Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aml-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:05 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/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.8-parrot-hancs/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-hancs.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-hancs.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 6566 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3291 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3027 (Rfree = 0.000) for 6566 atoms. Found 36 (36 requested) and removed 61 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 4.06 Search for helices and strands: 0 residues in 0 chains, 6706 seeds are put forward NCS extension: 0 residues added, 6706 seeds are put forward Round 1: 248 peptides, 52 chains. Longest chain 9 peptides. Score 0.277 Round 2: 331 peptides, 56 chains. Longest chain 16 peptides. Score 0.436 Round 3: 378 peptides, 54 chains. Longest chain 16 peptides. Score 0.550 Round 4: 393 peptides, 58 chains. Longest chain 16 peptides. Score 0.545 Round 5: 414 peptides, 56 chains. Longest chain 17 peptides. Score 0.599 Taking the results from Round 5 Chains 57, Residues 358, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12160 restraints for refining 5397 atoms. 10702 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2367 (Rfree = 0.000) for 5397 atoms. Found 29 (29 requested) and removed 51 (14 requested) atoms. Cycle 2: After refmac, R = 0.2115 (Rfree = 0.000) for 5300 atoms. Found 20 (29 requested) and removed 31 (14 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1754 (Rfree = 0.000) for 5243 atoms. Found 13 (29 requested) and removed 24 (14 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1918 (Rfree = 0.000) for 5204 atoms. Found 16 (28 requested) and removed 29 (14 requested) atoms. Cycle 5: After refmac, R = 0.1654 (Rfree = 0.000) for 5176 atoms. Found 6 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.97 Search for helices and strands: 0 residues in 0 chains, 5374 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5390 seeds are put forward Round 1: 324 peptides, 64 chains. Longest chain 11 peptides. Score 0.342 Round 2: 373 peptides, 61 chains. Longest chain 15 peptides. Score 0.480 Round 3: 370 peptides, 58 chains. Longest chain 13 peptides. Score 0.501 Round 4: 383 peptides, 57 chains. Longest chain 17 peptides. Score 0.535 Round 5: 378 peptides, 51 chains. Longest chain 23 peptides. Score 0.575 Taking the results from Round 5 Chains 54, Residues 327, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7174 reflections ( 99.71 % complete ) and 12175 restraints for refining 5381 atoms. 10814 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2141 (Rfree = 0.000) for 5381 atoms. Found 29 (29 requested) and removed 52 (14 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2193 (Rfree = 0.000) for 5308 atoms. Found 28 (29 requested) and removed 44 (14 requested) atoms. Cycle 8: After refmac, R = 0.2178 (Rfree = 0.000) for 5253 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2064 (Rfree = 0.000) for 5220 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2044 (Rfree = 0.000) for 5202 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5496 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 5509 seeds are put forward Round 1: 306 peptides, 59 chains. Longest chain 12 peptides. Score 0.349 Round 2: 358 peptides, 57 chains. Longest chain 20 peptides. Score 0.485 Round 3: 352 peptides, 57 chains. Longest chain 16 peptides. Score 0.472 Round 4: 363 peptides, 57 chains. Longest chain 14 peptides. Score 0.495 Round 5: 375 peptides, 57 chains. Longest chain 17 peptides. Score 0.519 Taking the results from Round 5 Chains 57, Residues 318, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7174 reflections ( 99.71 % complete ) and 11986 restraints for refining 5333 atoms. 