Tue 25 Dec 19:27:57 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 2ig6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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/2ig6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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 19:28:07 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/2ig6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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 249 and 0 Target number of residues in the AU: 249 Target solvent content: 0.6378 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 300 Adjusted target solvent content: 0.56 Input MTZ file: 2ig6-3.6-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2400 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: 55.977 3.600 Wilson plot Bfac: 70.35 4546 reflections ( 97.72 % complete ) and 0 restraints for refining 2668 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3146 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2939 (Rfree = 0.000) for 2668 atoms. Found 17 (17 requested) and removed 45 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 2691 seeds are put forward NCS extension: 0 residues added, 2691 seeds are put forward Round 1: 161 peptides, 27 chains. Longest chain 14 peptides. Score 0.420 Round 2: 184 peptides, 25 chains. Longest chain 16 peptides. Score 0.543 Round 3: 195 peptides, 22 chains. Longest chain 19 peptides. Score 0.625 Round 4: 198 peptides, 21 chains. Longest chain 27 peptides. Score 0.648 Round 5: 209 peptides, 20 chains. Longest chain 40 peptides. Score 0.691 Taking the results from Round 5 Chains 20, Residues 189, Estimated correctness of the model 46.8 % 1 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4239 restraints for refining 2175 atoms. 3337 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2513 (Rfree = 0.000) for 2175 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2310 (Rfree = 0.000) for 2119 atoms. Found 9 (13 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2209 (Rfree = 0.000) for 2100 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.2095 (Rfree = 0.000) for 2094 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2004 (Rfree = 0.000) for 2083 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 2134 seeds are put forward NCS extension: 33 residues added (10 deleted due to clashes), 2167 seeds are put forward Round 1: 190 peptides, 25 chains. Longest chain 22 peptides. Score 0.564 Round 2: 210 peptides, 23 chains. Longest chain 29 peptides. Score 0.656 Round 3: 195 peptides, 21 chains. Longest chain 18 peptides. Score 0.639 Round 4: 196 peptides, 18 chains. Longest chain 32 peptides. Score 0.682 Round 5: 191 peptides, 19 chains. Longest chain 20 peptides. Score 0.655 Taking the results from Round 4 Chains 20, Residues 178, Estimated correctness of the model 43.9 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4596 restraints for refining 2174 atoms. 3858 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2253 (Rfree = 0.000) for 2174 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 7: After refmac, R = 0.2038 (Rfree = 0.000) for 2167 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1962 (Rfree = 0.000) for 2162 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2081 (Rfree = 0.000) for 2159 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1929 (Rfree = 0.000) for 2155 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2245 seeds are put forward NCS extension: 42 residues added (3 deleted due to clashes), 2287 seeds are put forward Round 1: 182 peptides, 24 chains. Longest chain 16 peptides. Score 0.552 Round 2: 185 peptides, 20 chains. Longest chain 20 peptides. Score 0.623 Round 3: 189 peptides, 21 chains. Longest chain 31 peptides. Score 0.621 Round 4: 193 peptides, 21 chains. Longest chain 29 peptides. Score 0.633 Round 5: 181 peptides, 23 chains. Longest chain 19 peptides. Score 0.564 Taking the results from Round 4 Chains 21, Residues 172, Estimated correctness of the model 27.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4546 reflections ( 97.72 % complete ) and 4816 restraints for refining 2176 atoms. 4149 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2161 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1962 (Rfree = 0.000) for 2172 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1942 (Rfree = 0.000) for 2178 atoms. Found 5 (13 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.1833 (Rfree = 0.000) for 2168 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.1825 (Rfree = 0.000) for 2164 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 2280 seeds are put forward Round 1: 165 peptides, 24 chains. Longest chain 17 peptides. Score 0.489 Round 2: 167 peptides, 21 chains. Longest chain 22 peptides. Score 0.547 Round 3: 185 peptides, 21 chains. Longest chain 21 peptides. Score 0.608 Round 4: 183 peptides, 24 chains. Longest chain 23 peptides. Score 0.555 Round 5: 178 peptides, 19 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 5 Chains 19, Residues 159, Estimated correctness of the model 20.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4546 reflections ( 97.72 % complete ) and 4812 restraints for refining 2176 atoms. 4195 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2323 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.1917 (Rfree = 0.000) for 2165 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1845 (Rfree = 0.000) for 2156 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.1841 (Rfree = 0.000) for 2157 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.1802 (Rfree = 0.000) for 2149 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2207 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 2249 seeds are put forward Round 1: 158 peptides, 24 chains. Longest chain 14 peptides. Score 0.461 Round 2: 177 peptides, 20 chains. Longest chain 28 peptides. Score 0.597 Round 3: 167 peptides, 20 chains. Longest chain 21 peptides. Score 0.563 Round 4: 167 peptides, 23 chains. Longest chain 17 peptides. Score 0.514 Round 5: 177 peptides, 20 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 5 Chains 20, Residues 157, Estimated correctness of the model 13.