null Sun 23 Dec 22:23:10 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 2ig6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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/2ig6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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 22:23:19 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/2ig6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-4.0-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 240 and 0 Target number of residues in the AU: 240 Target solvent content: 0.6509 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: 2ig6-4.0-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: 2ig6-4.0-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 4.001 Wilson plot Bfac: 78.18 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3336 reflections ( 97.60 % complete ) and 0 restraints for refining 2651 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3489 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3257 (Rfree = 0.000) for 2651 atoms. Found 12 (12 requested) and removed 34 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 2663 seeds are put forward NCS extension: 0 residues added, 2663 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.299 Round 2: 131 peptides, 21 chains. Longest chain 14 peptides. Score 0.403 Round 3: 141 peptides, 22 chains. Longest chain 18 peptides. Score 0.427 Round 4: 151 peptides, 20 chains. Longest chain 17 peptides. Score 0.504 Round 5: 163 peptides, 21 chains. Longest chain 23 peptides. Score 0.532 Taking the results from Round 5 Chains 21, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4896 restraints for refining 2168 atoms. 4349 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2370 (Rfree = 0.000) for 2168 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.2481 (Rfree = 0.000) for 2138 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.2352 (Rfree = 0.000) for 2123 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 4: After refmac, R = 0.2249 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2198 (Rfree = 0.000) for 2097 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.33 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2172 seeds are put forward Round 1: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.377 Round 2: 164 peptides, 23 chains. Longest chain 15 peptides. Score 0.502 Round 3: 168 peptides, 21 chains. Longest chain 18 peptides. Score 0.550 Round 4: 157 peptides, 21 chains. Longest chain 16 peptides. Score 0.510 Round 5: 179 peptides, 20 chains. Longest chain 20 peptides. Score 0.604 Taking the results from Round 5 Chains 20, Residues 159, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4418 restraints for refining 2168 atoms. 3699 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2344 (Rfree = 0.000) for 2168 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.2213 (Rfree = 0.000) for 2144 atoms. Found 7 (10 requested) and removed 13 (5 requested) atoms. Cycle 8: After refmac, R = 0.2097 (Rfree = 0.000) for 2132 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.2069 (Rfree = 0.000) for 2127 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2016 (Rfree = 0.000) for 2117 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2166 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 2190 seeds are put forward Round 1: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.351 Round 2: 162 peptides, 26 chains. Longest chain 12 peptides. Score 0.442 Round 3: 162 peptides, 23 chains. Longest chain 15 peptides. Score 0.495 Round 4: 166 peptides, 21 chains. Longest chain 14 peptides. Score 0.543 Round 5: 176 peptides, 23 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 5 Chains 26, Residues 153, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4587 restraints for refining 2167 atoms. 3918 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2203 (Rfree = 0.000) for 2167 atoms. Found 8 (10 requested) and removed 25 (5 requested) atoms. Cycle 12: After refmac, R = 0.2076 (Rfree = 0.000) for 2139 atoms. Found 8 (10 requested) and removed 16 (5 requested) atoms. Cycle 13: After refmac, R = 0.2037 (Rfree = 0.000) for 2119 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 2107 atoms. Found 5 (10 requested) and removed 15 (5 requested) atoms. Cycle 15: After refmac, R = 0.1820 (Rfree = 0.000) for 2095 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 2154 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 2164 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 12 peptides. Score 0.355 Round 2: 144 peptides, 22 chains. Longest chain 14 peptides. Score 0.440 Round 3: 150 peptides, 22 chains. Longest chain 16 peptides. Score 0.465 Round 4: 154 peptides, 20 chains. Longest chain 18 peptides. Score 0.516 Round 5: 163 peptides, 22 chains. Longest chain 16 peptides. Score 0.516 Taking the results from Round 5 Chains 23, Residues 141, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4849 restraints for refining 2168 atoms. 4271 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2118 (Rfree = 0.000) for 2168 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.1982 (Rfree = 0.000) for 2149 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.1904 (Rfree = 0.000) for 2139 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.1862 (Rfree = 0.000) for 2130 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1848 (Rfree = 0.000) for 2125 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.37 Search for helices and strands: 0 residues in 0 chains, 2190 seeds are put forward NCS extension: 0 residues added, 2190 seeds are put forward Round 1: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.379 Round 2: 153 peptides, 23 chains. Longest chain 16 peptides. Score 0.459 Round 3: 149 peptides, 21 chains. Longest chain 17 peptides. Score 0.479 Round 4: 162 peptides, 22 chains. Longest chain 19 peptides. Score 0.512 Round 5: 161 peptides, 24 chains. Longest chain 12 peptides. Score 0.473 Taking the results from Round 4 Chains 22, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4942 restraints for refining 2168 atoms. 