Sun 23 Dec 22:23:05 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fna-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-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 22:23:15 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fna-3.6-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 525 and 0 Target number of residues in the AU: 525 Target solvent content: 0.6593 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.80 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 3.600 Wilson plot Bfac: 84.33 9441 reflections ( 98.49 % complete ) and 0 restraints for refining 6311 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3319 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2873 (Rfree = 0.000) for 6311 atoms. Found 40 (40 requested) and removed 65 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 6475 seeds are put forward NCS extension: 0 residues added, 6475 seeds are put forward Round 1: 314 peptides, 57 chains. Longest chain 12 peptides. Score 0.358 Round 2: 375 peptides, 53 chains. Longest chain 18 peptides. Score 0.504 Round 3: 376 peptides, 53 chains. Longest chain 18 peptides. Score 0.505 Round 4: 389 peptides, 52 chains. Longest chain 20 peptides. Score 0.534 Round 5: 406 peptides, 54 chains. Longest chain 21 peptides. Score 0.547 Taking the results from Round 5 Chains 54, Residues 352, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11704 restraints for refining 5172 atoms. 10299 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2178 (Rfree = 0.000) for 5172 atoms. Found 22 (33 requested) and removed 29 (16 requested) atoms. Cycle 2: After refmac, R = 0.2023 (Rfree = 0.000) for 5136 atoms. Found 6 (33 requested) and removed 19 (16 requested) atoms. Cycle 3: After refmac, R = 0.1976 (Rfree = 0.000) for 5107 atoms. Found 5 (32 requested) and removed 19 (16 requested) atoms. Cycle 4: After refmac, R = 0.1955 (Rfree = 0.000) for 5090 atoms. Found 5 (32 requested) and removed 16 (16 requested) atoms. Cycle 5: After refmac, R = 0.1932 (Rfree = 0.000) for 5075 atoms. Found 1 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 5256 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 5278 seeds are put forward Round 1: 341 peptides, 62 chains. Longest chain 13 peptides. Score 0.369 Round 2: 374 peptides, 54 chains. Longest chain 16 peptides. Score 0.494 Round 3: 382 peptides, 52 chains. Longest chain 20 peptides. Score 0.523 Round 4: 382 peptides, 50 chains. Longest chain 22 peptides. Score 0.538 Round 5: 381 peptides, 52 chains. Longest chain 21 peptides. Score 0.521 Taking the results from Round 4 Chains 51, Residues 332, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11691 restraints for refining 5176 atoms. 10354 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2332 (Rfree = 0.000) for 5176 atoms. Found 30 (33 requested) and removed 26 (16 requested) atoms. Cycle 7: After refmac, R = 0.2130 (Rfree = 0.000) for 5156 atoms. Found 9 (33 requested) and removed 22 (16 requested) atoms. Cycle 8: After refmac, R = 0.2060 (Rfree = 0.000) for 5125 atoms. Found 13 (32 requested) and removed 21 (16 requested) atoms. Cycle 9: After refmac, R = 0.1909 (Rfree = 0.000) for 5106 atoms. Found 7 (32 requested) and removed 21 (16 requested) atoms. Cycle 10: After refmac, R = 0.1953 (Rfree = 0.000) for 5079 atoms. Found 5 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 5279 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5298 seeds are put forward Round 1: 323 peptides, 59 chains. Longest chain 14 peptides. Score 0.359 Round 2: 367 peptides, 55 chains. Longest chain 17 peptides. Score 0.475 Round 3: 376 peptides, 57 chains. Longest chain 15 peptides. Score 0.475 Round 4: 376 peptides, 58 chains. Longest chain 18 peptides. Score 0.467 Round 5: 384 peptides, 52 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 5 Chains 52, Residues 332, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11771 restraints for refining 5177 atoms. 