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4546 reflections ( 97.72 % complete ) and 4930 restraints for refining 2176 atoms. 4322 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2218 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1971 (Rfree = 0.000) for 2171 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1898 (Rfree = 0.000) for 2173 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1819 (Rfree = 0.000) for 2177 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1766 (Rfree = 0.000) for 2174 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2272 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2295 seeds are put forward Round 1: 162 peptides, 24 chains. Longest chain 16 peptides. Score 0.477 Round 2: 187 peptides, 24 chains. Longest chain 23 peptides. Score 0.569 Round 3: 177 peptides, 21 chains. Longest chain 23 peptides. Score 0.582 Round 4: 187 peptides, 22 chains. Longest chain 23 peptides. Score 0.600 Round 5: 192 peptides, 27 chains. Longest chain 23 peptides. Score 0.540 Taking the results from Round 4 Chains 24, Residues 165, Estimated correctness of the model 14.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4680 restraints for refining 2175 atoms. 3999 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 2175 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 27: After refmac, R = 0.1904 (Rfree = 0.000) for 2166 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1920 (Rfree = 0.000) for 2162 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1850 (Rfree = 0.000) for 2160 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.1872 (Rfree = 0.000) for 2162 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 2244 seeds are put forward NCS extension: 7 residues added (9 deleted due to clashes), 2251 seeds are put forward Round 1: 153 peptides, 26 chains. Longest chain 15 peptides. Score 0.404 Round 2: 173 peptides, 22 chains. Longest chain 23 peptides. Score 0.552 Round 3: 178 peptides, 21 chains. Longest chain 23 peptides. Score 0.585 Round 4: 176 peptides, 23 chains. Longest chain 23 peptides. Score 0.547 Round 5: 193 peptides, 24 chains. Longest chain 23 peptides. Score 0.589 Taking the results from Round 5 Chains 24, Residues 169, Estimated correctness of the model 10.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4546 reflections ( 97.72 % complete ) and 4829 restraints for refining 2176 atoms. 4177 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2412 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2193 (Rfree = 0.000) for 2174 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2148 (Rfree = 0.000) for 2178 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1972 (Rfree = 0.000) for 2183 atoms. Found 12 (14 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.2132 (Rfree = 0.000) for 2184 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.21 Search for helices and strands: 0 residues in 0 chains, 2270 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 2294 seeds are put forward Round 1: 144 peptides, 27 chains. Longest chain 10 peptides. Score 0.345 Round 2: 163 peptides, 25 chains. Longest chain 19 peptides. Score 0.464 Round 3: 162 peptides, 23 chains. Longest chain 20 peptides. Score 0.495 Round 4: 172 peptides, 23 chains. Longest chain 21 peptides. Score 0.532 Round 5: 182 peptides, 18 chains. Longest chain 30 peptides. Score 0.642 Taking the results from Round 5 Chains 18, Residues 164, Estimated correctness of the model 30.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4800 restraints for refining 2176 atoms. 4162 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2504 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.2137 (Rfree = 0.000) for 2167 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2034 (Rfree = 0.000) for 2164 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.1971 (Rfree = 0.000) for 2165 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1858 (Rfree = 0.000) for 2164 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 2224 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 2261 seeds are put forward Round 1: 156 peptides, 28 chains. Longest chain 13 peptides. Score 0.380 Round 2: 172 peptides, 24 chains. Longest chain 20 peptides. Score 0.516 Round 3: 172 peptides, 23 chains. Longest chain 23 peptides. Score 0.532 Round 4: 174 peptides, 24 chains. Longest chain 22 peptides. Score 0.523 Round 5: 171 peptides, 25 chains. Longest chain 22 peptides. Score 0.495 Taking the results from Round 3 Chains 23, Residues 149, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4546 reflections ( 97.72 % complete ) and 4906 restraints for refining 2176 atoms. 4313 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2142 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2017 (Rfree = 0.000) for 2174 atoms. Found 12 (14 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1942 (Rfree = 0.000) for 2168 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1828 (Rfree = 0.000) for 2168 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.1851 (Rfree = 0.000) for 2160 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2245 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2263 seeds are put forward Round 1: 153 peptides, 28 chains. Longest chain 12 peptides. Score 0.366 Round 2: 171 peptides, 25 chains. Longest chain 13 peptides. Score 0.495 Round 3: 164 peptides, 20 chains. Longest chain 18 peptides. Score 0.552 Round 4: 153 peptides, 22 chains. Longest chain 19 peptides. Score 0.477 Round 5: 164 peptides, 21 chains. Longest chain 20 peptides. Score 0.536 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 144, 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 2ig6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4546 reflections ( 97.72 % complete ) and 5042 restraints for refining 2176 atoms. 4486 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1986 (Rfree = 0.000) for 2176 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2027 (Rfree = 0.000) for 2163 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2030 (Rfree = 0.000) for 2155 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1864 (Rfree = 0.000) for 2149 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:03 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 48.1