4404 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2041 (Rfree = 0.000) for 2168 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.1896 (Rfree = 0.000) for 2153 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.1800 (Rfree = 0.000) for 2142 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1741 (Rfree = 0.000) for 2132 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1718 (Rfree = 0.000) for 2125 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2187 seeds are put forward NCS extension: 35 residues added (5 deleted due to clashes), 2222 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 13 peptides. Score 0.355 Round 2: 151 peptides, 25 chains. Longest chain 11 peptides. Score 0.414 Round 3: 154 peptides, 24 chains. Longest chain 15 peptides. Score 0.445 Round 4: 146 peptides, 23 chains. Longest chain 16 peptides. Score 0.430 Round 5: 153 peptides, 20 chains. Longest chain 14 peptides. Score 0.512 Taking the results from Round 5 Chains 21, Residues 133, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4893 restraints for refining 2166 atoms. 4338 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2055 (Rfree = 0.000) for 2166 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.1881 (Rfree = 0.000) for 2133 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1850 (Rfree = 0.000) for 2124 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.1988 (Rfree = 0.000) for 2113 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2022 (Rfree = 0.000) for 2099 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 2164 seeds are put forward NCS extension: 0 residues added, 2164 seeds are put forward Round 1: 128 peptides, 24 chains. Longest chain 14 peptides. Score 0.330 Round 2: 134 peptides, 21 chains. Longest chain 14 peptides. Score 0.416 Round 3: 132 peptides, 20 chains. Longest chain 10 peptides. Score 0.427 Round 4: 122 peptides, 17 chains. Longest chain 16 peptides. Score 0.442 Round 5: 121 peptides, 17 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 4 Chains 17, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 5112 restraints for refining 2168 atoms. 4709 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1987 (Rfree = 0.000) for 2168 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2051 (Rfree = 0.000) for 2151 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2066 (Rfree = 0.000) for 2141 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 34: After refmac, R = 0.2080 (Rfree = 0.000) for 2124 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2057 (Rfree = 0.000) for 2108 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.32 Search for helices and strands: 0 residues in 0 chains, 2178 seeds are put forward NCS extension: 0 residues added, 2178 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.287 Round 2: 117 peptides, 19 chains. Longest chain 15 peptides. Score 0.380 Round 3: 113 peptides, 18 chains. Longest chain 22 peptides. Score 0.382 Round 4: 123 peptides, 19 chains. Longest chain 14 peptides. Score 0.407 Round 5: 130 peptides, 18 chains. Longest chain 25 peptides. Score 0.456 Taking the results from Round 5 Chains 18, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 5001 restraints for refining 2147 atoms. 4571 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2185 (Rfree = 0.000) for 2147 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 37: After refmac, R = 0.2048 (Rfree = 0.000) for 2116 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 38: After refmac, R = 0.2050 (Rfree = 0.000) for 2100 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2107 (Rfree = 0.000) for 2094 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.1856 (Rfree = 0.000) for 2084 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2159 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 2200 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 7 peptides. Score 0.223 Round 2: 132 peptides, 25 chains. Longest chain 12 peptides. Score 0.329 Round 3: 123 peptides, 22 chains. Longest chain 9 peptides. Score 0.347 Round 4: 127 peptides, 22 chains. Longest chain 12 peptides. Score 0.366 Round 5: 141 peptides, 23 chains. Longest chain 12 peptides. Score 0.409 Taking the results from Round 5 Chains 24, Residues 118, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3336 reflections ( 97.60 % complete ) and 4779 restraints for refining 2141 atoms. 4298 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1935 (Rfree = 0.000) for 2141 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.1761 (Rfree = 0.000) for 2126 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.1670 (Rfree = 0.000) for 2121 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.1645 (Rfree = 0.000) for 2115 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.1626 (Rfree = 0.000) for 2105 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 2141 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 2151 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.288 Round 2: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.355 Round 3: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.344 Round 4: 116 peptides, 18 chains. Longest chain 10 peptides. Score 0.396 Round 5: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 100, 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 2ig6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3336 reflections ( 97.60 % complete ) and 5153 restraints for refining 2168 atoms. 4771 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1849 (Rfree = 0.000) for 2168 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1767 (Rfree = 0.000) for 2153 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1747 (Rfree = 0.000) for 2146 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1745 (Rfree = 0.000) for 2139 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:06:13 GMT 2018 Job finished. TimeTaking 43.05 Used memory is bytes: 4329960