, R = 0.1412 (Rfree = 0.000) for 5090 atoms. Found 17 (28 requested) and removed 19 (14 requested) atoms. Cycle 35: After refmac, R = 0.1514 (Rfree = 0.000) for 5075 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 5275 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5293 seeds are put forward Round 1: 202 peptides, 45 chains. Longest chain 8 peptides. Score 0.231 Round 2: 245 peptides, 46 chains. Longest chain 14 peptides. Score 0.334 Round 3: 230 peptides, 41 chains. Longest chain 11 peptides. Score 0.350 Round 4: 214 peptides, 39 chains. Longest chain 12 peptides. Score 0.332 Round 5: 208 peptides, 34 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Chains 34, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12075 restraints for refining 5059 atoms. 11413 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2099 (Rfree = 0.000) for 5059 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 37: After refmac, R = 0.1975 (Rfree = 0.000) for 5034 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 38: After refmac, R = 0.1489 (Rfree = 0.000) for 5017 atoms. Found 16 (27 requested) and removed 22 (13 requested) atoms. Cycle 39: After refmac, R = 0.1402 (Rfree = 0.000) for 4997 atoms. Found 7 (27 requested) and removed 18 (13 requested) atoms. Cycle 40: After refmac, R = 0.1390 (Rfree = 0.000) for 4980 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 5093 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5111 seeds are put forward Round 1: 176 peptides, 37 chains. Longest chain 9 peptides. Score 0.252 Round 2: 197 peptides, 37 chains. Longest chain 16 peptides. Score 0.310 Round 3: 199 peptides, 35 chains. Longest chain 17 peptides. Score 0.338 Round 4: 193 peptides, 33 chains. Longest chain 17 peptides. Score 0.345 Round 5: 203 peptides, 33 chains. Longest chain 18 peptides. Score 0.371 Taking the results from Round 5 Chains 35, Residues 170, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 11714 restraints for refining 5011 atoms. 11035 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1995 (Rfree = 0.000) for 5011 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 42: After refmac, R = 0.1980 (Rfree = 0.000) for 4983 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 43: After refmac, R = 0.1919 (Rfree = 0.000) for 4982 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 44: After refmac, R = 0.2010 (Rfree = 0.000) for 4971 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.1379 (Rfree = 0.000) for 4968 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 5120 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5140 seeds are put forward Round 1: 169 peptides, 37 chains. Longest chain 8 peptides. Score 0.231 Round 2: 193 peptides, 37 chains. Longest chain 15 peptides. Score 0.299 Round 3: 195 peptides, 35 chains. Longest chain 12 peptides. Score 0.327 Round 4: 193 peptides, 34 chains. Longest chain 15 peptides. Score 0.334 Round 5: 197 peptides, 35 chains. Longest chain 12 peptides. Score 0.333 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 159, 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. 7174 reflections ( 99.71 % complete ) and 11271 restraints for refining 4850 atoms. 10669 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2018 (Rfree = 0.000) for 4850 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1839 (Rfree = 0.000) for 4825 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1807 (Rfree = 0.000) for 4797 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1365 (Rfree = 0.000) for 4773 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... TimeTaking 56.68