Sun 23 Dec 22:22:56 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 2fna-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.4-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/2fna-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.4-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 ============================================================ Sun 23 Dec 22:23:06 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/2fna-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.4-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 544 and 0 Target number of residues in the AU: 544 Target solvent content: 0.6469 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-3.4-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: 4 Cell parameters: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.75 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: 69.461 3.400 Wilson plot Bfac: 75.99 11204 reflections ( 98.52 % complete ) and 0 restraints for refining 6319 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2777 (Rfree = 0.000) for 6319 atoms. Found 38 (47 requested) and removed 62 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 6466 seeds are put forward NCS extension: 0 residues added, 6466 seeds are put forward Round 1: 347 peptides, 68 chains. Longest chain 10 peptides. Score 0.330 Round 2: 384 peptides, 64 chains. Longest chain 13 peptides. Score 0.435 Round 3: 392 peptides, 64 chains. Longest chain 16 peptides. Score 0.449 Round 4: 393 peptides, 61 chains. Longest chain 13 peptides. Score 0.474 Round 5: 411 peptides, 58 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 5 Chains 60, Residues 353, Estimated correctness of the model 3.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11654 restraints for refining 5191 atoms. 10264 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2317 (Rfree = 0.000) for 5191 atoms. Found 29 (39 requested) and removed 28 (19 requested) atoms. Cycle 2: After refmac, R = 0.2250 (Rfree = 0.000) for 5142 atoms. Found 15 (39 requested) and removed 19 (19 requested) atoms. Cycle 3: After refmac, R = 0.2235 (Rfree = 0.000) for 5127 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. Cycle 4: After refmac, R = 0.2198 (Rfree = 0.000) for 5108 atoms. Found 5 (38 requested) and removed 19 (19 requested) atoms. Cycle 5: After refmac, R = 0.2177 (Rfree = 0.000) for 5093 atoms. Found 5 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 5295 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 5306 seeds are put forward Round 1: 363 peptides, 64 chains. Longest chain 18 peptides. Score 0.395 Round 2: 389 peptides, 61 chains. Longest chain 16 peptides. Score 0.467 Round 3: 427 peptides, 61 chains. Longest chain 20 peptides. Score 0.531 Round 4: 396 peptides, 56 chains. Longest chain 22 peptides. Score 0.517 Round 5: 397 peptides, 53 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 5 Chains 53, Residues 344, Estimated correctness of the model 7.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11900 restraints for refining 5190 atoms. 10577 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2503 (Rfree = 0.000) for 5190 atoms. Found 30 (39 requested) and removed 22 (19 requested) atoms. Cycle 7: After refmac, R = 0.2346 (Rfree = 0.000) for 5176 atoms. Found 12 (39 requested) and removed 19 (19 requested) atoms. Cycle 8: After refmac, R = 0.2257 (Rfree = 0.000) for 5163 atoms. Found 7 (39 requested) and removed 19 (19 requested) atoms. Cycle 9: After refmac, R = 0.2189 (Rfree = 0.000) for 5144 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.2166 (Rfree = 0.000) for 5131 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 5310 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5330 seeds are put forward Round 1: 386 peptides, 68 chains. Longest chain 12 peptides. Score 0.406 Round 2: 401 peptides, 60 chains. Longest chain 17 peptides. Score 0.495 Round 3: 401 peptides, 54 chains. Longest chain 19 peptides. Score 0.539 Round 4: 408 peptides, 53 chains. Longest chain 20 peptides. Score 0.558 Round 5: 403 peptides, 54 chains. Longest chain 17 peptides. Score 0.543 Taking the results from Round 4 Chains 55, Residues 355, Estimated correctness of the model 14.4 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11357 restraints for refining 5192 atoms. 