Mon 24 Dec 08:01:32 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 2ig6-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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/2ig6-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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 08:01:36 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/2ig6-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.6-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 249 and 0 Target number of residues in the AU: 249 Target solvent content: 0.6378 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: 2ig6-3.6-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: 2ig6-3.6-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 3.600 Wilson plot Bfac: 70.35 4546 reflections ( 97.72 % complete ) and 0 restraints for refining 2641 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3358 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3000 (Rfree = 0.000) for 2641 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 2669 seeds are put forward NCS extension: 0 residues added, 2669 seeds are put forward Round 1: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.384 Round 2: 188 peptides, 25 chains. Longest chain 21 peptides. Score 0.557 Round 3: 185 peptides, 23 chains. Longest chain 33 peptides. Score 0.578 Round 4: 173 peptides, 22 chains. Longest chain 17 peptides. Score 0.552 Round 5: 183 peptides, 23 chains. Longest chain 28 peptides. Score 0.571 Taking the results from Round 3 Chains 23, Residues 162, Estimated correctness of the model 5.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4738 restraints for refining 2176 atoms. 4113 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2448 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2163 (Rfree = 0.000) for 2140 atoms. Found 5 (13 requested) and removed 15 (6 requested) atoms. Cycle 3: After refmac, R = 0.2073 (Rfree = 0.000) for 2121 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.1974 (Rfree = 0.000) for 2109 atoms. Found 8 (13 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.1891 (Rfree = 0.000) for 2102 atoms. Found 2 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 2162 seeds are put forward NCS extension: 42 residues added (3 deleted due to clashes), 2204 seeds are put forward Round 1: 176 peptides, 29 chains. Longest chain 15 peptides. Score 0.446 Round 2: 187 peptides, 23 chains. Longest chain 20 peptides. Score 0.585 Round 3: 189 peptides, 22 chains. Longest chain 16 peptides. Score 0.606 Round 4: 187 peptides, 19 chains. Longest chain 22 peptides. Score 0.643 Round 5: 195 peptides, 20 chains. Longest chain 25 peptides. Score 0.653 Taking the results from Round 5 Chains 20, Residues 175, Estimated correctness of the model 34.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4633 restraints for refining 2176 atoms. 3953 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2212 (Rfree = 0.000) for 2176 atoms. Found 6 (13 requested) and removed 17 (6 requested) atoms. Cycle 7: After refmac, R = 0.2089 (Rfree = 0.000) for 2154 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.1970 (Rfree = 0.000) for 2152 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.1975 (Rfree = 0.000) for 2146 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.1956 (Rfree = 0.000) for 2143 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2235 seeds are put forward Round 1: 162 peptides, 25 chains. Longest chain 15 peptides. Score 0.460 Round 2: 180 peptides, 22 chains. Longest chain 22 peptides. Score 0.576 Round 3: 182 peptides, 22 chains. Longest chain 18 peptides. Score 0.583 Round 4: 185 peptides, 22 chains. Longest chain 23 peptides. Score 0.593 Round 5: 185 peptides, 23 chains. Longest chain 31 peptides. Score 0.578 Taking the results from Round 4 Chains 22, Residues 163, Estimated correctness of the model 11.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4789 restraints for refining 2175 atoms. 4159 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2279 (Rfree = 0.000) for 2175 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 12: After refmac, R = 0.2220 (Rfree = 0.000) for 2173 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 13: After refmac, R = 0.2068 (Rfree = 0.000) for 2168 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2004 (Rfree = 0.000) for 2163 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1953 (Rfree = 0.000) for 2159 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2240 seeds are put forward Round 1: 175 peptides, 25 chains. Longest chain 18 peptides. Score 0.510 Round 2: 181 peptides, 22 chains. Longest chain 20 peptides. Score 0.580 Round 3: 179 peptides, 21 chains. Longest chain 20 peptides. Score 0.588 Round 4: 189 peptides, 24 chains. Longest chain 22 peptides. Score 0.576 Round 5: 193 peptides, 23 chains. Longest chain 17 peptides. Score 0.604 Taking the results from Round 5 Chains 23, Residues 170, Estimated correctness of the model 16.2 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4701 restraints for refining 2176 atoms. 4005 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2367 (Rfree = 0.000) for 2176 atoms. Found 9 (13 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.2118 (Rfree = 0.000) for 2161 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.1950 (Rfree = 0.000) for 2159 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1918 (Rfree = 0.000) for 2154 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.1852 (Rfree = 0.000) for 2152 atoms. Found 1 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2234 seeds are put forward Round 1: 171 peptides, 26 chains. Longest chain 17 peptides. Score 0.478 Round 2: 179 peptides, 23 chains. Longest chain 22 peptides. Score 0.557 Round 3: 185 peptides, 21 chains. Longest chain 22 peptides. Score 0.608 Round 4: 164 peptides, 21 chains. Longest chain 22 peptides. Score 0.536 Round 5: 161 peptides, 22 chains. Longest chain 22 peptides. Score 0.508 Taking the results from Round 3 Chains 21, Residues 164, Estimated correctness of the model 17.