Mon 24 Dec 00:56:34 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 2ig6-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-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/2ig6-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-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 00:56:38 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/2ig6-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-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 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-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: 2ig6-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2400 target number of atoms Had to go as low as 0.65 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 2653 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3100 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2687 (Rfree = 0.000) for 2653 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 2702 seeds are put forward NCS extension: 0 residues added, 2702 seeds are put forward Round 1: 174 peptides, 25 chains. Longest chain 14 peptides. Score 0.506 Round 2: 191 peptides, 25 chains. Longest chain 16 peptides. Score 0.568 Round 3: 196 peptides, 20 chains. Longest chain 19 peptides. Score 0.656 Round 4: 201 peptides, 21 chains. Longest chain 32 peptides. Score 0.656 Round 5: 204 peptides, 21 chains. Longest chain 33 peptides. Score 0.665 Taking the results from Round 5 Chains 21, Residues 183, Estimated correctness of the model 48.4 % 3 chains (66 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4000 restraints for refining 2207 atoms. 2998 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2563 (Rfree = 0.000) for 2207 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 2: After refmac, R = 0.2365 (Rfree = 0.000) for 2181 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2263 (Rfree = 0.000) for 2171 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2194 (Rfree = 0.000) for 2166 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.2144 (Rfree = 0.000) for 2155 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 20 residues added (9 deleted due to clashes), 2235 seeds are put forward Round 1: 178 peptides, 22 chains. Longest chain 15 peptides. Score 0.570 Round 2: 193 peptides, 21 chains. Longest chain 25 peptides. Score 0.633 Round 3: 189 peptides, 15 chains. Longest chain 29 peptides. Score 0.702 Round 4: 182 peptides, 17 chains. Longest chain 29 peptides. Score 0.656 Round 5: 188 peptides, 20 chains. Longest chain 19 peptides. Score 0.632 Taking the results from Round 3 Chains 18, Residues 174, Estimated correctness of the model 58.4 % 3 chains (42 residues) have been docked in sequence Building loops using Loopy2018 18 chains (174 residues) following loop building 3 chains (42 residues) in sequence following loop building ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4234 restraints for refining 2182 atoms. 3372 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2487 (Rfree = 0.000) for 2182 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 7: After refmac, R = 0.2325 (Rfree = 0.000) for 2173 atoms. Found 14 (16 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2253 (Rfree = 0.000) for 2172 atoms. Found 5 (15 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.2271 (Rfree = 0.000) for 2167 atoms. Found 3 (15 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2202 (Rfree = 0.000) for 2161 atoms. Found 2 (15 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2229 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 2265 seeds are put forward Round 1: 180 peptides, 24 chains. Longest chain 26 peptides. Score 0.545 Round 2: 201 peptides, 22 chains. Longest chain 27 peptides. Score 0.643 Round 3: 197 peptides, 21 chains. Longest chain 26 peptides. Score 0.645 Round 4: 203 peptides, 23 chains. Longest chain 22 peptides. Score 0.635 Round 5: 206 peptides, 22 chains. Longest chain 25 peptides. Score 0.657 Taking the results from Round 5 Chains 24, Residues 184, Estimated correctness of the model 46.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4680 restraints for refining 2182 atoms. 3922 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2467 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 12: After refmac, R = 0.2260 (Rfree = 0.000) for 2177 atoms. Found 2 (14 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.2206 (Rfree = 0.000) for 2167 atoms. Found 4 (14 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.2144 (Rfree = 0.000) for 2161 atoms. Found 5 (14 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2113 (Rfree = 0.000) for 2157 atoms. Found 6 (14 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 2204 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 2217 seeds are put forward Round 1: 189 peptides, 26 chains. Longest chain 17 peptides. Score 0.545 Round 2: 205 peptides, 23 chains. Longest chain 29 peptides. Score 0.641 Round 3: 213 peptides, 21 chains. Longest chain 29 peptides. Score 0.689 Round 4: 202 peptides, 21 chains. Longest chain 33 peptides. Score 0.659 Round 5: 215 peptides, 22 chains. Longest chain 23 peptides. Score 0.682 Taking the results from Round 3 Chains 23, Residues 192, Estimated correctness of the model 55.0 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4283 restraints for refining 2181 atoms. 3373 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2335 (Rfree = 0.000) for 2181 atoms. Found 12 (14 requested) and removed 18 (8 requested) atoms. Cycle 17: After refmac, R = 0.2201 (Rfree = 0.000) for 2171 atoms. Found 9 (14 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2121 (Rfree = 0.000) for 2168 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 2162 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2072 (Rfree = 0.000) for 2155 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.02 Search for helices and strands: 0 residues in 0 chains, 2198 seeds are put forward NCS extension: 46 residues added (5 deleted due to clashes), 2244 seeds are put forward Round 1: 179 peptides, 25 chains. Longest chain 26 peptides. Score 0.525 Round 2: 194 peptides, 22 chains. Longest chain 28 peptides. Score 0.622 Round 3: 185 peptides, 23 chains. Longest chain 22 peptides. Score 0.578 Round 4: 197 peptides, 22 chains. Longest chain 29 peptides. Score 0.631 Round 5: 204 peptides, 27 chains. Longest chain 19 peptides. Score 0.581 Taking the results from Round 4 Chains 25, Residues 175, Estimated correctness of the model 38.5 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4388 restraints for refining 2182 atoms. 