Sun 23 Dec 22:22:46 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 2afb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2afb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2afb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-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/2afb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-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 22:22:56 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/2afb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-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 464 and 0 Target number of residues in the AU: 464 Target solvent content: 0.6576 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-4.0-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 4.000 Wilson plot Bfac: 83.06 Failed to save intermediate PDB 6408 reflections ( 99.24 % complete ) and 0 restraints for refining 6260 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3341 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 6260 atoms. Found 29 (29 requested) and removed 58 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 6352 seeds are put forward NCS extension: 0 residues added, 6352 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 10 peptides. Score 0.306 Round 2: 283 peptides, 49 chains. Longest chain 11 peptides. Score 0.384 Round 3: 307 peptides, 47 chains. Longest chain 17 peptides. Score 0.455 Round 4: 334 peptides, 54 chains. Longest chain 14 peptides. Score 0.447 Round 5: 357 peptides, 51 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 54, Residues 306, Estimated correctness of the model 0.0 % 9 chains (74 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11268 restraints for refining 5070 atoms. 9864 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2482 (Rfree = 0.000) for 5070 atoms. Found 23 (24 requested) and removed 37 (12 requested) atoms. Cycle 2: After refmac, R = 0.2369 (Rfree = 0.000) for 4932 atoms. Found 15 (24 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2292 (Rfree = 0.000) for 4875 atoms. Found 8 (23 requested) and removed 20 (11 requested) atoms. Cycle 4: After refmac, R = 0.2161 (Rfree = 0.000) for 4835 atoms. Found 6 (23 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2121 (Rfree = 0.000) for 4810 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 4984 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5002 seeds are put forward Round 1: 278 peptides, 51 chains. Longest chain 14 peptides. Score 0.353 Round 2: 328 peptides, 52 chains. Longest chain 22 peptides. Score 0.453 Round 3: 316 peptides, 47 chains. Longest chain 18 peptides. Score 0.473 Round 4: 321 peptides, 47 chains. Longest chain 18 peptides. Score 0.483 Round 5: 322 peptides, 47 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 5 Chains 51, Residues 275, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11152 restraints for refining 4892 atoms. 9966 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2332 (Rfree = 0.000) for 4892 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 7: After refmac, R = 0.2080 (Rfree = 0.000) for 4841 atoms. Found 14 (23 requested) and removed 25 (11 requested) atoms. Cycle 8: After refmac, R = 0.1993 (Rfree = 0.000) for 4813 atoms. Found 4 (22 requested) and removed 19 (11 requested) atoms. Cycle 9: After refmac, R = 0.1929 (Rfree = 0.000) for 4792 atoms. Found 4 (22 requested) and removed 19 (11 requested) atoms. Cycle 10: After refmac, R = 0.1912 (Rfree = 0.000) for 4775 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 4933 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4954 seeds are put forward Round 1: 277 peptides, 49 chains. Longest chain 14 peptides. Score 0.371 Round 2: 316 peptides, 48 chains. Longest chain 22 peptides. Score 0.464 Round 3: 338 peptides, 55 chains. Longest chain 15 peptides. Score 0.447 Round 4: 328 peptides, 51 chains. Longest chain 15 peptides. Score 0.462 Round 5: 336 peptides, 48 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 5 Chains 49, Residues 288, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12014 restraints for refining 5071 atoms. 10853 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2187 (Rfree = 0.000) for 5071 atoms. Found 17 (24 requested) and removed 35 (12 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 5019 atoms. Found 10 (23 requested) and removed 14 (11 requested) atoms. Cycle 13: After refmac, R = 0.2148 (Rfree = 0.000) for 5007 atoms. Found 3 (23 requested) and removed 17 (11 requested) atoms. Cycle 14: After refmac, R = 0.2133 (Rfree = 0.000) for 4985 atoms. Found 7 (23 requested) and removed 16 (11 requested) atoms. Cycle 15: After refmac, R = 0.2111 (Rfree = 0.000) for 4975 atoms. Found 0 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5160 seeds are put forward Round 1: 291 peptides, 54 chains. Longest chain 11 peptides. Score 0.354 Round 2: 319 peptides, 49 chains. Longest chain 14 peptides. Score 0.461 Round 3: 323 peptides, 47 chains. Longest chain 19 peptides. Score 0.487 Round 4: 332 peptides, 49 chains. Longest chain 16 peptides. Score 0.488 Round 5: 340 peptides, 45 chains. Longest chain 21 peptides. Score 0.537 Taking the results from Round 5 Chains 47, Residues 295, Estimated correctness of the model 0.0 % 6 chains (46 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11464 restraints for refining 5072 atoms. 10161 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2213 (Rfree = 0.000) for 5072 atoms. Found 19 (24 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.2051 (Rfree = 0.000) for 5030 atoms. Found 10 (24 requested) and removed 18 (12 requested) atoms. Cycle 18: After refmac, R = 0.2003 (Rfree = 0.000) for 5001 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1979 (Rfree = 0.000) for 4984 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1917 (Rfree = 0.000) for 4968 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 5136 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 5173 seeds are put forward Round 1: 271 peptides, 53 chains. Longest chain 9 peptides. Score 0.317 Round 2: 305 peptides, 52 chains. Longest chain 17 peptides. Score 0.404 Round 3: 322 peptides, 51 chains. Longest chain 12 peptides. Score 0.450 Round 4: 331 peptides, 49 chains. Longest chain 25 peptides. Score 0.486 Round 5: 301 peptides, 51 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 4 Chains 50, Residues 282, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11864 restraints for refining 5072 atoms. 