Sun 23 Dec 22:22:56 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 2o8q-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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/2o8q-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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 22:23:05 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/2o8q-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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 256 and 0 Target number of residues in the AU: 256 Target solvent content: 0.6514 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-3.8-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.85 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: 29.026 3.801 Wilson plot Bfac: 78.53 4222 reflections ( 98.37 % complete ) and 0 restraints for refining 2371 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3103 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3001 (Rfree = 0.000) for 2371 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.06 Search for helices and strands: 0 residues in 0 chains, 2406 seeds are put forward NCS extension: 0 residues added, 2406 seeds are put forward Round 1: 158 peptides, 25 chains. Longest chain 13 peptides. Score 0.430 Round 2: 180 peptides, 24 chains. Longest chain 20 peptides. Score 0.528 Round 3: 179 peptides, 20 chains. Longest chain 27 peptides. Score 0.585 Round 4: 193 peptides, 22 chains. Longest chain 37 peptides. Score 0.600 Round 5: 187 peptides, 21 chains. Longest chain 19 peptides. Score 0.596 Taking the results from Round 4 Chains 22, Residues 171, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3985 restraints for refining 1939 atoms. 3290 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2435 (Rfree = 0.000) for 1888 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2470 (Rfree = 0.000) for 1865 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2428 (Rfree = 0.000) for 1845 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 5: After refmac, R = 0.2402 (Rfree = 0.000) for 1827 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.09 Search for helices and strands: 0 residues in 0 chains, 1900 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 1923 seeds are put forward Round 1: 179 peptides, 22 chains. Longest chain 19 peptides. Score 0.555 Round 2: 197 peptides, 23 chains. Longest chain 18 peptides. Score 0.598 Round 3: 176 peptides, 20 chains. Longest chain 26 peptides. Score 0.576 Round 4: 195 peptides, 21 chains. Longest chain 32 peptides. Score 0.620 Round 5: 192 peptides, 19 chains. Longest chain 25 peptides. Score 0.638 Taking the results from Round 5 Chains 19, Residues 173, Estimated correctness of the model 15.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4088 restraints for refining 1939 atoms. 3415 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2508 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 7: After refmac, R = 0.2551 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 8: After refmac, R = 0.2484 (Rfree = 0.000) for 1893 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2444 (Rfree = 0.000) for 1881 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2474 (Rfree = 0.000) for 1872 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 1950 seeds are put forward NCS extension: 28 residues added (6 deleted due to clashes), 1978 seeds are put forward Round 1: 157 peptides, 21 chains. Longest chain 25 peptides. Score 0.494 Round 2: 163 peptides, 18 chains. Longest chain 18 peptides. Score 0.564 Round 3: 172 peptides, 22 chains. Longest chain 17 peptides. Score 0.532 Round 4: 183 peptides, 19 chains. Longest chain 19 peptides. Score 0.612 Round 5: 170 peptides, 19 chains. Longest chain 33 peptides. Score 0.571 Taking the results from Round 4 Chains 20, Residues 164, Estimated correctness of the model 4.3 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4108 restraints for refining 1938 atoms. 3433 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2611 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2575 (Rfree = 0.000) for 1917 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 13: After refmac, R = 0.2455 (Rfree = 0.000) for 1912 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 14: After refmac, R = 0.2373 (Rfree = 0.000) for 1897 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.2338 (Rfree = 0.000) for 1890 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 2.96 Search for helices and strands: 0 residues in 0 chains, 1922 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1935 seeds are put forward Round 1: 169 peptides, 25 chains. Longest chain 18 peptides. Score 0.472 Round 2: 177 peptides, 19 chains. Longest chain 24 peptides. Score 0.593 Round 3: 183 peptides, 24 chains. Longest chain 21 peptides. Score 0.538 Round 4: 186 peptides, 23 chains. Longest chain 28 peptides. Score 0.563 Round 5: 179 peptides, 23 chains. Longest chain 19 peptides. Score 0.540 Taking the results from Round 2 Chains 20, Residues 158, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3895 restraints for refining 1939 atoms. 3191 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2432 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2532 (Rfree = 0.000) for 1918 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 18: After refmac, R = 0.2187 (Rfree = 0.000) for 1905 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2295 (Rfree = 0.000) for 1899 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2083 (Rfree = 0.000) for 1900 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 2.96 Search for helices and strands: 0 residues in 0 chains, 1928 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 1962 seeds are put forward Round 1: 164 peptides, 25 chains. Longest chain 13 peptides. Score 0.454 Round 2: 171 peptides, 22 chains. Longest chain 29 peptides. Score 0.528 Round 3: 172 peptides, 22 chains. Longest chain 19 peptides. Score 0.532 Round 4: 172 peptides, 21 chains. Longest chain 20 peptides. Score 0.547 Round 5: 168 peptides, 21 chains. Longest chain 15 peptides. Score 0.533 Taking the results from Round 4 Chains 21, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4351 restraints for refining 1938 atoms. 