Mon 24 Dec 07:30:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2afb-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2afb-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2afb-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-parrot-noncs ############### 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 07:30:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-4.0-parrot-noncs/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-noncs.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-noncs.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 6408 reflections ( 99.24 % complete ) and 0 restraints for refining 6231 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3357 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3269 (Rfree = 0.000) for 6231 atoms. Found 29 (29 requested) and removed 39 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 6343 seeds are put forward NCS extension: 0 residues added, 6343 seeds are put forward Round 1: 218 peptides, 42 chains. Longest chain 11 peptides. Score 0.302 Round 2: 266 peptides, 45 chains. Longest chain 12 peptides. Score 0.385 Round 3: 302 peptides, 49 chains. Longest chain 17 peptides. Score 0.426 Round 4: 315 peptides, 45 chains. Longest chain 15 peptides. Score 0.489 Round 5: 326 peptides, 50 chains. Longest chain 21 peptides. Score 0.467 Taking the results from Round 4 Chains 47, Residues 270, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12147 restraints for refining 5072 atoms. 11026 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2488 (Rfree = 0.000) for 5072 atoms. Found 14 (24 requested) and removed 32 (12 requested) atoms. Cycle 2: After refmac, R = 0.2302 (Rfree = 0.000) for 4964 atoms. Found 10 (24 requested) and removed 27 (12 requested) atoms. Cycle 3: After refmac, R = 0.2161 (Rfree = 0.000) for 4923 atoms. Found 6 (23 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2101 (Rfree = 0.000) for 4897 atoms. Found 5 (23 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2041 (Rfree = 0.000) for 4881 atoms. Found 2 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5038 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5054 seeds are put forward Round 1: 305 peptides, 54 chains. Longest chain 12 peptides. Score 0.385 Round 2: 341 peptides, 46 chains. Longest chain 19 peptides. Score 0.530 Round 3: 348 peptides, 45 chains. Longest chain 19 peptides. Score 0.551 Round 4: 342 peptides, 44 chains. Longest chain 22 peptides. Score 0.549 Round 5: 343 peptides, 49 chains. Longest chain 14 peptides. Score 0.509 Taking the results from Round 3 Chains 46, Residues 303, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11572 restraints for refining 4997 atoms. 10327 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2247 (Rfree = 0.000) for 4997 atoms. Found 13 (23 requested) and removed 31 (11 requested) atoms. Cycle 7: After refmac, R = 0.2101 (Rfree = 0.000) for 4947 atoms. Found 5 (23 requested) and removed 24 (11 requested) atoms. Cycle 8: After refmac, R = 0.2057 (Rfree = 0.000) for 4914 atoms. Found 4 (23 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.2005 (Rfree = 0.000) for 4900 atoms. Found 1 (23 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2007 (Rfree = 0.000) for 4880 atoms. Found 1 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.84 Search for helices and strands: 0 residues in 0 chains, 5022 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5037 seeds are put forward Round 1: 302 peptides, 52 chains. Longest chain 16 peptides. Score 0.398 Round 2: 333 peptides, 49 chains. Longest chain 13 peptides. Score 0.490 Round 3: 333 peptides, 43 chains. Longest chain 20 peptides. Score 0.541 Round 4: 326 peptides, 41 chains. Longest chain 25 peptides. Score 0.544 Round 5: 324 peptides, 43 chains. Longest chain 24 peptides. Score 0.524 Taking the results from Round 4 Chains 45, Residues 285, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11911 restraints for refining 5072 atoms. 