Mon 24 Dec 07:31:27 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 2ig6-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-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/2ig6-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-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 07:31:31 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/2ig6-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.6305 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: 2ig6-3.4-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: 2ig6-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 66.56 5383 reflections ( 97.84 % complete ) and 0 restraints for refining 2644 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3269 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3120 (Rfree = 0.000) for 2644 atoms. Found 19 (19 requested) and removed 46 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.02 Search for helices and strands: 0 residues in 0 chains, 2658 seeds are put forward NCS extension: 0 residues added, 2658 seeds are put forward Round 1: 165 peptides, 26 chains. Longest chain 21 peptides. Score 0.454 Round 2: 187 peptides, 23 chains. Longest chain 39 peptides. Score 0.585 Round 3: 186 peptides, 19 chains. Longest chain 40 peptides. Score 0.640 Round 4: 196 peptides, 21 chains. Longest chain 40 peptides. Score 0.642 Round 5: 205 peptides, 20 chains. Longest chain 41 peptides. Score 0.681 Taking the results from Round 5 Chains 21, Residues 185, Estimated correctness of the model 52.9 % 2 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 3987 restraints for refining 2182 atoms. 3041 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2554 (Rfree = 0.000) for 2182 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2414 (Rfree = 0.000) for 2150 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2275 (Rfree = 0.000) for 2134 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2178 (Rfree = 0.000) for 2119 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2124 (Rfree = 0.000) for 2110 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2167 seeds are put forward NCS extension: 47 residues added (9 deleted due to clashes), 2214 seeds are put forward Round 1: 176 peptides, 22 chains. Longest chain 26 peptides. Score 0.563 Round 2: 185 peptides, 19 chains. Longest chain 36 peptides. Score 0.637 Round 3: 186 peptides, 21 chains. Longest chain 26 peptides. Score 0.611 Round 4: 192 peptides, 19 chains. Longest chain 35 peptides. Score 0.658 Round 5: 192 peptides, 24 chains. Longest chain 18 peptides. Score 0.586 Taking the results from Round 4 Chains 19, Residues 173, Estimated correctness of the model 46.5 % 2 chains (51 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4197 restraints for refining 2182 atoms. 3288 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2473 (Rfree = 0.000) for 2182 atoms. Found 7 (16 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2278 (Rfree = 0.000) for 2167 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 8: After refmac, R = 0.2209 (Rfree = 0.000) for 2161 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2163 (Rfree = 0.000) for 2160 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2132 (Rfree = 0.000) for 2154 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward NCS extension: 35 residues added (11 deleted due to clashes), 2236 seeds are put forward Round 1: 188 peptides, 26 chains. Longest chain 26 peptides. Score 0.542 Round 2: 201 peptides, 22 chains. Longest chain 26 peptides. Score 0.643 Round 3: 203 peptides, 20 chains. Longest chain 30 peptides. Score 0.675 Round 4: 210 peptides, 19 chains. Longest chain 31 peptides. Score 0.706 Round 5: 217 peptides, 21 chains. Longest chain 27 peptides. Score 0.700 Taking the results from Round 4 Chains 20, Residues 191, Estimated correctness of the model 59.4 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4551 restraints for refining 2182 atoms. 3745 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2307 (Rfree = 0.000) for 2182 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. Cycle 12: After refmac, R = 0.2186 (Rfree = 0.000) for 2178 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.2141 (Rfree = 0.000) for 2172 atoms. Found 1 (15 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2113 (Rfree = 0.000) for 2164 atoms. Found 0 (15 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2077 (Rfree = 0.000) for 2155 atoms. Found 1 (15 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 2211 seeds are put forward NCS extension: 31 residues added (5 deleted due to clashes), 2242 seeds are put forward Round 1: 182 peptides, 24 chains. Longest chain 18 peptides. Score 0.552 Round 2: 201 peptides, 23 chains. Longest chain 26 peptides. Score 0.629 Round 3: 209 peptides, 18 chains. Longest chain 32 peptides. Score 0.716 Round 4: 226 peptides, 22 chains. Longest chain 34 peptides. Score 0.710 Round 5: 220 peptides, 25 chains. Longest chain 30 peptides. Score 0.658 Taking the results from Round 3 Chains 20, Residues 191, Estimated correctness of the model 61.9 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4384 restraints for refining 2182 atoms. 3512 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2333 (Rfree = 0.000) for 2182 atoms. Found 9 (14 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.2146 (Rfree = 0.000) for 2172 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2056 (Rfree = 0.000) for 2161 atoms. Found 8 (14 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2001 (Rfree = 0.000) for 2156 atoms. Found 3 (13 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1900 (Rfree = 0.000) for 2145 atoms. Found 3 (13 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 2204 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2229 seeds are put forward Round 1: 187 peptides, 23 chains. Longest chain 27 peptides. Score 0.585 Round 2: 208 peptides, 23 chains. Longest chain 27 peptides. Score 0.650 Round 3: 215 peptides, 21 chains. Longest chain 35 peptides. Score 0.695 Round 4: 207 peptides, 17 chains. Longest chain 35 peptides. Score 0.723 Round 5: 193 peptides, 20 chains. Longest chain 32 peptides. Score 0.647 Taking the results from Round 4 Chains 21, Residues 190, Estimated correctness of the model 63.6 % 3 chains (55 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 126 A 20 chains (190 residues) following loop building 2 chains (61 residues) in sequence following loop building ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 3978 restraints for refining 2181 atoms. 