null Sun 23 Dec 22:23:05 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 2ig6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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/2ig6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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 22:23:13 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/2ig6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.8-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 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-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: 2ig6-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2400 target number of atoms Had to go as low as 0.75 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 2662 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3313 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3082 (Rfree = 0.000) for 2662 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.23 Search for helices and strands: 0 residues in 0 chains, 2698 seeds are put forward NCS extension: 0 residues added, 2698 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 17 peptides. Score 0.352 Round 2: 166 peptides, 24 chains. Longest chain 18 peptides. Score 0.493 Round 3: 176 peptides, 24 chains. Longest chain 15 peptides. Score 0.530 Round 4: 188 peptides, 24 chains. Longest chain 23 peptides. Score 0.573 Round 5: 198 peptides, 23 chains. Longest chain 20 peptides. Score 0.620 Taking the results from Round 5 Chains 23, Residues 175, Estimated correctness of the model 8.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4779 restraints for refining 2169 atoms. 4102 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 2169 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 2: After refmac, R = 0.2448 (Rfree = 0.000) for 2128 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2332 (Rfree = 0.000) for 2106 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 2101 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.2063 (Rfree = 0.000) for 2097 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2200 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2218 seeds are put forward Round 1: 171 peptides, 27 chains. Longest chain 17 peptides. Score 0.461 Round 2: 176 peptides, 23 chains. Longest chain 21 peptides. Score 0.547 Round 3: 183 peptides, 23 chains. Longest chain 21 peptides. Score 0.571 Round 4: 176 peptides, 21 chains. Longest chain 21 peptides. Score 0.578 Round 5: 178 peptides, 20 chains. Longest chain 24 peptides. Score 0.600 Taking the results from Round 5 Chains 20, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4705 restraints for refining 2171 atoms. 4093 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2359 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.2184 (Rfree = 0.000) for 2132 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2223 (Rfree = 0.000) for 2119 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 9: After refmac, R = 0.2051 (Rfree = 0.000) for 2112 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1991 (Rfree = 0.000) for 2114 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 2190 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 2231 seeds are put forward Round 1: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.373 Round 2: 162 peptides, 22 chains. Longest chain 18 peptides. Score 0.512 Round 3: 177 peptides, 23 chains. Longest chain 17 peptides. Score 0.550 Round 4: 175 peptides, 23 chains. Longest chain 17 peptides. Score 0.543 Round 5: 163 peptides, 21 chains. Longest chain 15 peptides. Score 0.532 Taking the results from Round 3 Chains 23, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4743 restraints for refining 2169 atoms. 4150 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2315 (Rfree = 0.000) for 2169 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.1941 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1838 (Rfree = 0.000) for 2149 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.1761 (Rfree = 0.000) for 2147 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.1689 (Rfree = 0.000) for 2151 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2230 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2252 seeds are put forward Round 1: 146 peptides, 22 chains. Longest chain 13 peptides. Score 0.448 Round 2: 167 peptides, 22 chains. Longest chain 14 peptides. Score 0.530 Round 3: 163 peptides, 20 chains. Longest chain 19 peptides. Score 0.549 Round 4: 166 peptides, 19 chains. Longest chain 22 peptides. Score 0.576 Round 5: 168 peptides, 18 chains. Longest chain 19 peptides. Score 0.598 Taking the results from Round 5 Chains 18, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4889 restraints for refining 2171 atoms. 4307 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2413 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2120 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.1859 (Rfree = 0.000) for 2156 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.1852 (Rfree = 0.000) for 2151 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.1800 (Rfree = 0.000) for 2146 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 2218 seeds are put forward NCS extension: 0 residues added, 2218 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 11 peptides. Score 0.370 Round 2: 155 peptides, 21 chains. Longest chain 20 peptides. Score 0.502 Round 3: 155 peptides, 19 chains. Longest chain 13 peptides. Score 0.536 Round 4: 159 peptides, 20 chains. Longest chain 20 peptides. Score 0.534 Round 5: 149 peptides, 20 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 3 Chains 19, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4938 restraints for refining 2170 atoms. 