3768 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2485 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2328 (Rfree = 0.000) for 1924 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.2278 (Rfree = 0.000) for 1911 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2233 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2187 (Rfree = 0.000) for 1905 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 2.89 Search for helices and strands: 0 residues in 0 chains, 1976 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2002 seeds are put forward Round 1: 151 peptides, 24 chains. Longest chain 13 peptides. Score 0.420 Round 2: 168 peptides, 22 chains. Longest chain 15 peptides. Score 0.518 Round 3: 180 peptides, 25 chains. Longest chain 11 peptides. Score 0.512 Round 4: 179 peptides, 22 chains. Longest chain 21 peptides. Score 0.555 Round 5: 177 peptides, 19 chains. Longest chain 21 peptides. Score 0.593 Taking the results from Round 5 Chains 20, Residues 158, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3926 restraints for refining 1939 atoms. 3191 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2393 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.2286 (Rfree = 0.000) for 1916 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2155 (Rfree = 0.000) for 1917 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2190 (Rfree = 0.000) for 1909 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 30: After refmac, R = 0.2132 (Rfree = 0.000) for 1904 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.94 Search for helices and strands: 0 residues in 0 chains, 1939 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1957 seeds are put forward Round 1: 145 peptides, 22 chains. Longest chain 18 peptides. Score 0.431 Round 2: 152 peptides, 24 chains. Longest chain 20 peptides. Score 0.424 Round 3: 161 peptides, 25 chains. Longest chain 12 peptides. Score 0.442 Round 4: 161 peptides, 24 chains. Longest chain 12 peptides. Score 0.459 Round 5: 166 peptides, 23 chains. Longest chain 18 peptides. Score 0.494 Taking the results from Round 5 Chains 23, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4308 restraints for refining 1938 atoms. 3759 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2344 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.2178 (Rfree = 0.000) for 1921 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2099 (Rfree = 0.000) for 1912 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.1980 (Rfree = 0.000) for 1904 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2001 (Rfree = 0.000) for 1899 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 1955 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1977 seeds are put forward Round 1: 160 peptides, 27 chains. Longest chain 13 peptides. Score 0.403 Round 2: 162 peptides, 23 chains. Longest chain 15 peptides. Score 0.480 Round 3: 175 peptides, 24 chains. Longest chain 19 peptides. Score 0.510 Round 4: 176 peptides, 24 chains. Longest chain 15 peptides. Score 0.514 Round 5: 170 peptides, 24 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 4 Chains 24, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4291 restraints for refining 1939 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2382 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 37: After refmac, R = 0.2317 (Rfree = 0.000) for 1929 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2271 (Rfree = 0.000) for 1926 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2185 (Rfree = 0.000) for 1920 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2065 (Rfree = 0.000) for 1918 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 1967 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1985 seeds are put forward Round 1: 156 peptides, 28 chains. Longest chain 10 peptides. Score 0.369 Round 2: 174 peptides, 30 chains. Longest chain 13 peptides. Score 0.408 Round 3: 171 peptides, 22 chains. Longest chain 23 peptides. Score 0.528 Round 4: 171 peptides, 22 chains. Longest chain 24 peptides. Score 0.528 Round 5: 167 peptides, 20 chains. Longest chain 27 peptides. Score 0.546 Taking the results from Round 5 Chains 20, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4235 restraints for refining 1938 atoms. 3667 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2299 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.2221 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2193 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.2108 (Rfree = 0.000) for 1937 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.1845 (Rfree = 0.000) for 1937 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 1990 seeds are put forward NCS extension: 47 residues added (4 deleted due to clashes), 2037 seeds are put forward Round 1: 124 peptides, 24 chains. Longest chain 13 peptides. Score 0.304 Round 2: 146 peptides, 20 chains. Longest chain 18 peptides. Score 0.470 Round 3: 138 peptides, 21 chains. Longest chain 13 peptides. Score 0.421 Round 4: 131 peptides, 18 chains. Longest chain 13 peptides. Score 0.447 Round 5: 142 peptides, 18 chains. Longest chain 13 peptides. Score 0.490 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 124, 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 2o8q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4222 reflections ( 98.37 % complete ) and 4421 restraints for refining 1939 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2515 (Rfree = 0.000) for 1939 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2432 (Rfree = 0.000) for 1926 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2536 (Rfree = 0.000) for 1916 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2321 (Rfree = 0.000) for 1907 atoms. TimeTaking 44.47