10711 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2186 (Rfree = 0.000) for 5072 atoms. Found 13 (24 requested) and removed 47 (12 requested) atoms. Cycle 12: After refmac, R = 0.2051 (Rfree = 0.000) for 5017 atoms. Found 3 (23 requested) and removed 16 (11 requested) atoms. Cycle 13: After refmac, R = 0.1993 (Rfree = 0.000) for 4998 atoms. Found 0 (23 requested) and removed 15 (11 requested) atoms. Cycle 14: After refmac, R = 0.1965 (Rfree = 0.000) for 4978 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.1937 (Rfree = 0.000) for 4966 atoms. Found 0 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 5118 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5136 seeds are put forward Round 1: 284 peptides, 51 chains. Longest chain 12 peptides. Score 0.367 Round 2: 334 peptides, 47 chains. Longest chain 15 peptides. Score 0.509 Round 3: 341 peptides, 51 chains. Longest chain 17 peptides. Score 0.488 Round 4: 333 peptides, 48 chains. Longest chain 16 peptides. Score 0.498 Round 5: 340 peptides, 48 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 5 Chains 48, Residues 292, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12026 restraints for refining 5071 atoms. 10859 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2165 (Rfree = 0.000) for 5071 atoms. Found 7 (24 requested) and removed 30 (12 requested) atoms. Cycle 17: After refmac, R = 0.2023 (Rfree = 0.000) for 5028 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 18: After refmac, R = 0.1978 (Rfree = 0.000) for 5012 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. Cycle 19: After refmac, R = 0.1968 (Rfree = 0.000) for 4995 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1944 (Rfree = 0.000) for 4979 atoms. Found 1 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5158 seeds are put forward Round 1: 309 peptides, 57 chains. Longest chain 13 peptides. Score 0.366 Round 2: 330 peptides, 55 chains. Longest chain 12 peptides. Score 0.430 Round 3: 362 peptides, 57 chains. Longest chain 13 peptides. Score 0.478 Round 4: 365 peptides, 55 chains. Longest chain 26 peptides. Score 0.500 Round 5: 358 peptides, 53 chains. Longest chain 15 peptides. Score 0.504 Taking the results from Round 5 Chains 53, Residues 305, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 11856 restraints for refining 5070 atoms. 10622 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2121 (Rfree = 0.000) for 5070 atoms. Found 7 (24 requested) and removed 25 (12 requested) atoms. Cycle 22: After refmac, R = 0.1910 (Rfree = 0.000) for 5026 atoms. Found 8 (23 requested) and removed 21 (11 requested) atoms. Cycle 23: After refmac, R = 0.1909 (Rfree = 0.000) for 4997 atoms. Found 5 (23 requested) and removed 18 (11 requested) atoms. Cycle 24: After refmac, R = 0.1765 (Rfree = 0.000) for 4980 atoms. Found 6 (23 requested) and removed 16 (11 requested) atoms. Cycle 25: After refmac, R = 0.1757 (Rfree = 0.000) for 4964 atoms. Found 0 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 5128 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5146 seeds are put forward Round 1: 242 peptides, 50 chains. Longest chain 10 peptides. Score 0.277 Round 2: 301 peptides, 51 chains. Longest chain 11 peptides. Score 0.405 Round 3: 309 peptides, 48 chains. Longest chain 14 peptides. Score 0.450 Round 4: 306 peptides, 50 chains. Longest chain 13 peptides. Score 0.425 Round 5: 309 peptides, 47 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 5 Chains 50, Residues 262, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12110 restraints for refining 5072 atoms. 11020 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2084 (Rfree = 0.000) for 5072 atoms. Found 8 (24 requested) and removed 23 (12 requested) atoms. Cycle 27: After refmac, R = 0.1924 (Rfree = 0.000) for 5024 atoms. Found 12 (24 requested) and removed 18 (12 requested) atoms. Cycle 28: After refmac, R = 0.1886 (Rfree = 0.000) for 5000 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.1874 (Rfree = 0.000) for 4995 atoms. Found 1 (23 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.1729 (Rfree = 0.000) for 4967 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 5095 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5111 seeds are put forward Round 1: 258 peptides, 52 chains. Longest chain 11 peptides. Score 0.296 Round 2: 313 peptides, 56 chains. Longest chain 13 peptides. Score 0.384 Round 3: 307 peptides, 50 chains. Longest chain 12 peptides. Score 0.427 Round 4: 304 peptides, 46 chains. Longest chain 14 peptides. Score 0.458 Round 5: 308 peptides, 49 chains. Longest chain 16 peptides. Score 0.439 Taking the results from Round 4 Chains 47, Residues 258, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12148 restraints for refining 5070 atoms. 