Sun 23 Dec 22:23:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ig6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:16 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/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.4-parrot-hancs/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-hancs.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-hancs.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 2679 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3181 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2933 (Rfree = 0.000) for 2679 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 2706 seeds are put forward NCS extension: 0 residues added, 2706 seeds are put forward Round 1: 171 peptides, 27 chains. Longest chain 16 peptides. Score 0.461 Round 2: 203 peptides, 22 chains. Longest chain 36 peptides. Score 0.649 Round 3: 195 peptides, 22 chains. Longest chain 41 peptides. Score 0.625 Round 4: 202 peptides, 23 chains. Longest chain 32 peptides. Score 0.632 Round 5: 204 peptides, 20 chains. Longest chain 38 peptides. Score 0.678 Taking the results from Round 5 Chains 22, Residues 184, Estimated correctness of the model 52.0 % 3 chains (69 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4072 restraints for refining 2214 atoms. 3067 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2465 (Rfree = 0.000) for 2214 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 2: After refmac, R = 0.2235 (Rfree = 0.000) for 2183 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2099 (Rfree = 0.000) for 2178 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 4: After refmac, R = 0.2015 (Rfree = 0.000) for 2174 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.1953 (Rfree = 0.000) for 2173 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 49 residues added (7 deleted due to clashes), 2270 seeds are put forward Round 1: 191 peptides, 26 chains. Longest chain 25 peptides. Score 0.552 Round 2: 192 peptides, 21 chains. Longest chain 31 peptides. Score 0.630 Round 3: 206 peptides, 21 chains. Longest chain 30 peptides. Score 0.670 Round 4: 220 peptides, 18 chains. Longest chain 48 peptides. Score 0.741 Round 5: 202 peptides, 17 chains. Longest chain 49 peptides. Score 0.710 Taking the results from Round 4 Chains 19, Residues 202, Estimated correctness of the model 67.8 % 2 chains (82 residues) have been docked in sequence Building loops using Loopy2018 19 chains (202 residues) following loop building 2 chains (82 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5383 reflections ( 97.84 % complete ) and 3595 restraints for refining 2182 atoms. 2454 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2437 (Rfree = 0.000) for 2182 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2218 (Rfree = 0.000) for 2163 atoms. Found 12 (16 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.2127 (Rfree = 0.000) for 2154 atoms. Found 6 (15 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.2000 (Rfree = 0.000) for 2141 atoms. Found 9 (15 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 2140 atoms. Found 5 (15 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 2210 seeds are put forward NCS extension: 94 residues added (21 deleted due to clashes), 2304 seeds are put forward Round 1: 191 peptides, 23 chains. Longest chain 35 peptides. Score 0.598 Round 2: 203 peptides, 20 chains. Longest chain 32 peptides. Score 0.675 Round 3: 186 peptides, 17 chains. Longest chain 47 peptides. Score 0.668 Round 4: 192 peptides, 16 chains. Longest chain 55 peptides. Score 0.697 Round 5: 187 peptides, 19 chains. Longest chain 30 peptides. Score 0.643 Taking the results from Round 4 Chains 16, Residues 176, Estimated correctness of the model 57.1 % 1 chains (54 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4141 restraints for refining 2182 atoms. 3219 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2460 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. Cycle 12: After refmac, R = 0.2293 (Rfree = 0.000) for 2170 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.2221 (Rfree = 0.000) for 2166 atoms. Found 7 (14 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2166 (Rfree = 0.000) for 2162 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2138 (Rfree = 0.000) for 2153 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 64 residues added (9 deleted due to clashes), 2279 seeds are put forward Round 1: 179 peptides, 23 chains. Longest chain 16 peptides. Score 0.557 Round 2: 201 peptides, 19 chains. Longest chain 24 peptides. Score 0.683 Round 3: 188 peptides, 20 chains. Longest chain 20 peptides. Score 0.632 Round 4: 194 peptides, 21 chains. Longest chain 27 peptides. Score 0.636 Round 5: 202 peptides, 20 chains. Longest chain 23 peptides. Score 0.672 Taking the results from Round 2 Chains 19, Residues 182, Estimated correctness of the model 53.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4714 restraints for refining 2182 atoms. 4005 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2382 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 8 (8 requested) atoms. Cycle 17: After refmac, R = 0.2273 (Rfree = 0.000) for 2188 atoms. Found 11 (14 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2176 (Rfree = 0.000) for 2190 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2157 (Rfree = 0.000) for 2185 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2113 (Rfree = 0.000) for 2180 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 2244 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 2278 seeds are put forward Round 1: 176 peptides, 24 chains. Longest chain 22 peptides. Score 0.530 Round 2: 188 peptides, 19 chains. Longest chain 35 peptides. Score 0.646 Round 3: 186 peptides, 22 chains. Longest chain 18 peptides. Score 0.596 Round 4: 190 peptides, 23 chains. Longest chain 21 peptides. Score 0.595 Round 5: 187 peptides, 22 chains. Longest chain 18 peptides. Score 0.600 Taking the results from Round 2 Chains 22, Residues 169, Estimated correctness of the model 43.0 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4248 restraints for refining 2182 atoms. 