null Mon 24 Dec 00:45:33 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fna-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-parrot-mrncs ############### 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 00:45:38 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 6370 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3204 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2715 (Rfree = 0.000) for 6370 atoms. Found 57 (57 requested) and removed 41 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 6575 seeds are put forward NCS extension: 0 residues added, 6575 seeds are put forward Round 1: 360 peptides, 65 chains. Longest chain 13 peptides. Score 0.381 Round 2: 439 peptides, 64 chains. Longest chain 16 peptides. Score 0.529 Round 3: 477 peptides, 66 chains. Longest chain 17 peptides. Score 0.574 Round 4: 484 peptides, 59 chains. Longest chain 29 peptides. Score 0.628 Round 5: 479 peptides, 60 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 4 Chains 59, Residues 425, Estimated correctness of the model 48.4 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 10707 restraints for refining 5214 atoms. 8930 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2486 (Rfree = 0.000) for 5214 atoms. Found 37 (46 requested) and removed 32 (23 requested) atoms. Cycle 2: After refmac, R = 0.2309 (Rfree = 0.000) for 5179 atoms. Found 13 (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 24 (23 requested) atoms. Cycle 4: After refmac, R = 0.2184 (Rfree = 0.000) for 5123 atoms. Found 14 (46 requested) and removed 24 (23 requested) atoms. Cycle 5: After refmac, R = 0.2130 (Rfree = 0.000) for 5101 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 5294 seeds are put forward NCS extension: 27 residues added (6 deleted due to clashes), 5321 seeds are put forward Round 1: 427 peptides, 68 chains. Longest chain 16 peptides. Score 0.480 Round 2: 462 peptides, 56 chains. Longest chain 23 peptides. Score 0.617 Round 3: 469 peptides, 55 chains. Longest chain 26 peptides. Score 0.633 Round 4: 458 peptides, 56 chains. Longest chain 23 peptides. Score 0.611 Round 5: 443 peptides, 55 chains. Longest chain 29 peptides. Score 0.596 Taking the results from Round 3 Chains 59, Residues 414, Estimated correctness of the model 49.7 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 10812 restraints for refining 5213 atoms. 9037 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2395 (Rfree = 0.000) for 5213 atoms. Found 40 (46 requested) and removed 40 (23 requested) atoms. Cycle 7: After refmac, R = 0.2199 (Rfree = 0.000) for 5195 atoms. Found 15 (46 requested) and removed 24 (23 requested) atoms. Cycle 8: After refmac, R = 0.2365 (Rfree = 0.000) for 5179 atoms. Found 18 (46 requested) and removed 24 (23 requested) atoms. Cycle 9: After refmac, R = 0.2099 (Rfree = 0.000) for 5165 atoms. Found 9 (46 requested) and removed 25 (23 requested) atoms. Cycle 10: After refmac, R = 0.2108 (Rfree = 0.000) for 5140 atoms. Found 13 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 5315 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 5339 seeds are put forward Round 1: 387 peptides, 57 chains. Longest chain 18 peptides. Score 0.494 Round 2: 459 peptides, 61 chains. Longest chain 23 peptides. Score 0.580 Round 3: 457 peptides, 56 chains. Longest chain 29 peptides. Score 0.610 Round 4: 445 peptides, 56 chains. Longest chain 31 peptides. Score 0.593 Round 5: 452 peptides, 57 chains. Longest chain 26 peptides. Score 0.596 Taking the results from Round 3 Chains 59, Residues 401, Estimated correctness of the model 43.7 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 10735 restraints for refining 5215 atoms. 8981 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2370 (Rfree = 0.000) for 5215 atoms. Found 34 (46 requested) and removed 32 (23 requested) atoms. Cycle 12: After refmac, R = 0.2169 (Rfree = 0.000) for 5195 atoms. Found 13 (46 requested) and removed 24 (23 requested) atoms. Cycle 13: After refmac, R = 0.2122 (Rfree = 0.000) for 5177 atoms. Found 16 (46 requested) and removed 23 (23 requested) atoms. Cycle 14: After refmac, R = 0.2041 (Rfree = 0.000) for 5163 atoms. Found 5 (46 requested) and removed 23 (23 requested) atoms. Cycle 15: After refmac, R = 0.1987 (Rfree = 0.000) for 5140 atoms. Found 8 (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, 5320 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 5358 seeds are put forward Round 1: 389 peptides, 59 chains. Longest chain 17 peptides. Score 0.482 Round 2: 448 peptides, 59 chains. Longest chain 27 peptides. Score 0.577 Round 3: 424 peptides, 54 chains. Longest chain 28 peptides. Score 0.575 Round 4: 441 peptides, 57 chains. Longest chain 28 peptides. Score 0.580 Round 5: 443 peptides, 55 chains. Longest chain 28 peptides. Score 0.596 Taking the results from Round 5 Chains 58, Residues 388, Estimated correctness of the model 40.0 % 5 chains (68 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 10636 restraints for refining 5215 atoms. 