11116 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2170 (Rfree = 0.000) for 5070 atoms. Found 14 (24 requested) and removed 29 (12 requested) atoms. Cycle 32: After refmac, R = 0.2207 (Rfree = 0.000) for 5025 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 33: After refmac, R = 0.2119 (Rfree = 0.000) for 4998 atoms. Found 20 (23 requested) and removed 25 (11 requested) atoms. Cycle 34: After refmac, R = 0.2247 (Rfree = 0.000) for 4967 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 35: After refmac, R = 0.2002 (Rfree = 0.000) for 4938 atoms. Found 16 (23 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 5159 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5178 seeds are put forward Round 1: 171 peptides, 37 chains. Longest chain 9 peptides. Score 0.234 Round 2: 232 peptides, 44 chains. Longest chain 10 peptides. Score 0.315 Round 3: 248 peptides, 47 chains. Longest chain 13 peptides. Score 0.323 Round 4: 241 peptides, 44 chains. Longest chain 14 peptides. Score 0.337 Round 5: 248 peptides, 44 chains. Longest chain 12 peptides. Score 0.354 Taking the results from Round 5 Chains 44, Residues 204, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12325 restraints for refining 5017 atoms. 11549 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2131 (Rfree = 0.000) for 5017 atoms. Found 22 (23 requested) and removed 30 (11 requested) atoms. Cycle 37: After refmac, R = 0.1998 (Rfree = 0.000) for 4972 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 38: After refmac, R = 0.2077 (Rfree = 0.000) for 4960 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 39: After refmac, R = 0.1866 (Rfree = 0.000) for 4939 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 40: After refmac, R = 0.1933 (Rfree = 0.000) for 4932 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 5132 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5146 seeds are put forward Round 1: 192 peptides, 44 chains. Longest chain 6 peptides. Score 0.212 Round 2: 223 peptides, 44 chains. Longest chain 7 peptides. Score 0.293 Round 3: 223 peptides, 44 chains. Longest chain 8 peptides. Score 0.293 Round 4: 241 peptides, 45 chains. Longest chain 10 peptides. Score 0.327 Round 5: 252 peptides, 45 chains. Longest chain 12 peptides. Score 0.353 Taking the results from Round 5 Chains 45, Residues 207, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6408 reflections ( 99.24 % complete ) and 12144 restraints for refining 4959 atoms. 11343 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2164 (Rfree = 0.000) for 4959 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 42: After refmac, R = 0.2027 (Rfree = 0.000) for 4926 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 43: After refmac, R = 0.1918 (Rfree = 0.000) for 4906 atoms. Found 22 (23 requested) and removed 22 (11 requested) atoms. Cycle 44: After refmac, R = 0.1420 (Rfree = 0.000) for 4891 atoms. Found 7 (23 requested) and removed 15 (11 requested) atoms. Cycle 45: After refmac, R = 0.1294 (Rfree = 0.000) for 4871 atoms. Found 2 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 5007 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5023 seeds are put forward Round 1: 160 peptides, 36 chains. Longest chain 6 peptides. Score 0.215 Round 2: 208 peptides, 43 chains. Longest chain 8 peptides. Score 0.266 Round 3: 215 peptides, 37 chains. Longest chain 10 peptides. Score 0.348 Round 4: 215 peptides, 38 chains. Longest chain 11 peptides. Score 0.337 Round 5: 204 peptides, 36 chains. Longest chain 10 peptides. Score 0.332 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 178, 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 2afb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6408 reflections ( 99.24 % complete ) and 11985 restraints for refining 4909 atoms. 11310 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1945 (Rfree = 0.000) for 4909 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1777 (Rfree = 0.000) for 4883 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1769 (Rfree = 0.000) for 4863 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1214 (Rfree = 0.000) for 4840 atoms. TimeTaking 60.87