Sun 23 Dec 22:22:59 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-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 22:23:08 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-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 559 and 0 Target number of residues in the AU: 559 Target solvent content: 0.6372 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 70.45 13411 reflections ( 98.47 % complete ) and 0 restraints for refining 6343 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3248 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2698 (Rfree = 0.000) for 6343 atoms. Found 55 (56 requested) and removed 50 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 6506 seeds are put forward NCS extension: 0 residues added, 6506 seeds are put forward Round 1: 362 peptides, 73 chains. Longest chain 9 peptides. Score 0.318 Round 2: 417 peptides, 69 chains. Longest chain 15 peptides. Score 0.455 Round 3: 429 peptides, 68 chains. Longest chain 20 peptides. Score 0.484 Round 4: 433 peptides, 61 chains. Longest chain 18 peptides. Score 0.541 Round 5: 441 peptides, 61 chains. Longest chain 19 peptides. Score 0.553 Taking the results from Round 5 Chains 61, Residues 380, Estimated correctness of the model 27.8 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11374 restraints for refining 5213 atoms. 9812 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2505 (Rfree = 0.000) for 5213 atoms. Found 44 (46 requested) and removed 30 (23 requested) atoms. Cycle 2: After refmac, R = 0.2277 (Rfree = 0.000) for 5179 atoms. Found 17 (46 requested) and removed 27 (23 requested) atoms. Cycle 3: After refmac, R = 0.2237 (Rfree = 0.000) for 5144 atoms. Found 16 (46 requested) and removed 28 (23 requested) atoms. Cycle 4: After refmac, R = 0.2223 (Rfree = 0.000) for 5125 atoms. Found 11 (46 requested) and removed 26 (23 requested) atoms. Cycle 5: After refmac, R = 0.2174 (Rfree = 0.000) for 5104 atoms. Found 12 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 5287 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5309 seeds are put forward Round 1: 374 peptides, 59 chains. Longest chain 18 peptides. Score 0.456 Round 2: 418 peptides, 58 chains. Longest chain 19 peptides. Score 0.538 Round 3: 438 peptides, 57 chains. Longest chain 21 peptides. Score 0.576 Round 4: 455 peptides, 53 chains. Longest chain 23 peptides. Score 0.626 Round 5: 426 peptides, 53 chains. Longest chain 23 peptides. Score 0.585 Taking the results from Round 4 Chains 54, Residues 402, Estimated correctness of the model 47.9 % 3 chains (60 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 10613 restraints for refining 5215 atoms. 8769 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2487 (Rfree = 0.000) for 5215 atoms. Found 42 (46 requested) and removed 38 (23 requested) atoms. Cycle 7: After refmac, R = 0.2271 (Rfree = 0.000) for 5197 atoms. Found 13 (46 requested) and removed 27 (23 requested) atoms. Cycle 8: After refmac, R = 0.2203 (Rfree = 0.000) for 5167 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. Cycle 9: After refmac, R = 0.2181 (Rfree = 0.000) for 5147 atoms. Found 6 (46 requested) and removed 23 (23 requested) atoms. Cycle 10: After refmac, R = 0.2135 (Rfree = 0.000) for 5126 atoms. Found 8 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 5312 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5341 seeds are put forward Round 1: 391 peptides, 63 chains. Longest chain 19 peptides. Score 0.455 Round 2: 421 peptides, 60 chains. Longest chain 17 peptides. Score 0.529 Round 3: 427 peptides, 55 chains. Longest chain 15 peptides. Score 0.573 Round 4: 440 peptides, 57 chains. Longest chain 19 peptides. Score 0.579 Round 5: 425 peptides, 55 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 4 Chains 57, Residues 383, Estimated correctness of the model 35.3 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11559 restraints for refining 5215 atoms. 