10495 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2112 (Rfree = 0.000) for 5177 atoms. Found 20 (33 requested) and removed 22 (16 requested) atoms. Cycle 12: After refmac, R = 0.1954 (Rfree = 0.000) for 5150 atoms. Found 11 (33 requested) and removed 22 (16 requested) atoms. Cycle 13: After refmac, R = 0.1891 (Rfree = 0.000) for 5126 atoms. Found 7 (32 requested) and removed 20 (16 requested) atoms. Cycle 14: After refmac, R = 0.1847 (Rfree = 0.000) for 5105 atoms. Found 12 (32 requested) and removed 17 (16 requested) atoms. Cycle 15: After refmac, R = 0.1837 (Rfree = 0.000) for 5090 atoms. Found 7 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 5283 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 5311 seeds are put forward Round 1: 327 peptides, 55 chains. Longest chain 19 peptides. Score 0.401 Round 2: 341 peptides, 49 chains. Longest chain 20 peptides. Score 0.476 Round 3: 352 peptides, 49 chains. Longest chain 17 peptides. Score 0.495 Round 4: 356 peptides, 46 chains. Longest chain 19 peptides. Score 0.525 Round 5: 357 peptides, 46 chains. Longest chain 19 peptides. Score 0.526 Taking the results from Round 5 Chains 46, Residues 311, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11791 restraints for refining 5177 atoms. 10593 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1993 (Rfree = 0.000) for 5177 atoms. Found 20 (33 requested) and removed 23 (16 requested) atoms. Cycle 17: After refmac, R = 0.1785 (Rfree = 0.000) for 5145 atoms. Found 14 (33 requested) and removed 22 (16 requested) atoms. Cycle 18: After refmac, R = 0.1707 (Rfree = 0.000) for 5126 atoms. Found 9 (32 requested) and removed 18 (16 requested) atoms. Cycle 19: After refmac, R = 0.1677 (Rfree = 0.000) for 5111 atoms. Found 9 (32 requested) and removed 20 (16 requested) atoms. Cycle 20: After refmac, R = 0.1649 (Rfree = 0.000) for 5096 atoms. Found 14 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 5268 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5285 seeds are put forward Round 1: 303 peptides, 57 chains. Longest chain 12 peptides. Score 0.335 Round 2: 342 peptides, 55 chains. Longest chain 18 peptides. Score 0.429 Round 3: 342 peptides, 58 chains. Longest chain 18 peptides. Score 0.404 Round 4: 341 peptides, 54 chains. Longest chain 20 peptides. Score 0.435 Round 5: 348 peptides, 51 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 5 Chains 51, Residues 297, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 12021 restraints for refining 5176 atoms. 10884 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1961 (Rfree = 0.000) for 5176 atoms. Found 16 (33 requested) and removed 18 (16 requested) atoms. Cycle 22: After refmac, R = 0.1875 (Rfree = 0.000) for 5158 atoms. Found 20 (33 requested) and removed 21 (16 requested) atoms. Cycle 23: After refmac, R = 0.1737 (Rfree = 0.000) for 5147 atoms. Found 16 (33 requested) and removed 18 (16 requested) atoms. Cycle 24: After refmac, R = 0.1695 (Rfree = 0.000) for 5141 atoms. Found 16 (33 requested) and removed 17 (16 requested) atoms. Cycle 25: After refmac, R = 0.1576 (Rfree = 0.000) for 5138 atoms. Found 10 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.37 Failed to save intermediate PDB Search for helices and strands: 0 residues in 0 chains, 5338 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5353 seeds are put forward Round 1: 261 peptides, 49 chains. Longest chain 12 peptides. Score 0.319 Round 2: 306 peptides, 49 chains. Longest chain 18 peptides. Score 0.411 Round 3: 322 peptides, 49 chains. Longest chain 20 peptides. Score 0.441 Round 4: 317 peptides, 48 chains. Longest chain 23 peptides. Score 0.440 Round 5: 323 peptides, 50 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 3 Chains 49, Residues 273, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 12063 restraints for refining 5178 atoms. 11020 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1935 (Rfree = 0.000) for 5178 atoms. Found 21 (33 requested) and removed 18 (16 requested) atoms. Cycle 27: After refmac, R = 0.1781 (Rfree = 0.000) for 5166 atoms. Found 14 (33 requested) and removed 18 (16 requested) atoms. Cycle 28: After refmac, R = 0.1761 (Rfree = 0.000) for 5153 atoms. Found 15 (33 requested) and removed 19 (16 requested) atoms. Cycle 29: After refmac, R = 0.1673 (Rfree = 0.000) for 5143 atoms. Found 14 (33 requested) and removed 22 (16 requested) atoms. Cycle 30: After refmac, R = 0.1694 (Rfree = 0.000) for 5133 atoms. Found 23 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 5311 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 5349 seeds are put forward Round 1: 287 peptides, 57 chains. Longest chain 10 peptides. Score 0.302 Round 2: 318 peptides, 54 chains. Longest chain 14 peptides. Score 0.391 Round 3: 327 peptides, 53 chains. Longest chain 16 peptides. Score 0.417 Round 4: 347 peptides, 54 chains. Longest chain 13 peptides. Score 0.447 Round 5: 349 peptides, 50 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 5 Chains 50, Residues 299, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11776 restraints for refining 5178 atoms. 