3399 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2326 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.2154 (Rfree = 0.000) for 2178 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2130 (Rfree = 0.000) for 2176 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2101 (Rfree = 0.000) for 2173 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2080 (Rfree = 0.000) for 2166 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, 2241 seeds are put forward NCS extension: 51 residues added (4 deleted due to clashes), 2292 seeds are put forward Round 1: 174 peptides, 27 chains. Longest chain 13 peptides. Score 0.473 Round 2: 188 peptides, 20 chains. Longest chain 27 peptides. Score 0.632 Round 3: 189 peptides, 21 chains. Longest chain 29 peptides. Score 0.621 Round 4: 185 peptides, 20 chains. Longest chain 27 peptides. Score 0.623 Round 5: 201 peptides, 19 chains. Longest chain 32 peptides. Score 0.683 Taking the results from Round 5 Chains 20, Residues 182, Estimated correctness of the model 53.4 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4335 restraints for refining 2182 atoms. 3521 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2548 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2342 (Rfree = 0.000) for 2175 atoms. Found 4 (14 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2254 (Rfree = 0.000) for 2166 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 2159 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2165 (Rfree = 0.000) for 2148 atoms. Found 3 (14 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.02 Search for helices and strands: 0 residues in 0 chains, 2204 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2228 seeds are put forward Round 1: 165 peptides, 26 chains. Longest chain 17 peptides. Score 0.454 Round 2: 166 peptides, 22 chains. Longest chain 19 peptides. Score 0.527 Round 3: 188 peptides, 23 chains. Longest chain 28 peptides. Score 0.588 Round 4: 187 peptides, 24 chains. Longest chain 24 peptides. Score 0.569 Round 5: 174 peptides, 21 chains. Longest chain 26 peptides. Score 0.571 Taking the results from Round 3 Chains 24, Residues 165, Estimated correctness of the model 24.7 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4520 restraints for refining 2181 atoms. 3778 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2380 (Rfree = 0.000) for 2181 atoms. Found 9 (14 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.2217 (Rfree = 0.000) for 2172 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.2142 (Rfree = 0.000) for 2166 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2091 (Rfree = 0.000) for 2156 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2055 (Rfree = 0.000) for 2148 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 2197 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2227 seeds are put forward Round 1: 159 peptides, 25 chains. Longest chain 15 peptides. Score 0.447 Round 2: 186 peptides, 27 chains. Longest chain 21 peptides. Score 0.518 Round 3: 174 peptides, 23 chains. Longest chain 17 peptides. Score 0.539 Round 4: 181 peptides, 24 chains. Longest chain 18 peptides. Score 0.548 Round 5: 189 peptides, 22 chains. Longest chain 25 peptides. Score 0.606 Taking the results from Round 5 Chains 24, Residues 167, Estimated correctness of the model 30.6 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4654 restraints for refining 2182 atoms. 3917 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2346 (Rfree = 0.000) for 2182 atoms. Found 14 (14 requested) and removed 17 (8 requested) atoms. Cycle 37: After refmac, R = 0.2203 (Rfree = 0.000) for 2170 atoms. Found 8 (14 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2116 (Rfree = 0.000) for 2169 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2089 (Rfree = 0.000) for 2161 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2080 (Rfree = 0.000) for 2153 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, 2194 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2220 seeds are put forward Round 1: 142 peptides, 22 chains. Longest chain 14 peptides. Score 0.432 Round 2: 168 peptides, 22 chains. Longest chain 17 peptides. Score 0.534 Round 3: 165 peptides, 20 chains. Longest chain 21 peptides. Score 0.556 Round 4: 166 peptides, 21 chains. Longest chain 20 peptides. Score 0.543 Round 5: 157 peptides, 19 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 3 Chains 20, Residues 145, Estimated correctness of the model 13.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5383 reflections ( 97.84 % complete ) and 4866 restraints for refining 2181 atoms. 4283 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2349 (Rfree = 0.000) for 2181 atoms. Found 7 (14 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2255 (Rfree = 0.000) for 2176 atoms. Found 7 (14 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2198 (Rfree = 0.000) for 2174 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2135 (Rfree = 0.000) for 2167 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2101 (Rfree = 0.000) for 2157 atoms. Found 1 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.04 Search for helices and strands: 0 residues in 0 chains, 2213 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 2238 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 13 peptides. Score 0.387 Round 2: 153 peptides, 24 chains. Longest chain 18 peptides. Score 0.441 Round 3: 152 peptides, 24 chains. Longest chain 28 peptides. Score 0.437 Round 4: 158 peptides, 22 chains. Longest chain 27 peptides. Score 0.496 Round 5: 159 peptides, 24 chains. Longest chain 28 peptides. Score 0.465 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 136, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 9 % 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 4822 restraints for refining 2182 atoms. 4236 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2216 (Rfree = 0.000) for 2182 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2236 (Rfree = 0.000) for 2170 atoms. Found 0 (14 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2144 (Rfree = 0.000) for 2159 atoms. Found 0 (14 requested) and removed 6 (8 requested) atoms. Cycle 49: After refmac, R = 0.2046 (Rfree = 0.000) for 2151 atoms. TimeTaking 45.43