10699 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2298 (Rfree = 0.000) for 5333 atoms. Found 29 (29 requested) and removed 71 (14 requested) atoms. Cycle 12: After refmac, R = 0.1898 (Rfree = 0.000) for 5256 atoms. Found 25 (29 requested) and removed 31 (14 requested) atoms. Cycle 13: After refmac, R = 0.1824 (Rfree = 0.000) for 5235 atoms. Found 28 (28 requested) and removed 40 (14 requested) atoms. Cycle 14: After refmac, R = 0.1734 (Rfree = 0.000) for 5209 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1608 (Rfree = 0.000) for 5210 atoms. Found 22 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5431 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5452 seeds are put forward Round 1: 286 peptides, 57 chains. Longest chain 10 peptides. Score 0.320 Round 2: 312 peptides, 48 chains. Longest chain 16 peptides. Score 0.470 Round 3: 338 peptides, 50 chains. Longest chain 19 peptides. Score 0.506 Round 4: 354 peptides, 50 chains. Longest chain 18 peptides. Score 0.538 Round 5: 351 peptides, 51 chains. Longest chain 17 peptides. Score 0.524 Taking the results from Round 4 Chains 50, Residues 304, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7174 reflections ( 99.71 % complete ) and 12072 restraints for refining 5398 atoms. 10820 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1989 (Rfree = 0.000) for 5398 atoms. Found 29 (29 requested) and removed 44 (14 requested) atoms. Cycle 17: After refmac, R = 0.1899 (Rfree = 0.000) for 5358 atoms. Found 29 (29 requested) and removed 32 (14 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1874 (Rfree = 0.000) for 5344 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 19: After refmac, R = 0.1753 (Rfree = 0.000) for 5326 atoms. Found 25 (29 requested) and removed 28 (14 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1533 (Rfree = 0.000) for 5309 atoms. Found 8 (29 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 5488 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5508 seeds are put forward Round 1: 290 peptides, 59 chains. Longest chain 10 peptides. Score 0.309 Round 2: 319 peptides, 56 chains. Longest chain 16 peptides. Score 0.409 Round 3: 327 peptides, 56 chains. Longest chain 15 peptides. Score 0.427 Round 4: 335 peptides, 55 chains. Longest chain 14 peptides. Score 0.454 Round 5: 328 peptides, 54 chains. Longest chain 23 peptides. Score 0.448 Taking the results from Round 4 Chains 55, Residues 280, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12676 restraints for refining 5398 atoms. 11571 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1969 (Rfree = 0.000) for 5398 atoms. Found 29 (29 requested) and removed 68 (14 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2060 (Rfree = 0.000) for 5331 atoms. Found 29 (29 requested) and removed 39 (14 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1831 (Rfree = 0.000) for 5305 atoms. Found 29 (29 requested) and removed 38 (14 requested) atoms. Cycle 24: After refmac, R = 0.1816 (Rfree = 0.000) for 5284 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1441 (Rfree = 0.000) for 5274 atoms. Found 5 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 4.04 Search for helices and strands: 0 residues in 0 chains, 5423 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5444 seeds are put forward Round 1: 222 peptides, 48 chains. Longest chain 7 peptides. Score 0.252 Round 2: 286 peptides, 53 chains. Longest chain 9 peptides. Score 0.362 Round 3: 297 peptides, 49 chains. Longest chain 14 peptides. Score 0.428 Round 4: 285 peptides, 49 chains. Longest chain 12 peptides. Score 0.400 Round 5: 295 peptides, 50 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 3 Chains 49, Residues 248, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12792 restraints for refining 5381 atoms. 11849 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1891 (Rfree = 0.000) for 5381 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1779 (Rfree = 0.000) for 5357 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1352 (Rfree = 0.000) for 5348 atoms. Found 17 (29 requested) and removed 18 (14 requested) atoms. Cycle 29: After refmac, R = 0.1239 (Rfree = 0.000) for 5332 atoms. Found 8 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.1227 (Rfree = 0.000) for 5318 atoms. Found 7 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 5528 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5549 seeds are put forward Round 1: 242 peptides, 50 chains. Longest chain 9 peptides. Score 0.283 Round 2: 295 peptides, 50 chains. Longest chain 13 peptides. Score 0.413 Round 3: 299 peptides, 52 chains. Longest chain 13 peptides. Score 0.403 Round 4: 291 peptides, 46 chains. Longest chain 14 peptides. Score 0.444 Round 5: 303 peptides, 51 chains. Longest chain 21 peptides. Score 0.422 Taking the results from Round 4 Chains 49, Residues 245, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12691 restraints for refining 5397 atoms. 