3570 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2215 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.1977 (Rfree = 0.000) for 2176 atoms. Found 5 (14 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.1940 (Rfree = 0.000) for 2167 atoms. Found 4 (14 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1890 (Rfree = 0.000) for 2159 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1869 (Rfree = 0.000) for 2154 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.05 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: 170 peptides, 20 chains. Longest chain 26 peptides. Score 0.574 Round 2: 178 peptides, 21 chains. Longest chain 21 peptides. Score 0.585 Round 3: 185 peptides, 20 chains. Longest chain 17 peptides. Score 0.623 Round 4: 178 peptides, 20 chains. Longest chain 20 peptides. Score 0.600 Round 5: 182 peptides, 20 chains. Longest chain 39 peptides. Score 0.613 Taking the results from Round 3 Chains 21, Residues 165, Estimated correctness of the model 36.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4600 restraints for refining 2182 atoms. 3860 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2279 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.2097 (Rfree = 0.000) for 2179 atoms. Found 10 (14 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2063 (Rfree = 0.000) for 2179 atoms. Found 5 (14 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2007 (Rfree = 0.000) for 2175 atoms. Found 3 (14 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1998 (Rfree = 0.000) for 2168 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2206 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2219 seeds are put forward Round 1: 175 peptides, 24 chains. Longest chain 24 peptides. Score 0.527 Round 2: 191 peptides, 27 chains. Longest chain 19 peptides. Score 0.537 Round 3: 179 peptides, 21 chains. Longest chain 20 peptides. Score 0.588 Round 4: 167 peptides, 19 chains. Longest chain 26 peptides. Score 0.579 Round 5: 175 peptides, 22 chains. Longest chain 20 peptides. Score 0.559 Taking the results from Round 3 Chains 21, Residues 158, Estimated correctness of the model 24.7 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4438 restraints for refining 2182 atoms. 3675 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2267 (Rfree = 0.000) for 2182 atoms. Found 12 (14 requested) and removed 16 (8 requested) atoms. Cycle 32: After refmac, R = 0.2043 (Rfree = 0.000) for 2176 atoms. Found 7 (14 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1975 (Rfree = 0.000) for 2170 atoms. Found 4 (14 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1962 (Rfree = 0.000) for 2163 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1834 (Rfree = 0.000) for 2158 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 2213 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 2244 seeds are put forward Round 1: 158 peptides, 17 chains. Longest chain 27 peptides. Score 0.580 Round 2: 174 peptides, 20 chains. Longest chain 27 peptides. Score 0.587 Round 3: 191 peptides, 19 chains. Longest chain 27 peptides. Score 0.655 Round 4: 168 peptides, 17 chains. Longest chain 28 peptides. Score 0.613 Round 5: 174 peptides, 22 chains. Longest chain 28 peptides. Score 0.556 Taking the results from Round 3 Chains 20, Residues 172, Estimated correctness of the model 45.6 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4290 restraints for refining 2182 atoms. 3422 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2283 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. Cycle 37: After refmac, R = 0.2046 (Rfree = 0.000) for 2171 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1974 (Rfree = 0.000) for 2166 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1946 (Rfree = 0.000) for 2160 atoms. Found 1 (14 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1941 (Rfree = 0.000) for 2151 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2197 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2232 seeds are put forward Round 1: 167 peptides, 21 chains. Longest chain 27 peptides. Score 0.547 Round 2: 173 peptides, 17 chains. Longest chain 35 peptides. Score 0.629 Round 3: 167 peptides, 22 chains. Longest chain 22 peptides. Score 0.530 Round 4: 179 peptides, 20 chains. Longest chain 20 peptides. Score 0.604 Round 5: 179 peptides, 24 chains. Longest chain 27 peptides. Score 0.541 Taking the results from Round 2 Chains 18, Residues 156, Estimated correctness of the model 37.9 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4502 restraints for refining 2182 atoms. 3737 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2196 (Rfree = 0.000) for 2182 atoms. Found 9 (14 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.2049 (Rfree = 0.000) for 2174 atoms. Found 5 (14 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2023 (Rfree = 0.000) for 2170 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2008 (Rfree = 0.000) for 2164 atoms. Found 3 (14 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1994 (Rfree = 0.000) for 2157 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 2250 seeds are put forward Round 1: 157 peptides, 20 chains. Longest chain 19 peptides. Score 0.527 Round 2: 168 peptides, 21 chains. Longest chain 22 peptides. Score 0.550 Round 3: 175 peptides, 21 chains. Longest chain 22 peptides. Score 0.575 Round 4: 170 peptides, 19 chains. Longest chain 24 peptides. Score 0.589 Round 5: 175 peptides, 23 chains. Longest chain 21 peptides. Score 0.543 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 151, Estimated correctness of the model 25.0 % 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. 5383 reflections ( 97.84 % complete ) and 4890 restraints for refining 2182 atoms. 4305 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2181 (Rfree = 0.000) for 2182 atoms. Found 0 (14 requested) and removed 4 (8 requested) atoms. Cycle 47: After refmac, R = 0.2096 (Rfree = 0.000) for 2176 atoms. Found 0 (14 requested) and removed 0 (8 requested) atoms. Cycle 48: After refmac, R = 0.2077 (Rfree = 0.000) for 2175 atoms. Found 0 (14 requested) and removed 1 (8 requested) atoms. Cycle 49: After refmac, R = 0.2079 (Rfree = 0.000) for 2174 atoms. TimeTaking 29.55