10693 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2199 (Rfree = 0.000) for 5072 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 22: After refmac, R = 0.2076 (Rfree = 0.000) for 5049 atoms. Found 9 (24 requested) and removed 15 (12 requested) atoms. Cycle 23: After refmac, R = 0.2042 (Rfree = 0.000) for 5037 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.2023 (Rfree = 0.000) for 5023 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.2000 (Rfree = 0.000) for 5013 atoms. Found 0 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 5186 seeds are put forward NCS extension: 47 residues added (4 deleted due to clashes), 5233 seeds are put forward Round 1: 250 peptides, 50 chains. Longest chain 8 peptides. Score 0.297 Round 2: 308 peptides, 53 chains. Longest chain 11 peptides. Score 0.401 Round 3: 311 peptides, 52 chains. Longest chain 12 peptides. Score 0.417 Round 4: 298 peptides, 46 chains. Longest chain 17 peptides. Score 0.445 Round 5: 309 peptides, 47 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 5 Chains 47, Residues 262, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12152 restraints for refining 5072 atoms. 11096 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2122 (Rfree = 0.000) for 5072 atoms. Found 15 (24 requested) and removed 16 (12 requested) atoms. Cycle 27: After refmac, R = 0.1996 (Rfree = 0.000) for 5047 atoms. Found 9 (24 requested) and removed 15 (12 requested) atoms. Cycle 28: After refmac, R = 0.1935 (Rfree = 0.000) for 5034 atoms. Found 2 (23 requested) and removed 17 (11 requested) atoms. Cycle 29: After refmac, R = 0.1903 (Rfree = 0.000) for 5017 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.1887 (Rfree = 0.000) for 5009 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5160 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5177 seeds are put forward Round 1: 238 peptides, 48 chains. Longest chain 11 peptides. Score 0.288 Round 2: 279 peptides, 47 chains. Longest chain 20 peptides. Score 0.395 Round 3: 305 peptides, 52 chains. Longest chain 12 peptides. Score 0.404 Round 4: 312 peptides, 47 chains. Longest chain 25 peptides. Score 0.465 Round 5: 295 peptides, 46 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 4 Chains 47, Residues 265, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12212 restraints for refining 5071 atoms. 11157 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2023 (Rfree = 0.000) for 5071 atoms. Found 16 (24 requested) and removed 16 (12 requested) atoms. Cycle 32: After refmac, R = 0.1878 (Rfree = 0.000) for 5052 atoms. Found 6 (24 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.1837 (Rfree = 0.000) for 5036 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1834 (Rfree = 0.000) for 5023 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1815 (Rfree = 0.000) for 5009 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 5178 seeds are put forward Round 1: 217 peptides, 47 chains. Longest chain 8 peptides. Score 0.245 Round 2: 246 peptides, 45 chains. Longest chain 10 peptides. Score 0.339 Round 3: 253 peptides, 44 chains. Longest chain 11 peptides. Score 0.365 Round 4: 247 peptides, 38 chains. Longest chain 11 peptides. Score 0.412 Round 5: 256 peptides, 42 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 4 Chains 39, Residues 209, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12565 restraints for refining 5072 atoms. 11734 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1902 (Rfree = 0.000) for 5072 atoms. Found 15 (24 requested) and removed 24 (12 requested) atoms. Cycle 37: After refmac, R = 0.1790 (Rfree = 0.000) for 5047 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 5034 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1741 (Rfree = 0.000) for 5026 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1736 (Rfree = 0.000) for 5014 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5176 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5188 seeds are put forward Round 1: 210 peptides, 45 chains. Longest chain 9 peptides. Score 0.249 Round 2: 256 peptides, 46 chains. Longest chain 13 peptides. Score 0.352 Round 3: 251 peptides, 46 chains. Longest chain 14 peptides. Score 0.341 Round 4: 257 peptides, 43 chains. Longest chain 15 peptides. Score 0.385 Round 5: 248 peptides, 43 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 4 Chains 43, Residues 214, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12676 restraints for refining 5072 atoms. 11841 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1954 (Rfree = 0.000) for 5072 atoms. Found 17 (24 requested) and removed 14 (12 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1851 (Rfree = 0.000) for 5064 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1786 (Rfree = 0.000) for 5047 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1768 (Rfree = 0.000) for 5039 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1758 (Rfree = 0.000) for 5031 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5179 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 5203 seeds are put forward Round 1: 206 peptides, 43 chains. Longest chain 8 peptides. Score 0.260 Round 2: 238 peptides, 42 chains. Longest chain 13 peptides. Score 0.351 Round 3: 237 peptides, 44 chains. Longest chain 11 peptides. Score 0.328 Round 4: 241 peptides, 42 chains. Longest chain 12 peptides. Score 0.358 Round 5: 247 peptides, 42 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 205, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2afb-4_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (205 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6408 reflections ( 99.24 % complete ) and 12742 restraints for refining 5071 atoms. 11937 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2032 (Rfree = 0.000) for 5071 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1983 (Rfree = 0.000) for 5048 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2036 (Rfree = 0.000) for 5034 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2053 (Rfree = 0.000) for 5021 atoms. TimeTaking 76.02