Mon 24 Dec 00:44:10 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 2ig6-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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/2ig6-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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 ============================================================ Mon 24 Dec 00:44:14 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/2ig6-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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 240 and 0 Target number of residues in the AU: 240 Target solvent content: 0.6509 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: 2ig6-4.0-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-4.0-parrot-mrncs.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 4.001 Wilson plot Bfac: 78.18 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3336 reflections ( 97.60 % complete ) and 0 restraints for refining 2662 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3465 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3215 (Rfree = 0.000) for 2662 atoms. Found 12 (12 requested) and removed 39 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2664 seeds are put forward NCS extension: 0 residues added, 2664 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.296 Round 2: 137 peptides, 19 chains. Longest chain 16 peptides. Score 0.467 Round 3: 150 peptides, 19 chains. Longest chain 29 peptides. Score 0.518 Round 4: 162 peptides, 17 chains. Longest chain 26 peptides. Score 0.594 Round 5: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.463 Taking the results from Round 4 Chains 17, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4808 restraints for refining 2167 atoms. 4245 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2417 (Rfree = 0.000) for 2167 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.2411 (Rfree = 0.000) for 2126 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2424 (Rfree = 0.000) for 2108 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2379 (Rfree = 0.000) for 2094 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2304 (Rfree = 0.000) for 2075 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 2151 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 2172 seeds are put forward Round 1: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.392 Round 2: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.475 Round 3: 149 peptides, 20 chains. Longest chain 16 peptides. Score 0.496 Round 4: 158 peptides, 23 chains. Longest chain 13 peptides. Score 0.479 Round 5: 156 peptides, 22 chains. Longest chain 12 peptides. Score 0.489 Taking the results from Round 3 Chains 20, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4960 restraints for refining 2138 atoms. 4464 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2082 (Rfree = 0.000) for 2138 atoms. Found 3 (10 requested) and removed 15 (5 requested) atoms. Cycle 7: After refmac, R = 0.2009 (Rfree = 0.000) for 2099 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2247 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.2365 (Rfree = 0.000) for 2070 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 2054 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 2140 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2153 seeds are put forward Round 1: 123 peptides, 23 chains. Longest chain 10 peptides. Score 0.327 Round 2: 147 peptides, 22 chains. Longest chain 12 peptides. Score 0.452 Round 3: 160 peptides, 22 chains. Longest chain 13 peptides. Score 0.504 Round 4: 155 peptides, 22 chains. Longest chain 13 peptides. Score 0.485 Round 5: 151 peptides, 19 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 5 Chains 19, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4835 restraints for refining 2134 atoms. 4326 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2257 (Rfree = 0.000) for 2134 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 12: After refmac, R = 0.2291 (Rfree = 0.000) for 2119 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.2287 (Rfree = 0.000) for 2099 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 14: After refmac, R = 0.1970 (Rfree = 0.000) for 2075 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2275 (Rfree = 0.000) for 2069 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.40 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2166 seeds are put forward Round 1: 132 peptides, 24 chains. Longest chain 8 peptides. Score 0.349 Round 2: 144 peptides, 22 chains. Longest chain 11 peptides. Score 0.440 Round 3: 131 peptides, 20 chains. Longest chain 12 peptides. Score 0.423 Round 4: 149 peptides, 22 chains. Longest chain 14 peptides. Score 0.461 Round 5: 155 peptides, 19 chains. Longest chain 17 peptides. Score 0.536 Taking the results from Round 5 Chains 19, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4856 restraints for refining 2162 atoms. 4331 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2161 (Rfree = 0.000) for 2162 atoms. Found 10 (10 requested) and removed 35 (5 requested) atoms. Cycle 17: After refmac, R = 0.2276 (Rfree = 0.000) for 2123 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 18: After refmac, R = 0.2174 (Rfree = 0.000) for 2104 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.2239 (Rfree = 0.000) for 2090 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 20: After refmac, R = 0.2110 (Rfree = 0.000) for 2076 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 2136 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2154 seeds are put forward Round 1: 130 peptides, 24 chains. Longest chain 10 peptides. Score 0.340 Round 2: 143 peptides, 26 chains. Longest chain 11 peptides. Score 0.360 Round 3: 150 peptides, 26 chains. Longest chain 13 peptides. Score 0.391 Round 4: 157 peptides, 27 chains. Longest chain 11 peptides. Score 0.403 Round 5: 143 peptides, 21 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 21, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4956 restraints for refining 2166 atoms. 