4413 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2009 (Rfree = 0.000) for 2170 atoms. Found 9 (11 requested) and removed 10 (5 requested) atoms. Cycle 22: After refmac, R = 0.1890 (Rfree = 0.000) for 2150 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.1911 (Rfree = 0.000) for 2148 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 24: After refmac, R = 0.1808 (Rfree = 0.000) for 2145 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.1785 (Rfree = 0.000) for 2145 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 2205 seeds are put forward NCS extension: 0 residues added, 2205 seeds are put forward Round 1: 140 peptides, 26 chains. Longest chain 9 peptides. Score 0.346 Round 2: 156 peptides, 24 chains. Longest chain 19 peptides. Score 0.453 Round 3: 143 peptides, 19 chains. Longest chain 20 peptides. Score 0.491 Round 4: 157 peptides, 22 chains. Longest chain 21 peptides. Score 0.493 Round 5: 151 peptides, 20 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 5 Chains 20, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5054 restraints for refining 2171 atoms. 4550 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2108 (Rfree = 0.000) for 2171 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.2038 (Rfree = 0.000) for 2159 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.1686 (Rfree = 0.000) for 2163 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 29: After refmac, R = 0.1812 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.1619 (Rfree = 0.000) for 2158 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2221 seeds are put forward Round 1: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.385 Round 2: 157 peptides, 21 chains. Longest chain 19 peptides. Score 0.510 Round 3: 156 peptides, 22 chains. Longest chain 17 peptides. Score 0.489 Round 4: 157 peptides, 21 chains. Longest chain 16 peptides. Score 0.510 Round 5: 168 peptides, 25 chains. Longest chain 18 peptides. Score 0.483 Taking the results from Round 4 Chains 21, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5004 restraints for refining 2171 atoms. 4481 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2211 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2244 (Rfree = 0.000) for 2154 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2722 (Rfree = 0.000) for 2140 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 34: After refmac, R = 0.2234 (Rfree = 0.000) for 2114 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 35: After refmac, R = 0.2376 (Rfree = 0.000) for 2110 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 2187 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2214 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 11 peptides. Score 0.302 Round 2: 144 peptides, 25 chains. Longest chain 14 peptides. Score 0.384 Round 3: 142 peptides, 23 chains. Longest chain 14 peptides. Score 0.413 Round 4: 121 peptides, 17 chains. Longest chain 13 peptides. Score 0.438 Round 5: 130 peptides, 20 chains. Longest chain 13 peptides. Score 0.418 Taking the results from Round 4 Chains 17, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 5164 restraints for refining 2171 atoms. 4765 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2097 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.1976 (Rfree = 0.000) for 2166 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.1946 (Rfree = 0.000) for 2162 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.1950 (Rfree = 0.000) for 2160 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 40: After refmac, R = 0.2033 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 2224 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2239 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 11 peptides. Score 0.266 Round 2: 141 peptides, 23 chains. Longest chain 15 peptides. Score 0.409 Round 3: 147 peptides, 24 chains. Longest chain 12 peptides. Score 0.415 Round 4: 147 peptides, 21 chains. Longest chain 16 peptides. Score 0.471 Round 5: 160 peptides, 23 chains. Longest chain 16 peptides. Score 0.487 Taking the results from Round 5 Chains 25, Residues 137, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3878 reflections ( 97.63 % complete ) and 4908 restraints for refining 2171 atoms. 4333 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2080 (Rfree = 0.000) for 2171 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2061 (Rfree = 0.000) for 2153 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.1955 (Rfree = 0.000) for 2148 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 44: After refmac, R = 0.2049 (Rfree = 0.000) for 2140 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.1867 (Rfree = 0.000) for 2131 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2203 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 8 peptides. Score 0.296 Round 2: 139 peptides, 24 chains. Longest chain 12 peptides. Score 0.381 Round 3: 129 peptides, 19 chains. Longest chain 15 peptides. Score 0.433 Round 4: 132 peptides, 20 chains. Longest chain 21 peptides. Score 0.427 Round 5: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 110, 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 5109 restraints for refining 2171 atoms. 4688 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2164 (Rfree = 0.000) for 2171 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2095 (Rfree = 0.000) for 2162 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1919 (Rfree = 0.000) for 2146 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1690 (Rfree = 0.000) for 2137 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:44 GMT 2018 Job finished. TimeTaking 43.66 Used memory is bytes: 9858312