10061 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2272 (Rfree = 0.000) for 5215 atoms. Found 28 (46 requested) and removed 25 (23 requested) atoms. Cycle 12: After refmac, R = 0.2140 (Rfree = 0.000) for 5205 atoms. Found 8 (46 requested) and removed 23 (23 requested) atoms. Cycle 13: After refmac, R = 0.2083 (Rfree = 0.000) for 5179 atoms. Found 15 (46 requested) and removed 23 (23 requested) atoms. Cycle 14: After refmac, R = 0.2013 (Rfree = 0.000) for 5166 atoms. Found 8 (46 requested) and removed 23 (23 requested) atoms. Cycle 15: After refmac, R = 0.1972 (Rfree = 0.000) for 5146 atoms. Found 12 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 5321 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5337 seeds are put forward Round 1: 387 peptides, 67 chains. Longest chain 16 peptides. Score 0.416 Round 2: 422 peptides, 60 chains. Longest chain 19 peptides. Score 0.530 Round 3: 414 peptides, 57 chains. Longest chain 20 peptides. Score 0.539 Round 4: 411 peptides, 51 chains. Longest chain 21 peptides. Score 0.576 Round 5: 425 peptides, 56 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 4 Chains 53, Residues 360, Estimated correctness of the model 34.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11617 restraints for refining 5215 atoms. 10155 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2258 (Rfree = 0.000) for 5215 atoms. Found 20 (46 requested) and removed 26 (23 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2175 (Rfree = 0.000) for 5199 atoms. Found 13 (46 requested) and removed 23 (23 requested) atoms. Cycle 18: After refmac, R = 0.2118 (Rfree = 0.000) for 5183 atoms. Found 11 (46 requested) and removed 23 (23 requested) atoms. Cycle 19: After refmac, R = 0.2065 (Rfree = 0.000) for 5165 atoms. Found 8 (46 requested) and removed 24 (23 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 5143 atoms. Found 6 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 5319 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 5336 seeds are put forward Round 1: 378 peptides, 58 chains. Longest chain 21 peptides. Score 0.471 Round 2: 421 peptides, 58 chains. Longest chain 19 peptides. Score 0.543 Round 3: 404 peptides, 58 chains. Longest chain 19 peptides. Score 0.515 Round 4: 409 peptides, 57 chains. Longest chain 20 peptides. Score 0.531 Round 5: 400 peptides, 55 chains. Longest chain 26 peptides. Score 0.531 Taking the results from Round 2 Chains 60, Residues 363, Estimated correctness of the model 24.8 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11451 restraints for refining 5215 atoms. 9981 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2175 (Rfree = 0.000) for 5215 atoms. Found 19 (46 requested) and removed 29 (23 requested) atoms. Cycle 22: After refmac, R = 0.2120 (Rfree = 0.000) for 5193 atoms. Found 14 (46 requested) and removed 23 (23 requested) atoms. Cycle 23: After refmac, R = 0.2042 (Rfree = 0.000) for 5177 atoms. Found 5 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2028 (Rfree = 0.000) for 5156 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. Cycle 25: After refmac, R = 0.2330 (Rfree = 0.000) for 5139 atoms. Found 29 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 5325 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5345 seeds are put forward Round 1: 375 peptides, 65 chains. Longest chain 19 peptides. Score 0.410 Round 2: 402 peptides, 55 chains. Longest chain 21 peptides. Score 0.534 Round 3: 396 peptides, 54 chains. Longest chain 20 peptides. Score 0.531 Round 4: 379 peptides, 56 chains. Longest chain 22 peptides. Score 0.488 Round 5: 394 peptides, 56 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 2 Chains 55, Residues 347, Estimated correctness of the model 22.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11566 restraints for refining 5215 atoms. 10233 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2184 (Rfree = 0.000) for 5215 atoms. Found 19 (46 requested) and removed 23 (23 requested) atoms. Cycle 27: After refmac, R = 0.2061 (Rfree = 0.000) for 5198 atoms. Found 16 (46 requested) and removed 23 (23 requested) atoms. Cycle 28: After refmac, R = 0.2002 (Rfree = 0.000) for 5185 atoms. Found 19 (46 requested) and removed 23 (23 requested) atoms. Cycle 29: After refmac, R = 0.2118 (Rfree = 0.000) for 5178 atoms. Found 22 (46 requested) and removed 23 (23 requested) atoms. Cycle 30: After refmac, R = 0.1867 (Rfree = 0.000) for 5173 atoms. Found 5 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 5356 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5377 seeds are put forward Round 1: 351 peptides, 65 chains. Longest chain 14 peptides. Score 0.363 Round 2: 357 peptides, 59 chains. Longest chain 19 peptides. Score 0.425 Round 3: 373 peptides, 58 chains. Longest chain 20 peptides. Score 0.462 Round 4: 382 peptides, 57 chains. Longest chain 16 peptides. Score 0.485 Round 5: 411 peptides, 59 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 5 Chains 59, Residues 352, Estimated correctness of the model 17.