Mon 24 Dec 00:09:09 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 2ig6-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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/2ig6-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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 ============================================================ Mon 24 Dec 00:09:14 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/2ig6-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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 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-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2400 target number of atoms Had to go as low as 0.70 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 2677 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3115 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2991 (Rfree = 0.000) for 2677 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 2715 seeds are put forward NCS extension: 0 residues added, 2715 seeds are put forward Round 1: 156 peptides, 24 chains. Longest chain 14 peptides. Score 0.453 Round 2: 191 peptides, 25 chains. Longest chain 17 peptides. Score 0.568 Round 3: 189 peptides, 22 chains. Longest chain 21 peptides. Score 0.606 Round 4: 204 peptides, 22 chains. Longest chain 21 peptides. Score 0.652 Round 5: 189 peptides, 24 chains. Longest chain 16 peptides. Score 0.576 Taking the results from Round 4 Chains 22, Residues 182, Estimated correctness of the model 33.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4681 restraints for refining 2176 atoms. 3975 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2305 (Rfree = 0.000) for 2176 atoms. Found 11 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2095 (Rfree = 0.000) for 2138 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.1962 (Rfree = 0.000) for 2123 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2113 (Rfree = 0.000) for 2111 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.1873 (Rfree = 0.000) for 2109 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 2200 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 2231 seeds are put forward Round 1: 172 peptides, 26 chains. Longest chain 17 peptides. Score 0.482 Round 2: 178 peptides, 23 chains. Longest chain 18 peptides. Score 0.554 Round 3: 180 peptides, 25 chains. Longest chain 16 peptides. Score 0.529 Round 4: 189 peptides, 23 chains. Longest chain 18 peptides. Score 0.591 Round 5: 195 peptides, 23 chains. Longest chain 20 peptides. Score 0.611 Taking the results from Round 5 Chains 23, Residues 172, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4798 restraints for refining 2175 atoms. 4133 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2224 (Rfree = 0.000) for 2175 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 7: After refmac, R = 0.2078 (Rfree = 0.000) for 2159 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 8: After refmac, R = 0.2020 (Rfree = 0.000) for 2153 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.1873 (Rfree = 0.000) for 2143 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.1868 (Rfree = 0.000) for 2133 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 2198 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2219 seeds are put forward Round 1: 175 peptides, 25 chains. Longest chain 24 peptides. Score 0.510 Round 2: 191 peptides, 24 chains. Longest chain 17 peptides. Score 0.583 Round 3: 197 peptides, 23 chains. Longest chain 18 peptides. Score 0.617 Round 4: 201 peptides, 23 chains. Longest chain 35 peptides. Score 0.629 Round 5: 192 peptides, 23 chains. Longest chain 24 peptides. Score 0.601 Taking the results from Round 4 Chains 23, Residues 178, Estimated correctness of the model 25.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4779 restraints for refining 2176 atoms. 4090 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 2176 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 12: After refmac, R = 0.2045 (Rfree = 0.000) for 2172 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1914 (Rfree = 0.000) for 2168 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1823 (Rfree = 0.000) for 2161 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1799 (Rfree = 0.000) for 2157 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 2212 seeds are put forward NCS extension: 49 residues added (2 deleted due to clashes), 2261 seeds are put forward Round 1: 162 peptides, 22 chains. Longest chain 14 peptides. Score 0.512 Round 2: 202 peptides, 26 chains. Longest chain 16 peptides. Score 0.589 Round 3: 197 peptides, 25 chains. Longest chain 21 peptides. Score 0.588 Round 4: 194 peptides, 25 chains. Longest chain 21 peptides. Score 0.578 Round 5: 187 peptides, 23 chains. Longest chain 19 peptides. Score 0.585 Taking the results from Round 2 Chains 27, Residues 176, Estimated correctness of the model 10.3 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4653 restraints for refining 2176 atoms. 3913 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2111 (Rfree = 0.000) for 2176 atoms. Found 9 (13 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.2107 (Rfree = 0.000) for 2163 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1967 (Rfree = 0.000) for 2158 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1890 (Rfree = 0.000) for 2162 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1893 (Rfree = 0.000) for 2160 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 2216 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2232 seeds are put forward Round 1: 172 peptides, 27 chains. Longest chain 13 peptides. Score 0.465 Round 2: 189 peptides, 24 chains. Longest chain 19 peptides. Score 0.576 Round 3: 174 peptides, 24 chains. Longest chain 19 peptides. Score 0.523 Round 4: 188 peptides, 20 chains. Longest chain 21 peptides. Score 0.632 Round 5: 174 peptides, 22 chains. Longest chain 34 peptides. Score 0.556 Taking the results from Round 4 Chains 22, Residues 168, Estimated correctness of the model 26.