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4769 restraints for refining 2176 atoms. 4134 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2074 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.1968 (Rfree = 0.000) for 2174 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1879 (Rfree = 0.000) for 2172 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1801 (Rfree = 0.000) for 2169 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1726 (Rfree = 0.000) for 2162 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 2267 seeds are put forward Round 1: 148 peptides, 25 chains. Longest chain 14 peptides. Score 0.401 Round 2: 171 peptides, 24 chains. Longest chain 19 peptides. Score 0.512 Round 3: 173 peptides, 22 chains. Longest chain 18 peptides. Score 0.552 Round 4: 181 peptides, 23 chains. Longest chain 23 peptides. Score 0.564 Round 5: 185 peptides, 21 chains. Longest chain 23 peptides. Score 0.608 Taking the results from Round 5 Chains 22, Residues 164, Estimated correctness of the model 17.8 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4546 reflections ( 97.72 % complete ) and 4316 restraints for refining 2176 atoms. 3506 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2461 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 27: After refmac, R = 0.2267 (Rfree = 0.000) for 2163 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.2204 (Rfree = 0.000) for 2160 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2212 (Rfree = 0.000) for 2159 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.2076 (Rfree = 0.000) for 2162 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2246 seeds are put forward Round 1: 151 peptides, 23 chains. Longest chain 19 peptides. Score 0.451 Round 2: 161 peptides, 20 chains. Longest chain 17 peptides. Score 0.542 Round 3: 172 peptides, 22 chains. Longest chain 19 peptides. Score 0.549 Round 4: 164 peptides, 18 chains. Longest chain 34 peptides. Score 0.585 Round 5: 158 peptides, 19 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 4 Chains 20, Residues 146, Estimated correctness of the model 8.7 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4783 restraints for refining 2175 atoms. 4123 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2283 (Rfree = 0.000) for 2175 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.2168 (Rfree = 0.000) for 2173 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2062 (Rfree = 0.000) for 2171 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1807 (Rfree = 0.000) for 2169 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1767 (Rfree = 0.000) for 2167 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 2244 seeds are put forward NCS extension: 47 residues added (6 deleted due to clashes), 2291 seeds are put forward Round 1: 148 peptides, 24 chains. Longest chain 12 peptides. Score 0.420 Round 2: 156 peptides, 23 chains. Longest chain 14 peptides. Score 0.471 Round 3: 163 peptides, 24 chains. Longest chain 15 peptides. Score 0.481 Round 4: 175 peptides, 21 chains. Longest chain 23 peptides. Score 0.575 Round 5: 164 peptides, 22 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 4 Chains 21, Residues 154, Estimated correctness of the model 4.6 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4669 restraints for refining 2174 atoms. 3976 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2160 (Rfree = 0.000) for 2174 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.1964 (Rfree = 0.000) for 2168 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.1903 (Rfree = 0.000) for 2159 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1871 (Rfree = 0.000) for 2155 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1927 (Rfree = 0.000) for 2148 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 2217 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 2244 seeds are put forward Round 1: 142 peptides, 23 chains. Longest chain 14 peptides. Score 0.413 Round 2: 161 peptides, 23 chains. Longest chain 18 peptides. Score 0.491 Round 3: 160 peptides, 22 chains. Longest chain 15 peptides. Score 0.504 Round 4: 171 peptides, 21 chains. Longest chain 19 peptides. Score 0.561 Round 5: 173 peptides, 20 chains. Longest chain 19 peptides. Score 0.584 Taking the results from Round 5 Chains 21, Residues 153, Estimated correctness of the model 8.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4546 reflections ( 97.72 % complete ) and 4879 restraints for refining 2176 atoms. 4249 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2251 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2152 (Rfree = 0.000) for 2174 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2040 (Rfree = 0.000) for 2166 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.1995 (Rfree = 0.000) for 2156 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1924 (Rfree = 0.000) for 2151 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 2188 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2211 seeds are put forward Round 1: 124 peptides, 21 chains. Longest chain 9 peptides. Score 0.372 Round 2: 136 peptides, 19 chains. Longest chain 11 peptides. Score 0.463 Round 3: 138 peptides, 22 chains. Longest chain 12 peptides. Score 0.415 Round 4: 133 peptides, 19 chains. Longest chain 15 peptides. Score 0.450 Round 5: 130 peptides, 18 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 117, 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. 4546 reflections ( 97.72 % complete ) and 5213 restraints for refining 2175 atoms. 4764 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2181 (Rfree = 0.000) for 2175 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2037 (Rfree = 0.000) for 2164 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1937 (Rfree = 0.000) for 2156 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1849 (Rfree = 0.000) for 2147 atoms. TimeTaking 28.05