8845 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2383 (Rfree = 0.000) for 5215 atoms. Found 30 (46 requested) and removed 35 (23 requested) atoms. Cycle 17: After refmac, R = 0.2238 (Rfree = 0.000) for 5191 atoms. Found 14 (46 requested) and removed 25 (23 requested) atoms. Cycle 18: After refmac, R = 0.2566 (Rfree = 0.000) for 5173 atoms. Found 46 (46 requested) and removed 26 (23 requested) atoms. Cycle 19: After refmac, R = 0.2155 (Rfree = 0.000) for 5185 atoms. Found 13 (46 requested) and removed 24 (23 requested) atoms. Cycle 20: After refmac, R = 0.2208 (Rfree = 0.000) for 5167 atoms. Found 16 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 5361 seeds are put forward NCS extension: 24 residues added (10 deleted due to clashes), 5385 seeds are put forward Round 1: 375 peptides, 61 chains. Longest chain 17 peptides. Score 0.442 Round 2: 422 peptides, 57 chains. Longest chain 19 peptides. Score 0.551 Round 3: 413 peptides, 59 chains. Longest chain 17 peptides. Score 0.523 Round 4: 438 peptides, 51 chains. Longest chain 32 peptides. Score 0.615 Round 5: 419 peptides, 58 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 4 Chains 52, Residues 387, Estimated correctness of the model 45.0 % 3 chains (60 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 10563 restraints for refining 5213 atoms. 8771 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2381 (Rfree = 0.000) for 5213 atoms. Found 31 (46 requested) and removed 37 (23 requested) atoms. Cycle 22: After refmac, R = 0.2179 (Rfree = 0.000) for 5189 atoms. Found 11 (46 requested) and removed 24 (23 requested) atoms. Cycle 23: After refmac, R = 0.2160 (Rfree = 0.000) for 5171 atoms. Found 14 (46 requested) and removed 23 (23 requested) atoms. Cycle 24: After refmac, R = 0.2104 (Rfree = 0.000) for 5160 atoms. Found 11 (46 requested) and removed 23 (23 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 5146 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 5320 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 5344 seeds are put forward Round 1: 378 peptides, 61 chains. Longest chain 17 peptides. Score 0.447 Round 2: 407 peptides, 54 chains. Longest chain 23 peptides. Score 0.549 Round 3: 409 peptides, 52 chains. Longest chain 23 peptides. Score 0.566 Round 4: 405 peptides, 50 chains. Longest chain 22 peptides. Score 0.574 Round 5: 402 peptides, 53 chains. Longest chain 19 peptides. Score 0.548 Taking the results from Round 4 Chains 52, Residues 355, Estimated correctness of the model 33.9 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11174 restraints for refining 5215 atoms. 9616 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2281 (Rfree = 0.000) for 5215 atoms. Found 35 (46 requested) and removed 24 (23 requested) atoms. Cycle 27: After refmac, R = 0.2138 (Rfree = 0.000) for 5208 atoms. Found 22 (46 requested) and removed 27 (23 requested) atoms. Cycle 28: After refmac, R = 0.2253 (Rfree = 0.000) for 5195 atoms. Found 46 (46 requested) and removed 29 (23 requested) atoms. Cycle 29: After refmac, R = 0.2119 (Rfree = 0.000) for 5209 atoms. Found 35 (46 requested) and removed 24 (23 requested) atoms. Cycle 30: After refmac, R = 0.2201 (Rfree = 0.000) for 5210 atoms. Found 44 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 5412 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5425 seeds are put forward Round 1: 325 peptides, 57 chains. Longest chain 17 peptides. Score 0.380 Round 2: 374 peptides, 56 chains. Longest chain 17 peptides. Score 0.479 Round 3: 375 peptides, 57 chains. Longest chain 17 peptides. Score 0.473 Round 4: 368 peptides, 50 chains. Longest chain 24 peptides. Score 0.515 Round 5: 372 peptides, 56 chains. Longest chain 18 peptides. Score 0.476 Taking the results from Round 4 Chains 50, Residues 318, Estimated correctness of the model 16.1 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11316 restraints for refining 5214 atoms. 