3024 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2420 (Rfree = 0.000) for 2181 atoms. Found 13 (13 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.2212 (Rfree = 0.000) for 2164 atoms. Found 6 (12 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2071 (Rfree = 0.000) for 2155 atoms. Found 3 (12 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.2091 (Rfree = 0.000) for 2145 atoms. Found 7 (12 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1999 (Rfree = 0.000) for 2141 atoms. Found 4 (12 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2192 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 2223 seeds are put forward Round 1: 174 peptides, 27 chains. Longest chain 13 peptides. Score 0.473 Round 2: 190 peptides, 22 chains. Longest chain 27 peptides. Score 0.609 Round 3: 178 peptides, 19 chains. Longest chain 21 peptides. Score 0.615 Round 4: 174 peptides, 20 chains. Longest chain 20 peptides. Score 0.587 Round 5: 171 peptides, 20 chains. Longest chain 23 peptides. Score 0.577 Taking the results from Round 3 Chains 20, Residues 159, Estimated correctness of the model 33.5 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4610 restraints for refining 2182 atoms. 3907 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2279 (Rfree = 0.000) for 2182 atoms. Found 11 (11 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 2183 atoms. Found 9 (11 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2018 (Rfree = 0.000) for 2179 atoms. Found 4 (11 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1992 (Rfree = 0.000) for 2174 atoms. Found 2 (11 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1943 (Rfree = 0.000) for 2168 atoms. Found 2 (11 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 2230 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 2250 seeds are put forward Round 1: 168 peptides, 24 chains. Longest chain 29 peptides. Score 0.501 Round 2: 177 peptides, 21 chains. Longest chain 24 peptides. Score 0.582 Round 3: 182 peptides, 26 chains. Longest chain 16 peptides. Score 0.520 Round 4: 182 peptides, 23 chains. Longest chain 26 peptides. Score 0.568 Round 5: 186 peptides, 25 chains. Longest chain 27 peptides. Score 0.550 Taking the results from Round 2 Chains 21, Residues 156, Estimated correctness of the model 22.7 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4649 restraints for refining 2182 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2185 (Rfree = 0.000) for 2182 atoms. Found 11 (11 requested) and removed 8 (8 requested) atoms. Cycle 32: After refmac, R = 0.2079 (Rfree = 0.000) for 2180 atoms. Found 9 (11 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1976 (Rfree = 0.000) for 2177 atoms. Found 5 (11 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1984 (Rfree = 0.000) for 2173 atoms. Found 5 (11 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1874 (Rfree = 0.000) for 2170 atoms. Found 2 (11 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 2261 seeds are put forward Round 1: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.412 Round 2: 175 peptides, 24 chains. Longest chain 18 peptides. Score 0.527 Round 3: 178 peptides, 27 chains. Longest chain 12 peptides. Score 0.488 Round 4: 183 peptides, 24 chains. Longest chain 28 peptides. Score 0.555 Round 5: 175 peptides, 22 chains. Longest chain 24 peptides. Score 0.559 Taking the results from Round 5 Chains 22, Residues 153, Estimated correctness of the model 14.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4944 restraints for refining 2181 atoms. 4354 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2191 (Rfree = 0.000) for 2181 atoms. Found 11 (11 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.2104 (Rfree = 0.000) for 2178 atoms. Found 11 (11 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1986 (Rfree = 0.000) for 2176 atoms. Found 5 (11 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1978 (Rfree = 0.000) for 2169 atoms. Found 9 (11 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1931 (Rfree = 0.000) for 2169 atoms. Found 4 (11 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 0 residues added, 2247 seeds are put forward Round 1: 141 peptides, 23 chains. Longest chain 13 peptides. Score 0.409 Round 2: 154 peptides, 23 chains. Longest chain 15 peptides. Score 0.463 Round 3: 157 peptides, 21 chains. Longest chain 30 peptides. Score 0.510 Round 4: 157 peptides, 22 chains. Longest chain 16 peptides. Score 0.493 Round 5: 160 peptides, 21 chains. Longest chain 26 peptides. Score 0.521 Taking the results from Round 5 Chains 21, Residues 139, Estimated correctness of the model 0.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 5028 restraints for refining 2182 atoms. 4493 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2072 (Rfree = 0.000) for 2182 atoms. Found 11 (11 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1923 (Rfree = 0.000) for 2179 atoms. Found 10 (11 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1922 (Rfree = 0.000) for 2175 atoms. Found 11 (11 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.1875 (Rfree = 0.000) for 2175 atoms. Found 11 (11 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1863 (Rfree = 0.000) for 2177 atoms. Found 4 (11 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 2263 seeds are put forward Round 1: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.367 Round 2: 153 peptides, 18 chains. Longest chain 28 peptides. Score 0.546 Round 3: 154 peptides, 22 chains. Longest chain 17 peptides. Score 0.481 Round 4: 159 peptides, 21 chains. Longest chain 37 peptides. Score 0.517 Round 5: 164 peptides, 23 chains. Longest chain 17 peptides. Score 0.502 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 135, Estimated correctness of the model 10.1 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2ig6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5383 reflections ( 97.84 % complete ) and 4730 restraints for refining 2182 atoms. 4123 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2169 (Rfree = 0.000) for 2182 atoms. Found 0 (11 requested) and removed 4 (8 requested) atoms. Cycle 47: After refmac, R = 0.2126 (Rfree = 0.000) for 2167 atoms. Found 0 (11 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2023 (Rfree = 0.000) for 2158 atoms. Found 0 (11 requested) and removed 4 (8 requested) atoms. Cycle 49: After refmac, R = 0.2007 (Rfree = 0.000) for 2153 atoms. TimeTaking 30.62