11660 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1874 (Rfree = 0.000) for 5397 atoms. Found 29 (29 requested) and removed 42 (14 requested) atoms. Cycle 32: After refmac, R = 0.1886 (Rfree = 0.000) for 5361 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 33: After refmac, R = 0.1482 (Rfree = 0.000) for 5341 atoms. Found 18 (29 requested) and removed 20 (14 requested) atoms. Cycle 34: After refmac, R = 0.1394 (Rfree = 0.000) for 5328 atoms. Found 11 (29 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.1356 (Rfree = 0.000) for 5310 atoms. Found 11 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 5489 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5503 seeds are put forward Round 1: 208 peptides, 45 chains. Longest chain 9 peptides. Score 0.247 Round 2: 260 peptides, 48 chains. Longest chain 11 peptides. Score 0.350 Round 3: 260 peptides, 45 chains. Longest chain 10 peptides. Score 0.382 Round 4: 266 peptides, 44 chains. Longest chain 11 peptides. Score 0.406 Round 5: 271 peptides, 44 chains. Longest chain 10 peptides. Score 0.418 Taking the results from Round 5 Chains 44, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12855 restraints for refining 5397 atoms. 11991 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1836 (Rfree = 0.000) for 5397 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2005 (Rfree = 0.000) for 5380 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 38: After refmac, R = 0.1537 (Rfree = 0.000) for 5370 atoms. Found 12 (29 requested) and removed 22 (14 requested) atoms. Cycle 39: After refmac, R = 0.1878 (Rfree = 0.000) for 5351 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 40: After refmac, R = 0.1849 (Rfree = 0.000) for 5348 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5553 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5564 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 8 peptides. Score 0.260 Round 2: 240 peptides, 44 chains. Longest chain 13 peptides. Score 0.343 Round 3: 240 peptides, 42 chains. Longest chain 11 peptides. Score 0.365 Round 4: 244 peptides, 43 chains. Longest chain 12 peptides. Score 0.364 Round 5: 243 peptides, 43 chains. Longest chain 11 peptides. Score 0.361 Taking the results from Round 3 Chains 42, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7174 reflections ( 99.71 % complete ) and 12632 restraints for refining 5259 atoms. 11882 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2008 (Rfree = 0.000) for 5259 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. Cycle 42: After refmac, R = 0.1950 (Rfree = 0.000) for 5240 atoms. Found 28 (28 requested) and removed 59 (14 requested) atoms. Cycle 43: After refmac, R = 0.1387 (Rfree = 0.000) for 5195 atoms. Found 4 (28 requested) and removed 24 (14 requested) atoms. Cycle 44: After refmac, R = 0.1324 (Rfree = 0.000) for 5167 atoms. Found 14 (28 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.1255 (Rfree = 0.000) for 5159 atoms. Found 8 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 5328 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5343 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 7 peptides. Score 0.260 Round 2: 209 peptides, 38 chains. Longest chain 9 peptides. Score 0.330 Round 3: 196 peptides, 36 chains. Longest chain 11 peptides. Score 0.319 Round 4: 201 peptides, 33 chains. Longest chain 14 peptides. Score 0.366 Round 5: 184 peptides, 33 chains. Longest chain 12 peptides. Score 0.321 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 168, Estimated correctness of the model 0.0 % 1 chains (11 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. 7174 reflections ( 99.71 % complete ) and 12286 restraints for refining 5181 atoms. 11615 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1871 (Rfree = 0.000) for 5181 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2012 (Rfree = 0.000) for 5161 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1346 (Rfree = 0.000) for 5141 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1287 (Rfree = 0.000) for 5116 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:46:00 GMT 2018 Job finished. TimeTaking 78.09