null Mon 24 Dec 07:40:45 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 2ig6-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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/2ig6-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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 07:40:49 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/2ig6-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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 244 and 0 Target number of residues in the AU: 244 Target solvent content: 0.6451 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: 2ig6-3.8-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-3.8-parrot-noncs.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 3.800 Wilson plot Bfac: 74.43 3878 reflections ( 97.63 % complete ) and 0 restraints for refining 2667 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3436 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3355 (Rfree = 0.000) for 2667 atoms. Found 14 (14 requested) and removed 66 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2663 seeds are put forward NCS extension: 0 residues added, 2663 seeds are put forward Round 1: 143 peptides, 28 chains. Longest chain 11 peptides. Score 0.321 Round 2: 159 peptides, 26 chains. Longest chain 12 peptides. Score 0.429 Round 3: 169 peptides, 23 chains. Longest chain 22 peptides. Score 0.521 Round 4: 160 peptides, 22 chains. Longest chain 18 peptides. Score 0.504 Round 5: 172 peptides, 23 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 5 Chains 23, Residues 149, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4613 restraints for refining 2171 atoms. 3968 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2486 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.2234 (Rfree = 0.000) for 2130 atoms. Found 7 (11 requested) and removed 14 (5 requested) atoms. Cycle 3: After refmac, R = 0.2093 (Rfree = 0.000) for 2111 atoms. Found 7 (11 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.2052 (Rfree = 0.000) for 2097 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.1920 (Rfree = 0.000) for 2087 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 2197 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 10 peptides. Score 0.354 Round 2: 170 peptides, 19 chains. Longest chain 18 peptides. Score 0.589 Round 3: 164 peptides, 21 chains. Longest chain 18 peptides. Score 0.536 Round 4: 174 peptides, 22 chains. Longest chain 16 peptides. Score 0.556 Round 5: 175 peptides, 23 chains. Longest chain 15 peptides. Score 0.543 Taking the results from Round 2 Chains 19, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4893 restraints for refining 2171 atoms. 4308 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2235 (Rfree = 0.000) for 2171 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 7: After refmac, R = 0.2076 (Rfree = 0.000) for 2157 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2115 (Rfree = 0.000) for 2147 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.2133 (Rfree = 0.000) for 2141 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.1995 (Rfree = 0.000) for 2135 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2209 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2230 seeds are put forward Round 1: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.358 Round 2: 171 peptides, 26 chains. Longest chain 13 peptides. Score 0.478 Round 3: 176 peptides, 25 chains. Longest chain 24 peptides. Score 0.514 Round 4: 180 peptides, 25 chains. Longest chain 14 peptides. Score 0.529 Round 5: 173 peptides, 21 chains. Longest chain 20 peptides. Score 0.568 Taking the results from Round 5 Chains 21, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4888 restraints for refining 2169 atoms. 4301 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2202 (Rfree = 0.000) for 2169 atoms. Found 8 (11 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2129 (Rfree = 0.000) for 2139 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 2134 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.1895 (Rfree = 0.000) for 2120 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.1893 (Rfree = 0.000) for 2118 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2165 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2197 seeds are put forward Round 1: 150 peptides, 28 chains. Longest chain 11 peptides. Score 0.353 Round 2: 156 peptides, 24 chains. Longest chain 15 peptides. Score 0.453 Round 3: 165 peptides, 23 chains. Longest chain 14 peptides. Score 0.506 Round 4: 164 peptides, 19 chains. Longest chain 16 peptides. Score 0.569 Round 5: 168 peptides, 22 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 4 Chains 19, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4923 restraints for refining 2171 atoms. 4362 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2156 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 17: After refmac, R = 0.2015 (Rfree = 0.000) for 2161 atoms. Found 8 (11 requested) and removed 12 (5 requested) atoms. Cycle 18: After refmac, R = 0.1934 (Rfree = 0.000) for 2149 atoms. Found 9 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.1836 (Rfree = 0.000) for 2145 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 20: After refmac, R = 0.1832 (Rfree = 0.000) for 2137 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2223 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 10 peptides. Score 0.352 Round 2: 141 peptides, 22 chains. Longest chain 14 peptides. Score 0.427 Round 3: 144 peptides, 22 chains. Longest chain 14 peptides. Score 0.440 Round 4: 153 peptides, 21 chains. Longest chain 15 peptides. Score 0.494 Round 5: 142 peptides, 21 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 4 Chains 21, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5071 restraints for refining 2171 atoms. 