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4626 restraints for refining 2175 atoms. 3928 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2263 (Rfree = 0.000) for 2175 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2106 (Rfree = 0.000) for 2172 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2028 (Rfree = 0.000) for 2166 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1968 (Rfree = 0.000) for 2158 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1935 (Rfree = 0.000) for 2151 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2194 seeds are put forward NCS extension: 0 residues added, 2194 seeds are put forward Round 1: 150 peptides, 22 chains. Longest chain 26 peptides. Score 0.465 Round 2: 154 peptides, 18 chains. Longest chain 19 peptides. Score 0.550 Round 3: 176 peptides, 19 chains. Longest chain 29 peptides. Score 0.609 Round 4: 174 peptides, 20 chains. Longest chain 39 peptides. Score 0.587 Round 5: 179 peptides, 24 chains. Longest chain 13 peptides. Score 0.541 Taking the results from Round 3 Chains 19, Residues 157, Estimated correctness of the model 18.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4933 restraints for refining 2176 atoms. 4324 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2206 (Rfree = 0.000) for 2176 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2250 (Rfree = 0.000) for 2175 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2082 (Rfree = 0.000) for 2176 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.2036 (Rfree = 0.000) for 2170 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1978 (Rfree = 0.000) for 2173 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 2239 seeds are put forward NCS extension: 56 residues added (2 deleted due to clashes), 2295 seeds are put forward Round 1: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.429 Round 2: 164 peptides, 22 chains. Longest chain 16 peptides. Score 0.519 Round 3: 162 peptides, 16 chains. Longest chain 23 peptides. Score 0.609 Round 4: 171 peptides, 21 chains. Longest chain 16 peptides. Score 0.561 Round 5: 175 peptides, 20 chains. Longest chain 21 peptides. Score 0.590 Taking the results from Round 3 Chains 16, Residues 146, Estimated correctness of the model 18.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4936 restraints for refining 2176 atoms. 4368 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2039 (Rfree = 0.000) for 2176 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.2010 (Rfree = 0.000) for 2167 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1881 (Rfree = 0.000) for 2166 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1966 (Rfree = 0.000) for 2168 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1984 (Rfree = 0.000) for 2168 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 2240 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 2249 seeds are put forward Round 1: 162 peptides, 23 chains. Longest chain 19 peptides. Score 0.495 Round 2: 168 peptides, 20 chains. Longest chain 22 peptides. Score 0.567 Round 3: 163 peptides, 21 chains. Longest chain 19 peptides. Score 0.532 Round 4: 152 peptides, 17 chains. Longest chain 21 peptides. Score 0.559 Round 5: 154 peptides, 18 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 2 Chains 20, Residues 148, Estimated correctness of the model 1.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4887 restraints for refining 2176 atoms. 4315 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2056 (Rfree = 0.000) for 2176 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2143 (Rfree = 0.000) for 2175 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.1891 (Rfree = 0.000) for 2176 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1912 (Rfree = 0.000) for 2176 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1847 (Rfree = 0.000) for 2174 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2245 seeds are put forward Round 1: 141 peptides, 25 chains. Longest chain 11 peptides. Score 0.370 Round 2: 160 peptides, 20 chains. Longest chain 25 peptides. Score 0.538 Round 3: 169 peptides, 23 chains. Longest chain 17 peptides. Score 0.521 Round 4: 162 peptides, 18 chains. Longest chain 23 peptides. Score 0.578 Round 5: 158 peptides, 20 chains. Longest chain 26 peptides. Score 0.531 Taking the results from Round 4 Chains 18, Residues 144, Estimated correctness of the model 5.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4915 restraints for refining 2176 atoms. 4357 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2180 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2084 (Rfree = 0.000) for 2175 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2013 (Rfree = 0.000) for 2173 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1931 (Rfree = 0.000) for 2178 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1883 (Rfree = 0.000) for 2171 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 2262 seeds are put forward Round 1: 143 peptides, 23 chains. Longest chain 15 peptides. Score 0.417 Round 2: 149 peptides, 18 chains. Longest chain 21 peptides. Score 0.531 Round 3: 145 peptides, 19 chains. Longest chain 14 peptides. Score 0.499 Round 4: 159 peptides, 20 chains. Longest chain 20 peptides. Score 0.534 Round 5: 147 peptides, 20 chains. Longest chain 17 peptides. Score 0.489 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 139, 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 4963 restraints for refining 2175 atoms. 4427 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2257 (Rfree = 0.000) for 2175 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2016 (Rfree = 0.000) for 2161 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1929 (Rfree = 0.000) for 2150 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1951 (Rfree = 0.000) for 2141 atoms. TimeTaking 29.83