9899 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2180 (Rfree = 0.000) for 5214 atoms. Found 32 (46 requested) and removed 29 (23 requested) atoms. Cycle 32: After refmac, R = 0.2088 (Rfree = 0.000) for 5209 atoms. Found 21 (46 requested) and removed 25 (23 requested) atoms. Cycle 33: After refmac, R = 0.1991 (Rfree = 0.000) for 5199 atoms. Found 17 (46 requested) and removed 23 (23 requested) atoms. Cycle 34: After refmac, R = 0.1969 (Rfree = 0.000) for 5186 atoms. Found 7 (46 requested) and removed 23 (23 requested) atoms. Cycle 35: After refmac, R = 0.1926 (Rfree = 0.000) for 5165 atoms. Found 12 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 5318 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 5339 seeds are put forward Round 1: 328 peptides, 57 chains. Longest chain 13 peptides. Score 0.386 Round 2: 352 peptides, 52 chains. Longest chain 21 peptides. Score 0.471 Round 3: 344 peptides, 50 chains. Longest chain 18 peptides. Score 0.473 Round 4: 353 peptides, 52 chains. Longest chain 20 peptides. Score 0.473 Round 5: 358 peptides, 48 chains. Longest chain 27 peptides. Score 0.513 Taking the results from Round 5 Chains 50, Residues 310, Estimated correctness of the model 15.5 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11684 restraints for refining 5214 atoms. 10386 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2195 (Rfree = 0.000) for 5214 atoms. Found 35 (46 requested) and removed 24 (23 requested) atoms. Cycle 37: After refmac, R = 0.2154 (Rfree = 0.000) for 5214 atoms. Found 21 (46 requested) and removed 24 (23 requested) atoms. Cycle 38: After refmac, R = 0.2049 (Rfree = 0.000) for 5209 atoms. Found 12 (46 requested) and removed 23 (23 requested) atoms. Cycle 39: After refmac, R = 0.2011 (Rfree = 0.000) for 5195 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.1962 (Rfree = 0.000) for 5176 atoms. Found 18 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 5318 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 5350 seeds are put forward Round 1: 326 peptides, 62 chains. Longest chain 13 peptides. Score 0.339 Round 2: 354 peptides, 58 chains. Longest chain 17 peptides. Score 0.427 Round 3: 370 peptides, 59 chains. Longest chain 18 peptides. Score 0.449 Round 4: 368 peptides, 55 chains. Longest chain 18 peptides. Score 0.476 Round 5: 337 peptides, 54 chains. Longest chain 18 peptides. Score 0.428 Taking the results from Round 4 Chains 55, Residues 313, Estimated correctness of the model 3.4 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 13411 reflections ( 98.47 % complete ) and 11491 restraints for refining 5215 atoms. 10178 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2088 (Rfree = 0.000) for 5215 atoms. Found 35 (46 requested) and removed 24 (23 requested) atoms. Cycle 42: After refmac, R = 0.1990 (Rfree = 0.000) for 5219 atoms. Found 18 (46 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.1928 (Rfree = 0.000) for 5208 atoms. Found 13 (46 requested) and removed 23 (23 requested) atoms. Cycle 44: After refmac, R = 0.1926 (Rfree = 0.000) for 5196 atoms. Found 14 (46 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.1914 (Rfree = 0.000) for 5182 atoms. Found 20 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 5320 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5337 seeds are put forward Round 1: 336 peptides, 66 chains. Longest chain 13 peptides. Score 0.325 Round 2: 347 peptides, 54 chains. Longest chain 19 peptides. Score 0.447 Round 3: 346 peptides, 54 chains. Longest chain 13 peptides. Score 0.445 Round 4: 341 peptides, 52 chains. Longest chain 17 peptides. Score 0.452 Round 5: 331 peptides, 51 chains. Longest chain 22 peptides. Score 0.441 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 289, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 4 % 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 11831 restraints for refining 5214 atoms. 10668 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2042 (Rfree = 0.000) for 5214 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.1966 (Rfree = 0.000) for 5180 atoms. Found 0 (46 requested) and removed 17 (23 requested) atoms. Cycle 48: After refmac, R = 0.1889 (Rfree = 0.000) for 5154 atoms. Found 0 (46 requested) and removed 11 (23 requested) atoms. Cycle 49: After refmac, R = 0.1860 (Rfree = 0.000) for 5136 atoms. Found 0 (46 requested) and removed 8 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:48:51 GMT 2018 Job finished. TimeTaking 63.29 Used memory is bytes: 22588440