9794 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2442 (Rfree = 0.000) for 5192 atoms. Found 39 (39 requested) and removed 27 (19 requested) atoms. Cycle 12: After refmac, R = 0.2207 (Rfree = 0.000) for 5180 atoms. Found 14 (39 requested) and removed 21 (19 requested) atoms. Cycle 13: After refmac, R = 0.2134 (Rfree = 0.000) for 5162 atoms. Found 8 (39 requested) and removed 19 (19 requested) atoms. Cycle 14: After refmac, R = 0.2073 (Rfree = 0.000) for 5142 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 15: After refmac, R = 0.2046 (Rfree = 0.000) for 5122 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 5334 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5363 seeds are put forward Round 1: 369 peptides, 66 chains. Longest chain 12 peptides. Score 0.390 Round 2: 397 peptides, 61 chains. Longest chain 16 peptides. Score 0.481 Round 3: 403 peptides, 58 chains. Longest chain 26 peptides. Score 0.514 Round 4: 428 peptides, 58 chains. Longest chain 20 peptides. Score 0.554 Round 5: 415 peptides, 58 chains. Longest chain 19 peptides. Score 0.533 Taking the results from Round 4 Chains 58, Residues 370, Estimated correctness of the model 13.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11493 restraints for refining 5191 atoms. 10045 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2288 (Rfree = 0.000) for 5191 atoms. Found 25 (39 requested) and removed 23 (19 requested) atoms. Cycle 17: After refmac, R = 0.2110 (Rfree = 0.000) for 5179 atoms. Found 15 (39 requested) and removed 19 (19 requested) atoms. Cycle 18: After refmac, R = 0.2050 (Rfree = 0.000) for 5169 atoms. Found 6 (39 requested) and removed 20 (19 requested) atoms. Cycle 19: After refmac, R = 0.1998 (Rfree = 0.000) for 5153 atoms. Found 3 (38 requested) and removed 19 (19 requested) atoms. Cycle 20: After refmac, R = 0.1997 (Rfree = 0.000) for 5132 atoms. Found 3 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 5286 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 5310 seeds are put forward Round 1: 326 peptides, 60 chains. Longest chain 12 peptides. Score 0.356 Round 2: 368 peptides, 60 chains. Longest chain 19 peptides. Score 0.437 Round 3: 383 peptides, 58 chains. Longest chain 20 peptides. Score 0.479 Round 4: 377 peptides, 56 chains. Longest chain 20 peptides. Score 0.484 Round 5: 385 peptides, 59 chains. Longest chain 22 peptides. Score 0.475 Taking the results from Round 4 Chains 56, Residues 321, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11983 restraints for refining 5191 atoms. 10755 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2221 (Rfree = 0.000) for 5191 atoms. Found 26 (39 requested) and removed 20 (19 requested) atoms. Cycle 22: After refmac, R = 0.2115 (Rfree = 0.000) for 5188 atoms. Found 11 (39 requested) and removed 19 (19 requested) atoms. Cycle 23: After refmac, R = 0.2069 (Rfree = 0.000) for 5175 atoms. Found 6 (39 requested) and removed 20 (19 requested) atoms. Cycle 24: After refmac, R = 0.2071 (Rfree = 0.000) for 5157 atoms. Found 11 (38 requested) and removed 19 (19 requested) atoms. Cycle 25: After refmac, R = 0.2042 (Rfree = 0.000) for 5143 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 5298 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5324 seeds are put forward Round 1: 354 peptides, 69 chains. Longest chain 11 peptides. Score 0.336 Round 2: 376 peptides, 59 chains. Longest chain 15 peptides. Score 0.459 Round 3: 371 peptides, 58 chains. Longest chain 20 peptides. Score 0.458 Round 4: 395 peptides, 59 chains. Longest chain 18 peptides. Score 0.493 Round 5: 395 peptides, 60 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 4 Chains 59, Residues 336, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11822 restraints for refining 5192 atoms. 10537 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2230 (Rfree = 0.000) for 5192 atoms. Found 32 (39 requested) and removed 20 (19 requested) atoms. Cycle 27: After refmac, R = 0.2063 (Rfree = 0.000) for 5191 atoms. Found 9 (39 requested) and removed 20 (19 requested) atoms. Cycle 28: After refmac, R = 0.2023 (Rfree = 0.000) for 5177 atoms. Found 7 (39 requested) and removed 20 (19 requested) atoms. Cycle 29: After refmac, R = 0.2030 (Rfree = 0.000) for 5159 atoms. Found 7 (38 requested) and removed 20 (19 requested) atoms. Cycle 30: After refmac, R = 0.2009 (Rfree = 0.000) for 5139 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 5304 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5321 seeds are put forward Round 1: 302 peptides, 54 chains. Longest chain 13 peptides. Score 0.360 Round 2: 336 peptides, 56 chains. Longest chain 16 peptides. Score 0.409 Round 3: 356 peptides, 56 chains. Longest chain 15 peptides. Score 0.447 Round 4: 352 peptides, 54 chains. Longest chain 16 peptides. Score 0.456 Round 5: 379 peptides, 58 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 58, Residues 321, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11823 restraints for refining 5191 atoms. 