Sun 23 Dec 23:52:26 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 2eth-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-4.0-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/2eth-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-4.0-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 ============================================================ Sun 23 Dec 23:52:30 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/2eth-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-4.0-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 227 and 0 Target number of residues in the AU: 227 Target solvent content: 0.6735 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.56 Input MTZ file: 2eth-4.0-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.85 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: 65.143 4.000 Wilson plot Bfac: 94.99 3175 reflections ( 98.08 % complete ) and 0 restraints for refining 2723 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3402 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3371 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.99 3.68 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 0 residues added, 2772 seeds are put forward Round 1: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.300 Round 2: 120 peptides, 17 chains. Longest chain 12 peptides. Score 0.431 Round 3: 122 peptides, 15 chains. Longest chain 19 peptides. Score 0.478 Round 4: 132 peptides, 17 chains. Longest chain 18 peptides. Score 0.481 Round 5: 140 peptides, 19 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 4 Chains 17, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 5409 restraints for refining 2221 atoms. 4966 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2554 (Rfree = 0.000) for 2221 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2607 (Rfree = 0.000) for 2170 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 3: After refmac, R = 0.2422 (Rfree = 0.000) for 2128 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.2389 (Rfree = 0.000) for 2092 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2319 (Rfree = 0.000) for 2064 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.01 3.70 Search for helices and strands: 0 residues in 0 chains, 2160 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2183 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.285 Round 2: 134 peptides, 18 chains. Longest chain 18 peptides. Score 0.471 Round 3: 127 peptides, 15 chains. Longest chain 18 peptides. Score 0.498 Round 4: 129 peptides, 14 chains. Longest chain 18 peptides. Score 0.524 Round 5: 132 peptides, 16 chains. Longest chain 16 peptides. Score 0.499 Taking the results from Round 4 Chains 14, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4608 restraints for refining 2007 atoms. 4162 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 2007 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 7: After refmac, R = 0.2365 (Rfree = 0.000) for 1979 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2315 (Rfree = 0.000) for 1962 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 9: After refmac, R = 0.2344 (Rfree = 0.000) for 1949 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 10: After refmac, R = 0.2188 (Rfree = 0.000) for 1923 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.94 3.64 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2064 seeds are put forward Round 1: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.332 Round 2: 133 peptides, 19 chains. Longest chain 20 peptides. Score 0.448 Round 3: 138 peptides, 20 chains. Longest chain 16 peptides. Score 0.450 Round 4: 142 peptides, 20 chains. Longest chain 16 peptides. Score 0.466 Round 5: 134 peptides, 18 chains. Longest chain 16 peptides. Score 0.471 Taking the results from Round 5 Chains 18, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4558 restraints for refining 2022 atoms. 4112 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2257 (Rfree = 0.000) for 2022 atoms. Found 7 (9 requested) and removed 25 (4 requested) atoms. Cycle 12: After refmac, R = 0.2350 (Rfree = 0.000) for 1973 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2190 (Rfree = 0.000) for 1951 atoms. Found 7 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2313 (Rfree = 0.000) for 1940 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2042 (Rfree = 0.000) for 1932 atoms. Found 2 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.99 3.68 Search for helices and strands: 0 residues in 0 chains, 2042 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2063 seeds are put forward Round 1: 120 peptides, 23 chains. Longest chain 12 peptides. Score 0.311 Round 2: 134 peptides, 20 chains. Longest chain 13 peptides. Score 0.433 Round 3: 144 peptides, 24 chains. Longest chain 11 peptides. Score 0.401 Round 4: 143 peptides, 22 chains. Longest chain 13 peptides. Score 0.434 Round 5: 139 peptides, 23 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 4 Chains 22, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4783 restraints for refining 2119 atoms. 4321 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2319 (Rfree = 0.000) for 2119 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 17: After refmac, R = 0.2138 (Rfree = 0.000) for 2086 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 18: After refmac, R = 0.2182 (Rfree = 0.000) for 2068 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.2398 (Rfree = 0.000) for 2062 atoms. Found 6 (9 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.2075 (Rfree = 0.000) for 2040 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.97 3.66 Search for helices and strands: 0 residues in 0 chains, 2141 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2160 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 8 peptides. Score 0.266 Round 2: 135 peptides, 23 chains. Longest chain 12 peptides. Score 0.380 Round 3: 127 peptides, 20 chains. Longest chain 11 peptides. Score 0.403 Round 4: 134 peptides, 22 chains. Longest chain 13 peptides. Score 0.395 Round 5: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 3 Chains 20, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4871 restraints for refining 2118 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2160 (Rfree = 0.000) for 2118 atoms. Found 6 (10 requested) and removed 21 (5 requested) atoms. Cycle 22: After refmac, R = 0.2268 (Rfree = 0.000) for 2089 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 23: After refmac, R = 0.2295 (Rfree = 0.000) for 2072 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 24: After refmac, R = 0.2219 (Rfree = 0.000) for 2043 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2250 (Rfree = 0.000) for 2032 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.99 3.68 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward NCS extension: 0 residues added, 2126 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 11 peptides. Score 0.268 Round 2: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.352 Round 3: 124 peptides, 20 chains. Longest chain 11 peptides. Score 0.390 Round 4: 126 peptides, 19 chains. Longest chain 13 peptides. Score 0.418 Round 5: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.381 Taking the results from Round 4 Chains 19, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4856 restraints for refining 2137 atoms. 4447 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2542 (Rfree = 0.000) for 2137 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 27: After refmac, R = 0.2383 (Rfree = 0.000) for 2108 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.2295 (Rfree = 0.000) for 2098 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2323 (Rfree = 0.000) for 2087 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 30: After refmac, R = 0.2228 (Rfree = 0.000) for 2080 atoms. Found 7 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.99 3.68 Search for helices and strands: 0 residues in 0 chains, 2187 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2201 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 9 peptides. Score 0.240 Round 2: 137 peptides, 21 chains. Longest chain 13 peptides. Score 0.427 Round 3: 135 peptides, 21 chains. Longest chain 13 peptides. Score 0.419 Round 4: 121 peptides, 19 chains. Longest chain 14 peptides. Score 0.396 Round 5: 128 peptides, 20 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 2 Chains 21, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4942 restraints for refining 2146 atoms. 4499 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2415 (Rfree = 0.000) for 2146 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 32: After refmac, R = 0.2390 (Rfree = 0.000) for 2126 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 33: After refmac, R = 0.2105 (Rfree = 0.000) for 2111 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 34: After refmac, R = 0.2141 (Rfree = 0.000) for 2102 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.2216 (Rfree = 0.000) for 2098 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.92 3.62 Search for helices and strands: 0 residues in 0 chains, 2181 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2184 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 10 peptides. Score 0.282 Round 2: 104 peptides, 18 chains. Longest chain 13 peptides. Score 0.338 Round 3: 122 peptides, 19 chains. Longest chain 16 peptides. Score 0.401 Round 4: 118 peptides, 19 chains. Longest chain 16 peptides. Score 0.383 Round 5: 122 peptides, 17 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 5 Chains 17, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4899 restraints for refining 2131 atoms. 4496 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2320 (Rfree = 0.000) for 2131 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2279 (Rfree = 0.000) for 2122 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.2226 (Rfree = 0.000) for 2112 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.2271 (Rfree = 0.000) for 2098 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2268 (Rfree = 0.000) for 2092 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.92 3.62 Search for helices and strands: 0 residues in 0 chains, 2203 seeds are put forward NCS extension: 0 residues added, 2203 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 7 peptides. Score 0.222 Round 2: 113 peptides, 21 chains. Longest chain 9 peptides. Score 0.319 Round 3: 116 peptides, 19 chains. Longest chain 11 peptides. Score 0.374 Round 4: 108 peptides, 16 chains. Longest chain 10 peptides. Score 0.399 Round 5: 111 peptides, 16 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 16, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3175 reflections ( 98.08 % complete ) and 4963 restraints for refining 2143 atoms. 4599 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2493 (Rfree = 0.000) for 2143 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2544 (Rfree = 0.000) for 2122 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 43: After refmac, R = 0.2147 (Rfree = 0.000) for 2106 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.2102 (Rfree = 0.000) for 2088 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2487 (Rfree = 0.000) for 2077 atoms. Found 7 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 3.56 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 2186 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 9 peptides. Score 0.259 Round 2: 103 peptides, 18 chains. Longest chain 14 peptides. Score 0.334 Round 3: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.365 Round 4: 115 peptides, 18 chains. Longest chain 14 peptides. Score 0.390 Round 5: 122 peptides, 19 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 103, 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 2eth-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3175 reflections ( 98.08 % complete ) and 4433 restraints for refining 2030 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2345 (Rfree = 0.000) for 2030 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2331 (Rfree = 0.000) for 2014 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2283 (Rfree = 0.000) for 1998 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2517 (Rfree = 0.000) for 1989 atoms. TimeTaking 30.5