null Tue 25 Dec 19:27:56 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 2eth-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-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/2eth-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-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 ============================================================ Tue 25 Dec 19:28:10 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/2eth-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6563 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-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2464 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: 65.143 3.600 Wilson plot Bfac: 82.21 4336 reflections ( 98.17 % complete ) and 0 restraints for refining 2737 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3339 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 2737 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward NCS extension: 0 residues added, 2787 seeds are put forward Round 1: 122 peptides, 24 chains. Longest chain 8 peptides. Score 0.301 Round 2: 155 peptides, 22 chains. Longest chain 14 peptides. Score 0.482 Round 3: 142 peptides, 22 chains. Longest chain 11 peptides. Score 0.429 Round 4: 159 peptides, 21 chains. Longest chain 16 peptides. Score 0.515 Round 5: 168 peptides, 20 chains. Longest chain 16 peptides. Score 0.564 Taking the results from Round 5 Chains 20, Residues 148, Estimated correctness of the model 0.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5058 restraints for refining 2182 atoms. 4486 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2643 (Rfree = 0.000) for 2182 atoms. Found 5 (14 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2730 (Rfree = 0.000) for 2140 atoms. Found 6 (13 requested) and removed 16 (6 requested) atoms. Cycle 3: After refmac, R = 0.2455 (Rfree = 0.000) for 2124 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2397 (Rfree = 0.000) for 2110 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2344 (Rfree = 0.000) for 2104 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.38 Search for helices and strands: 0 residues in 0 chains, 2208 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2227 seeds are put forward Round 1: 148 peptides, 24 chains. Longest chain 10 peptides. Score 0.418 Round 2: 142 peptides, 18 chains. Longest chain 12 peptides. Score 0.502 Round 3: 148 peptides, 20 chains. Longest chain 18 peptides. Score 0.490 Round 4: 150 peptides, 18 chains. Longest chain 18 peptides. Score 0.532 Round 5: 155 peptides, 21 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 4 Chains 18, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5285 restraints for refining 2209 atoms. 4775 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2428 (Rfree = 0.000) for 2209 atoms. Found 8 (14 requested) and removed 20 (7 requested) atoms. Cycle 7: After refmac, R = 0.2432 (Rfree = 0.000) for 2181 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2367 (Rfree = 0.000) for 2170 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2297 (Rfree = 0.000) for 2165 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2131 (Rfree = 0.000) for 2157 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 2257 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 2282 seeds are put forward Round 1: 131 peptides, 21 chains. Longest chain 10 peptides. Score 0.401 Round 2: 144 peptides, 21 chains. Longest chain 16 peptides. Score 0.456 Round 3: 156 peptides, 21 chains. Longest chain 17 peptides. Score 0.503 Round 4: 151 peptides, 22 chains. Longest chain 17 peptides. Score 0.466 Round 5: 140 peptides, 19 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 3 Chains 21, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5212 restraints for refining 2231 atoms. 4693 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2259 (Rfree = 0.000) for 2231 atoms. Found 5 (14 requested) and removed 14 (7 requested) atoms. Cycle 12: After refmac, R = 0.2367 (Rfree = 0.000) for 2212 atoms. Found 4 (14 requested) and removed 16 (7 requested) atoms. Cycle 13: After refmac, R = 0.2265 (Rfree = 0.000) for 2195 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2020 (Rfree = 0.000) for 2183 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1941 (Rfree = 0.000) for 2172 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 2272 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 2299 seeds are put forward Round 1: 134 peptides, 24 chains. Longest chain 9 peptides. Score 0.356 Round 2: 151 peptides, 22 chains. Longest chain 14 peptides. Score 0.466 Round 3: 144 peptides, 22 chains. Longest chain 12 peptides. Score 0.438 Round 4: 159 peptides, 23 chains. Longest chain 19 peptides. Score 0.480 Round 5: 140 peptides, 22 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 4 Chains 23, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5191 restraints for refining 2233 atoms. 4670 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2315 (Rfree = 0.000) for 2233 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 17: After refmac, R = 0.2132 (Rfree = 0.000) for 2220 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.2051 (Rfree = 0.000) for 2213 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 2205 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1953 (Rfree = 0.000) for 2199 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 2302 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2320 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 8 peptides. Score 0.351 Round 2: 153 peptides, 23 chains. Longest chain 13 peptides. Score 0.456 Round 3: 141 peptides, 21 chains. Longest chain 12 peptides. Score 0.444 Round 4: 148 peptides, 23 chains. Longest chain 12 peptides. Score 0.436 Round 5: 139 peptides, 21 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 2 Chains 23, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5267 restraints for refining 2232 atoms. 