10597 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2140 (Rfree = 0.000) for 5191 atoms. Found 21 (39 requested) and removed 20 (19 requested) atoms. Cycle 32: After refmac, R = 0.2006 (Rfree = 0.000) for 5181 atoms. Found 7 (39 requested) and removed 19 (19 requested) atoms. Cycle 33: After refmac, R = 0.1971 (Rfree = 0.000) for 5154 atoms. Found 7 (39 requested) and removed 22 (19 requested) atoms. Cycle 34: After refmac, R = 0.1859 (Rfree = 0.000) for 5130 atoms. Found 4 (38 requested) and removed 20 (19 requested) atoms. Cycle 35: After refmac, R = 0.2006 (Rfree = 0.000) for 5109 atoms. Found 27 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 5309 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5325 seeds are put forward Round 1: 293 peptides, 60 chains. Longest chain 10 peptides. Score 0.287 Round 2: 316 peptides, 54 chains. Longest chain 11 peptides. Score 0.388 Round 3: 330 peptides, 55 chains. Longest chain 12 peptides. Score 0.406 Round 4: 359 peptides, 55 chains. Longest chain 17 peptides. Score 0.460 Round 5: 354 peptides, 53 chains. Longest chain 20 peptides. Score 0.467 Taking the results from Round 5 Chains 53, Residues 301, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11204 reflections ( 98.52 % complete ) and 11916 restraints for refining 5193 atoms. 10765 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2107 (Rfree = 0.000) for 5193 atoms. Found 32 (39 requested) and removed 20 (19 requested) atoms. Cycle 37: After refmac, R = 0.1991 (Rfree = 0.000) for 5192 atoms. Found 13 (39 requested) and removed 19 (19 requested) atoms. Cycle 38: After refmac, R = 0.1915 (Rfree = 0.000) for 5181 atoms. Found 3 (39 requested) and removed 19 (19 requested) atoms. Cycle 39: After refmac, R = 0.1886 (Rfree = 0.000) for 5154 atoms. Found 12 (38 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.1881 (Rfree = 0.000) for 5138 atoms. Found 4 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 5293 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5319 seeds are put forward Round 1: 272 peptides, 56 chains. Longest chain 10 peptides. Score 0.278 Round 2: 309 peptides, 51 chains. Longest chain 18 peptides. Score 0.399 Round 3: 331 peptides, 58 chains. Longest chain 18 peptides. Score 0.383 Round 4: 332 peptides, 53 chains. Longest chain 26 peptides. Score 0.427 Round 5: 332 peptides, 54 chains. Longest chain 20 peptides. Score 0.419 Taking the results from Round 4 Chains 54, Residues 279, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11204 reflections ( 98.52 % complete ) and 11699 restraints for refining 5193 atoms. 10533 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 5193 atoms. Found 27 (39 requested) and removed 23 (19 requested) atoms. Cycle 42: After refmac, R = 0.1986 (Rfree = 0.000) for 5188 atoms. Found 9 (39 requested) and removed 22 (19 requested) atoms. Cycle 43: After refmac, R = 0.2059 (Rfree = 0.000) for 5165 atoms. Found 14 (39 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.1855 (Rfree = 0.000) for 5149 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.1835 (Rfree = 0.000) for 5130 atoms. Found 1 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 5258 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5275 seeds are put forward Round 1: 269 peptides, 54 chains. Longest chain 11 peptides. Score 0.290 Round 2: 310 peptides, 49 chains. Longest chain 16 peptides. Score 0.418 Round 3: 305 peptides, 49 chains. Longest chain 14 peptides. Score 0.409 Round 4: 305 peptides, 51 chains. Longest chain 14 peptides. Score 0.392 Round 5: 311 peptides, 53 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 261, 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 2fna-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11204 reflections ( 98.52 % complete ) and 12064 restraints for refining 5192 atoms. 11069 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1935 (Rfree = 0.000) for 5192 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1877 (Rfree = 0.000) for 5164 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1875 (Rfree = 0.000) for 5140 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1857 (Rfree = 0.000) for 5113 atoms. TimeTaking 70.67