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11679 restraints for refining 5214 atoms. 10330 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2087 (Rfree = 0.000) for 5214 atoms. Found 28 (46 requested) and removed 24 (23 requested) atoms. Cycle 32: After refmac, R = 0.1990 (Rfree = 0.000) for 5214 atoms. Found 17 (46 requested) and removed 23 (23 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 5204 atoms. Found 33 (46 requested) and removed 23 (23 requested) atoms. Cycle 34: After refmac, R = 0.2134 (Rfree = 0.000) for 5209 atoms. Found 36 (46 requested) and removed 23 (23 requested) atoms. Cycle 35: After refmac, R = 0.1963 (Rfree = 0.000) for 5218 atoms. Found 17 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 5393 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5408 seeds are put forward Round 1: 324 peptides, 60 chains. Longest chain 12 peptides. Score 0.352 Round 2: 375 peptides, 57 chains. Longest chain 18 peptides. Score 0.473 Round 3: 388 peptides, 62 chains. Longest chain 14 peptides. Score 0.457 Round 4: 385 peptides, 56 chains. Longest chain 19 peptides. Score 0.498 Round 5: 379 peptides, 53 chains. Longest chain 18 peptides. Score 0.511 Taking the results from Round 5 Chains 53, Residues 326, Estimated correctness of the model 14.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11820 restraints for refining 5214 atoms. 10569 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2080 (Rfree = 0.000) for 5214 atoms. Found 24 (46 requested) and removed 25 (23 requested) atoms. Cycle 37: After refmac, R = 0.1993 (Rfree = 0.000) for 5203 atoms. Found 19 (46 requested) and removed 23 (23 requested) atoms. Cycle 38: After refmac, R = 0.2292 (Rfree = 0.000) for 5194 atoms. Found 38 (46 requested) and removed 23 (23 requested) atoms. Cycle 39: After refmac, R = 0.1836 (Rfree = 0.000) for 5199 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.1858 (Rfree = 0.000) for 5181 atoms. Found 18 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 5340 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5357 seeds are put forward Round 1: 314 peptides, 57 chains. Longest chain 17 peptides. Score 0.358 Round 2: 362 peptides, 58 chains. Longest chain 16 peptides. Score 0.442 Round 3: 370 peptides, 56 chains. Longest chain 18 peptides. Score 0.472 Round 4: 361 peptides, 56 chains. Longest chain 16 peptides. Score 0.456 Round 5: 378 peptides, 53 chains. Longest chain 19 peptides. Score 0.509 Taking the results from Round 5 Chains 54, Residues 325, Estimated correctness of the model 14.2 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11393 restraints for refining 5214 atoms. 10059 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2120 (Rfree = 0.000) for 5214 atoms. Found 27 (46 requested) and removed 27 (23 requested) atoms. Cycle 42: After refmac, R = 0.2033 (Rfree = 0.000) for 5198 atoms. Found 18 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1981 (Rfree = 0.000) for 5182 atoms. Found 17 (46 requested) and removed 23 (23 requested) atoms. Cycle 44: After refmac, R = 0.1940 (Rfree = 0.000) for 5165 atoms. Found 16 (46 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.1916 (Rfree = 0.000) for 5156 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 5307 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5325 seeds are put forward Round 1: 317 peptides, 53 chains. Longest chain 17 peptides. Score 0.398 Round 2: 354 peptides, 54 chains. Longest chain 16 peptides. Score 0.459 Round 3: 364 peptides, 55 chains. Longest chain 17 peptides. Score 0.469 Round 4: 350 peptides, 51 chains. Longest chain 17 peptides. Score 0.476 Round 5: 347 peptides, 55 chains. Longest chain 14 peptides. Score 0.438 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 299, Estimated correctness of the model 3.4 % 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. 13411 reflections ( 98.47 % complete ) and 11827 restraints for refining 5215 atoms. 10682 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2040 (Rfree = 0.000) for 5215 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2048 (Rfree = 0.000) for 5178 atoms. Found 0 (46 requested) and removed 19 (23 requested) atoms. Cycle 48: After refmac, R = 0.1994 (Rfree = 0.000) for 5157 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1961 (Rfree = 0.000) for 5127 atoms. TimeTaking 72.32