10565 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1855 (Rfree = 0.000) for 5178 atoms. Found 8 (33 requested) and removed 20 (16 requested) atoms. Cycle 32: After refmac, R = 0.1653 (Rfree = 0.000) for 5145 atoms. Found 7 (33 requested) and removed 18 (16 requested) atoms. Cycle 33: After refmac, R = 0.1614 (Rfree = 0.000) for 5126 atoms. Found 10 (32 requested) and removed 17 (16 requested) atoms. Cycle 34: After refmac, R = 0.1538 (Rfree = 0.000) for 5113 atoms. Found 10 (32 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.1518 (Rfree = 0.000) for 5102 atoms. Found 9 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 5265 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5291 seeds are put forward Round 1: 269 peptides, 53 chains. Longest chain 12 peptides. Score 0.299 Round 2: 319 peptides, 50 chains. Longest chain 17 peptides. Score 0.427 Round 3: 328 peptides, 53 chains. Longest chain 17 peptides. Score 0.419 Round 4: 339 peptides, 51 chains. Longest chain 18 peptides. Score 0.456 Round 5: 333 peptides, 51 chains. Longest chain 17 peptides. Score 0.445 Taking the results from Round 4 Chains 53, Residues 288, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 11730 restraints for refining 5178 atoms. 10531 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1957 (Rfree = 0.000) for 5178 atoms. Found 20 (33 requested) and removed 21 (16 requested) atoms. Cycle 37: After refmac, R = 0.1789 (Rfree = 0.000) for 5167 atoms. Found 8 (33 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.1785 (Rfree = 0.000) for 5144 atoms. Found 11 (33 requested) and removed 20 (16 requested) atoms. Cycle 39: After refmac, R = 0.1742 (Rfree = 0.000) for 5131 atoms. Found 14 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.1770 (Rfree = 0.000) for 5121 atoms. Found 16 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 5296 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 5329 seeds are put forward Round 1: 266 peptides, 52 chains. Longest chain 11 peptides. Score 0.302 Round 2: 313 peptides, 55 chains. Longest chain 19 peptides. Score 0.373 Round 3: 314 peptides, 50 chains. Longest chain 19 peptides. Score 0.418 Round 4: 309 peptides, 51 chains. Longest chain 16 peptides. Score 0.399 Round 5: 302 peptides, 49 chains. Longest chain 21 peptides. Score 0.403 Taking the results from Round 3 Chains 50, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9441 reflections ( 98.49 % complete ) and 12121 restraints for refining 5178 atoms. 11115 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1865 (Rfree = 0.000) for 5178 atoms. Found 20 (33 requested) and removed 16 (16 requested) atoms. Cycle 42: After refmac, R = 0.1794 (Rfree = 0.000) for 5170 atoms. Found 11 (33 requested) and removed 16 (16 requested) atoms. Cycle 43: After refmac, R = 0.1735 (Rfree = 0.000) for 5157 atoms. Found 11 (33 requested) and removed 20 (16 requested) atoms. Cycle 44: After refmac, R = 0.1698 (Rfree = 0.000) for 5147 atoms. Found 11 (33 requested) and removed 18 (16 requested) atoms. Cycle 45: After refmac, R = 0.1681 (Rfree = 0.000) for 5136 atoms. Found 16 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 5320 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5340 seeds are put forward Round 1: 239 peptides, 50 chains. Longest chain 13 peptides. Score 0.261 Round 2: 270 peptides, 51 chains. Longest chain 12 peptides. Score 0.320 Round 3: 291 peptides, 48 chains. Longest chain 17 peptides. Score 0.390 Round 4: 285 peptides, 49 chains. Longest chain 14 peptides. Score 0.369 Round 5: 297 peptides, 53 chains. Longest chain 13 peptides. Score 0.358 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 243, 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. 9441 reflections ( 98.49 % complete ) and 12252 restraints for refining 5178 atoms. 11328 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1726 (Rfree = 0.000) for 5178 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1696 (Rfree = 0.000) for 5150 atoms. Found 0 (33 requested) and removed 15 (16 requested) atoms. Cycle 48: After refmac, R = 0.1717 (Rfree = 0.000) for 5132 atoms. Found 0 (32 requested) and removed 12 (16 requested) atoms. Cycle 49: After refmac, R = 0.1756 (Rfree = 0.000) for 5115 atoms. Found 0 (32 requested) and removed 10 (16 requested) atoms. Writing output files ... TimeTaking 70.75