4564 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2016 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 22: After refmac, R = 0.2013 (Rfree = 0.000) for 2162 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 23: After refmac, R = 0.1978 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 24: After refmac, R = 0.1804 (Rfree = 0.000) for 2148 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.1933 (Rfree = 0.000) for 2148 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2204 seeds are put forward NCS extension: 0 residues added, 2204 seeds are put forward Round 1: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.333 Round 2: 134 peptides, 19 chains. Longest chain 14 peptides. Score 0.454 Round 3: 149 peptides, 23 chains. Longest chain 13 peptides. Score 0.443 Round 4: 142 peptides, 20 chains. Longest chain 15 peptides. Score 0.469 Round 5: 145 peptides, 20 chains. Longest chain 16 peptides. Score 0.481 Taking the results from Round 5 Chains 20, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5039 restraints for refining 2171 atoms. 4559 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2020 (Rfree = 0.000) for 2171 atoms. Found 8 (11 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.1803 (Rfree = 0.000) for 2153 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 28: After refmac, R = 0.1807 (Rfree = 0.000) for 2146 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.1804 (Rfree = 0.000) for 2143 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 30: After refmac, R = 0.1729 (Rfree = 0.000) for 2142 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2250 seeds are put forward Round 1: 125 peptides, 23 chains. Longest chain 12 peptides. Score 0.336 Round 2: 145 peptides, 22 chains. Longest chain 12 peptides. Score 0.444 Round 3: 157 peptides, 22 chains. Longest chain 14 peptides. Score 0.493 Round 4: 160 peptides, 21 chains. Longest chain 23 peptides. Score 0.521 Round 5: 142 peptides, 22 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 4 Chains 21, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4846 restraints for refining 2171 atoms. 4311 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3009 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 32: After refmac, R = 0.1980 (Rfree = 0.000) for 2144 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 33: After refmac, R = 0.2082 (Rfree = 0.000) for 2130 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2016 (Rfree = 0.000) for 2126 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2277 (Rfree = 0.000) for 2124 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2212 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 9 peptides. Score 0.267 Round 2: 136 peptides, 21 chains. Longest chain 17 peptides. Score 0.425 Round 3: 139 peptides, 23 chains. Longest chain 12 peptides. Score 0.400 Round 4: 142 peptides, 18 chains. Longest chain 18 peptides. Score 0.505 Round 5: 141 peptides, 20 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 4 Chains 18, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5024 restraints for refining 2170 atoms. 4546 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1997 (Rfree = 0.000) for 2170 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.1811 (Rfree = 0.000) for 2165 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.1728 (Rfree = 0.000) for 2162 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1555 (Rfree = 0.000) for 2165 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1595 (Rfree = 0.000) for 2159 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2207 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2226 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 7 peptides. Score 0.242 Round 2: 146 peptides, 24 chains. Longest chain 11 peptides. Score 0.411 Round 3: 155 peptides, 26 chains. Longest chain 12 peptides. Score 0.412 Round 4: 150 peptides, 22 chains. Longest chain 13 peptides. Score 0.465 Round 5: 151 peptides, 23 chains. Longest chain 14 peptides. Score 0.451 Taking the results from Round 4 Chains 22, Residues 128, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4810 restraints for refining 2169 atoms. 4275 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2272 (Rfree = 0.000) for 2169 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 42: After refmac, R = 0.2572 (Rfree = 0.000) for 2153 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 43: After refmac, R = 0.2186 (Rfree = 0.000) for 2137 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2036 (Rfree = 0.000) for 2136 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.1963 (Rfree = 0.000) for 2135 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 2212 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2225 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.309 Round 2: 135 peptides, 20 chains. Longest chain 13 peptides. Score 0.440 Round 3: 128 peptides, 21 chains. Longest chain 14 peptides. Score 0.390 Round 4: 136 peptides, 20 chains. Longest chain 17 peptides. Score 0.444 Round 5: 132 peptides, 21 chains. Longest chain 16 peptides. Score 0.408 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 116, 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. 3878 reflections ( 97.63 % complete ) and 5014 restraints for refining 2171 atoms. 4570 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2127 (Rfree = 0.000) for 2171 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 2160 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2093 (Rfree = 0.000) for 2155 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2079 (Rfree = 0.000) for 2145 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:08:50 GMT 2018 Job finished. TimeTaking 28.08 Used memory is bytes: 10714520