4770 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2118 (Rfree = 0.000) for 2232 atoms. Found 9 (14 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.1932 (Rfree = 0.000) for 2221 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1869 (Rfree = 0.000) for 2213 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1844 (Rfree = 0.000) for 2207 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1839 (Rfree = 0.000) for 2200 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 2278 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2286 seeds are put forward Round 1: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.286 Round 2: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.395 Round 3: 142 peptides, 20 chains. Longest chain 14 peptides. Score 0.466 Round 4: 136 peptides, 20 chains. Longest chain 11 peptides. Score 0.442 Round 5: 151 peptides, 23 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 3 Chains 20, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5247 restraints for refining 2232 atoms. 4779 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2074 (Rfree = 0.000) for 2232 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.1962 (Rfree = 0.000) for 2226 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1912 (Rfree = 0.000) for 2217 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1890 (Rfree = 0.000) for 2210 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1874 (Rfree = 0.000) for 2202 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2313 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.314 Round 2: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.353 Round 3: 129 peptides, 24 chains. Longest chain 8 peptides. Score 0.334 Round 4: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.404 Round 5: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 4 Chains 22, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5382 restraints for refining 2232 atoms. 4948 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2125 (Rfree = 0.000) for 2232 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.2158 (Rfree = 0.000) for 2220 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 2208 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2104 (Rfree = 0.000) for 2198 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2423 (Rfree = 0.000) for 2197 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.26 Search for helices and strands: 0 residues in 0 chains, 2313 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2326 seeds are put forward Round 1: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.286 Round 2: 122 peptides, 21 chains. Longest chain 10 peptides. Score 0.361 Round 3: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.324 Round 4: 128 peptides, 22 chains. Longest chain 12 peptides. Score 0.369 Round 5: 127 peptides, 21 chains. Longest chain 10 peptides. Score 0.384 Taking the results from Round 5 Chains 21, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5409 restraints for refining 2233 atoms. 5006 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2148 (Rfree = 0.000) for 2233 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 37: After refmac, R = 0.2243 (Rfree = 0.000) for 2227 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.2178 (Rfree = 0.000) for 2228 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2209 (Rfree = 0.000) for 2222 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.1776 (Rfree = 0.000) for 2222 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.38 Search for helices and strands: 0 residues in 0 chains, 2310 seeds are put forward NCS extension: 0 residues added, 2310 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 7 peptides. Score 0.261 Round 2: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.316 Round 3: 128 peptides, 19 chains. Longest chain 13 peptides. Score 0.427 Round 4: 117 peptides, 19 chains. Longest chain 10 peptides. Score 0.378 Round 5: 130 peptides, 19 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 5 Chains 19, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4336 reflections ( 98.17 % complete ) and 5327 restraints for refining 2233 atoms. 4902 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 2233 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.1881 (Rfree = 0.000) for 2226 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1952 (Rfree = 0.000) for 2216 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1793 (Rfree = 0.000) for 2208 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1810 (Rfree = 0.000) for 2205 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 2307 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2321 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.248 Round 2: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.298 Round 3: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.343 Round 4: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.357 Round 5: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 94, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4336 reflections ( 98.17 % complete ) and 5404 restraints for refining 2233 atoms. 5046 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2018 (Rfree = 0.000) for 2233 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2111 (Rfree = 0.000) for 2222 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1990 (Rfree = 0.000) for 2214 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1928 (Rfree = 0.000) for 2204 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:25:03 GMT 2018 Job finished. TimeTaking 57.13 Used memory is bytes: 19014648