4489 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2122 (Rfree = 0.000) for 2166 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 22: After refmac, R = 0.2182 (Rfree = 0.000) for 2138 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.1986 (Rfree = 0.000) for 2123 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2125 (Rfree = 0.000) for 2115 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2006 (Rfree = 0.000) for 2116 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 2199 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2220 seeds are put forward Round 1: 129 peptides, 27 chains. Longest chain 9 peptides. Score 0.274 Round 2: 145 peptides, 23 chains. Longest chain 21 peptides. Score 0.426 Round 3: 152 peptides, 24 chains. Longest chain 21 peptides. Score 0.437 Round 4: 164 peptides, 22 chains. Longest chain 22 peptides. Score 0.519 Round 5: 170 peptides, 23 chains. Longest chain 24 peptides. Score 0.525 Taking the results from Round 5 Chains 25, Residues 147, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4722 restraints for refining 2168 atoms. 4067 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2025 (Rfree = 0.000) for 2168 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 27: After refmac, R = 0.2088 (Rfree = 0.000) for 2154 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 28: After refmac, R = 0.1954 (Rfree = 0.000) for 2140 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 29: After refmac, R = 0.1929 (Rfree = 0.000) for 2127 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.1856 (Rfree = 0.000) for 2119 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2196 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2216 seeds are put forward Round 1: 132 peptides, 27 chains. Longest chain 13 peptides. Score 0.289 Round 2: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.398 Round 3: 137 peptides, 22 chains. Longest chain 17 peptides. Score 0.410 Round 4: 135 peptides, 24 chains. Longest chain 14 peptides. Score 0.363 Round 5: 128 peptides, 22 chains. Longest chain 10 peptides. Score 0.370 Taking the results from Round 3 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 5125 restraints for refining 2162 atoms. 4687 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1979 (Rfree = 0.000) for 2162 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.2104 (Rfree = 0.000) for 2148 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.1949 (Rfree = 0.000) for 2124 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.2215 (Rfree = 0.000) for 2117 atoms. Found 10 (10 requested) and removed 27 (5 requested) atoms. Cycle 35: After refmac, R = 0.1831 (Rfree = 0.000) for 2092 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 2136 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2156 seeds are put forward Round 1: 115 peptides, 25 chains. Longest chain 8 peptides. Score 0.246 Round 2: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.344 Round 3: 122 peptides, 23 chains. Longest chain 9 peptides. Score 0.322 Round 4: 127 peptides, 22 chains. Longest chain 9 peptides. Score 0.366 Round 5: 134 peptides, 24 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 4 Chains 22, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4981 restraints for refining 2092 atoms. 4583 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1864 (Rfree = 0.000) for 2092 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 37: After refmac, R = 0.2063 (Rfree = 0.000) for 2079 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1909 (Rfree = 0.000) for 2072 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.1764 (Rfree = 0.000) for 2068 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1605 (Rfree = 0.000) for 2067 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.32 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: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.304 Round 2: 108 peptides, 18 chains. Longest chain 9 peptides. Score 0.359 Round 3: 113 peptides, 19 chains. Longest chain 10 peptides. Score 0.362 Round 4: 116 peptides, 18 chains. Longest chain 11 peptides. Score 0.396 Round 5: 115 peptides, 18 chains. Longest chain 9 peptides. Score 0.391 Taking the results from Round 4 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 5138 restraints for refining 2167 atoms. 4764 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2162 (Rfree = 0.000) for 2167 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.1848 (Rfree = 0.000) for 2154 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1917 (Rfree = 0.000) for 2154 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.1910 (Rfree = 0.000) for 2147 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 45: After refmac, R = 0.1919 (Rfree = 0.000) for 2135 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 2186 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2200 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 6 peptides. Score 0.212 Round 2: 112 peptides, 21 chains. Longest chain 11 peptides. Score 0.315 Round 3: 116 peptides, 23 chains. Longest chain 8 peptides. Score 0.293 Round 4: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.344 Round 5: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.333 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 97, 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 2ig6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3336 reflections ( 97.60 % complete ) and 5135 restraints for refining 2168 atoms. 4768 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1944 (Rfree = 0.000) for 2168 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1952 (Rfree = 0.000) for 2148 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2009 (Rfree = 0.000) for 2135 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2139 (Rfree = 0.000) for 2120 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 31