Sun 23 Dec 23:55:22 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 2ig6-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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/2ig6-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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 ============================================================ Sun 23 Dec 23:55:27 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/2ig6-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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 244 and 0 Target number of residues in the AU: 244 Target solvent content: 0.6451 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: 2ig6-3.8-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: 2ig6-3.8-parrot-mrncs.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 3.800 Wilson plot Bfac: 74.43 3878 reflections ( 97.63 % complete ) and 0 restraints for refining 2660 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3271 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3244 (Rfree = 0.000) for 2660 atoms. Found 14 (14 requested) and removed 48 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2671 seeds are put forward NCS extension: 0 residues added, 2671 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 11 peptides. Score 0.332 Round 2: 159 peptides, 20 chains. Longest chain 14 peptides. Score 0.534 Round 3: 155 peptides, 18 chains. Longest chain 16 peptides. Score 0.553 Round 4: 171 peptides, 18 chains. Longest chain 25 peptides. Score 0.608 Round 5: 158 peptides, 18 chains. Longest chain 20 peptides. Score 0.564 Taking the results from Round 4 Chains 20, Residues 153, Estimated correctness of the model 2.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4721 restraints for refining 2166 atoms. 4071 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2609 (Rfree = 0.000) for 2166 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.2376 (Rfree = 0.000) for 2124 atoms. Found 6 (11 requested) and removed 15 (5 requested) atoms. Cycle 3: After refmac, R = 0.2263 (Rfree = 0.000) for 2088 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2161 (Rfree = 0.000) for 2068 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2032 (Rfree = 0.000) for 2061 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2143 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2175 seeds are put forward Round 1: 154 peptides, 22 chains. Longest chain 27 peptides. Score 0.481 Round 2: 179 peptides, 27 chains. Longest chain 25 peptides. Score 0.492 Round 3: 190 peptides, 29 chains. Longest chain 15 peptides. Score 0.501 Round 4: 197 peptides, 24 chains. Longest chain 33 peptides. Score 0.602 Round 5: 181 peptides, 24 chains. Longest chain 20 peptides. Score 0.548 Taking the results from Round 4 Chains 24, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4728 restraints for refining 2171 atoms. 4060 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2121 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 7: After refmac, R = 0.1942 (Rfree = 0.000) for 2143 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.1886 (Rfree = 0.000) for 2124 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.1875 (Rfree = 0.000) for 2106 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1866 (Rfree = 0.000) for 2102 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2178 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2205 seeds are put forward Round 1: 158 peptides, 28 chains. Longest chain 14 peptides. Score 0.388 Round 2: 163 peptides, 24 chains. Longest chain 14 peptides. Score 0.481 Round 3: 173 peptides, 21 chains. Longest chain 17 peptides. Score 0.568 Round 4: 178 peptides, 22 chains. Longest chain 18 peptides. Score 0.570 Round 5: 176 peptides, 22 chains. Longest chain 33 peptides. Score 0.563 Taking the results from Round 4 Chains 22, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4872 restraints for refining 2171 atoms. 4270 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2303 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 12: After refmac, R = 0.2349 (Rfree = 0.000) for 2146 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.2153 (Rfree = 0.000) for 2136 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.1990 (Rfree = 0.000) for 2130 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.1903 (Rfree = 0.000) for 2126 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.23 Search for helices and strands: 0 residues in 0 chains, 2230 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2258 seeds are put forward Round 1: 161 peptides, 24 chains. Longest chain 15 peptides. Score 0.473 Round 2: 171 peptides, 23 chains. Longest chain 15 peptides. Score 0.529 Round 3: 170 peptides, 23 chains. Longest chain 17 peptides. Score 0.525 Round 4: 169 peptides, 22 chains. Longest chain 15 peptides. Score 0.538 Round 5: 158 peptides, 21 chains. Longest chain 14 peptides. Score 0.514 Taking the results from Round 4 Chains 23, Residues 147, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4805 restraints for refining 2171 atoms. 4178 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2118 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.1966 (Rfree = 0.000) for 2148 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.1928 (Rfree = 0.000) for 2137 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.1639 (Rfree = 0.000) for 2130 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.1707 (Rfree = 0.000) for 2121 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2191 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2204 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 16 peptides. Score 0.366 Round 2: 149 peptides, 25 chains. Longest chain 12 peptides. Score 0.405 Round 3: 153 peptides, 21 chains. Longest chain 18 peptides. Score 0.494 Round 4: 154 peptides, 22 chains. Longest chain 14 peptides. Score 0.481 Round 5: 168 peptides, 22 chains. Longest chain 18 peptides. Score 0.534 Taking the results from Round 5 Chains 22, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5007 restraints for refining 2171 atoms. 4445 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2298 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.1884 (Rfree = 0.000) for 2153 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.1742 (Rfree = 0.000) for 2149 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1636 (Rfree = 0.000) for 2147 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1615 (Rfree = 0.000) for 2141 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 2239 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 2263 seeds are put forward Round 1: 148 peptides, 29 chains. Longest chain 13 peptides. Score 0.325 Round 2: 184 peptides, 29 chains. Longest chain 26 peptides. Score 0.478 Round 3: 167 peptides, 25 chains. Longest chain 20 peptides. Score 0.480 Round 4: 174 peptides, 27 chains. Longest chain 21 peptides. Score 0.473 Round 5: 164 peptides, 24 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 5 Chains 24, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5007 restraints for refining 2171 atoms. 4471 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1929 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.1902 (Rfree = 0.000) for 2162 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1808 (Rfree = 0.000) for 2159 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.1839 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.1541 (Rfree = 0.000) for 2153 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2210 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 2234 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 7 peptides. Score 0.258 Round 2: 135 peptides, 22 chains. Longest chain 14 peptides. Score 0.401 Round 3: 147 peptides, 24 chains. Longest chain 15 peptides. Score 0.415 Round 4: 135 peptides, 22 chains. Longest chain 12 peptides. Score 0.401 Round 5: 145 peptides, 23 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 5 Chains 23, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5139 restraints for refining 2170 atoms. 4674 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2099 (Rfree = 0.000) for 2170 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2295 (Rfree = 0.000) for 2158 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1933 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.1964 (Rfree = 0.000) for 2150 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 2146 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.26 Search for helices and strands: 0 residues in 0 chains, 2214 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2233 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 10 peptides. Score 0.265 Round 2: 147 peptides, 27 chains. Longest chain 9 peptides. Score 0.359 Round 3: 141 peptides, 24 chains. Longest chain 10 peptides. Score 0.389 Round 4: 152 peptides, 24 chains. Longest chain 14 peptides. Score 0.437 Round 5: 137 peptides, 24 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 4 Chains 24, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5085 restraints for refining 2170 atoms. 4597 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2171 (Rfree = 0.000) for 2170 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.2283 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.2378 (Rfree = 0.000) for 2141 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.1935 (Rfree = 0.000) for 2136 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.1831 (Rfree = 0.000) for 2132 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2213 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2226 seeds are put forward Round 1: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Round 2: 128 peptides, 23 chains. Longest chain 8 peptides. Score 0.350 Round 3: 137 peptides, 21 chains. Longest chain 14 peptides. Score 0.429 Round 4: 135 peptides, 20 chains. Longest chain 12 peptides. Score 0.440 Round 5: 155 peptides, 20 chains. Longest chain 21 peptides. Score 0.519 Taking the results from Round 5 Chains 20, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5002 restraints for refining 2170 atoms. 4482 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2257 (Rfree = 0.000) for 2170 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 42: After refmac, R = 0.2040 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1844 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.1891 (Rfree = 0.000) for 2154 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1728 (Rfree = 0.000) for 2153 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2245 seeds are put forward NCS extension: 42 residues added (1 deleted due to clashes), 2287 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.252 Round 2: 130 peptides, 23 chains. Longest chain 8 peptides. Score 0.360 Round 3: 143 peptides, 24 chains. Longest chain 15 peptides. Score 0.398 Round 4: 151 peptides, 22 chains. Longest chain 15 peptides. Score 0.469 Round 5: 131 peptides, 22 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 129, 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. 3878 reflections ( 97.63 % complete ) and 5175 restraints for refining 2171 atoms. 4681 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1972 (Rfree = 0.000) for 2171 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1777 (Rfree = 0.000) for 2160 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1753 (Rfree = 0.000) for 2154 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1710 (Rfree = 0.000) for 2148 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 28.7