Sun 23 Dec 23:42:50 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 2glz-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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/2glz-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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 23:42:55 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/2glz-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-4.0-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 263 and 0 Target number of residues in the AU: 263 Target solvent content: 0.6409 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.58 Input MTZ file: 2glz-4.0-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: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 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: 29.894 4.000 Wilson plot Bfac: 72.38 3639 reflections ( 99.62 % complete ) and 0 restraints for refining 2708 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3499 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2639 (Rfree = 0.000) for 2708 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.37 Search for helices and strands: 0 residues in 0 chains, 2743 seeds are put forward NCS extension: 0 residues added, 2743 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 10 peptides. Score 0.300 Round 2: 177 peptides, 27 chains. Longest chain 18 peptides. Score 0.470 Round 3: 185 peptides, 28 chains. Longest chain 14 peptides. Score 0.483 Round 4: 182 peptides, 25 chains. Longest chain 15 peptides. Score 0.520 Round 5: 186 peptides, 25 chains. Longest chain 22 peptides. Score 0.534 Taking the results from Round 5 Chains 25, Residues 161, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5012 restraints for refining 2211 atoms. 4357 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2595 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2428 (Rfree = 0.000) for 2192 atoms. Found 6 (10 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.2390 (Rfree = 0.000) for 2172 atoms. Found 6 (10 requested) and removed 18 (5 requested) atoms. Cycle 4: After refmac, R = 0.2371 (Rfree = 0.000) for 2156 atoms. Found 3 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2300 (Rfree = 0.000) for 2144 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.27 Search for helices and strands: 0 residues in 0 chains, 2253 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2276 seeds are put forward Round 1: 162 peptides, 28 chains. Longest chain 12 peptides. Score 0.395 Round 2: 167 peptides, 23 chains. Longest chain 19 peptides. Score 0.499 Round 3: 175 peptides, 25 chains. Longest chain 23 peptides. Score 0.495 Round 4: 171 peptides, 22 chains. Longest chain 18 peptides. Score 0.529 Round 5: 173 peptides, 23 chains. Longest chain 19 peptides. Score 0.520 Taking the results from Round 4 Chains 22, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5120 restraints for refining 2211 atoms. 4546 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2691 (Rfree = 0.000) for 2211 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.2480 (Rfree = 0.000) for 2203 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 2197 atoms. Found 0 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2377 (Rfree = 0.000) for 2189 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2337 (Rfree = 0.000) for 2188 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.36 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2289 seeds are put forward Round 1: 133 peptides, 22 chains. Longest chain 10 peptides. Score 0.383 Round 2: 156 peptides, 21 chains. Longest chain 14 peptides. Score 0.491 Round 3: 171 peptides, 23 chains. Longest chain 17 peptides. Score 0.513 Round 4: 174 peptides, 22 chains. Longest chain 18 peptides. Score 0.539 Round 5: 163 peptides, 23 chains. Longest chain 15 peptides. Score 0.484 Taking the results from Round 4 Chains 22, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 4981 restraints for refining 2211 atoms. 4395 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2596 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 12: After refmac, R = 0.2376 (Rfree = 0.000) for 2211 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2300 (Rfree = 0.000) for 2207 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2268 (Rfree = 0.000) for 2200 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2238 (Rfree = 0.000) for 2195 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.35 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2296 seeds are put forward Round 1: 146 peptides, 23 chains. Longest chain 19 peptides. Score 0.418 Round 2: 157 peptides, 22 chains. Longest chain 20 peptides. Score 0.478 Round 3: 154 peptides, 21 chains. Longest chain 18 peptides. Score 0.484 Round 4: 168 peptides, 20 chains. Longest chain 17 peptides. Score 0.550 Round 5: 154 peptides, 19 chains. Longest chain 13 peptides. Score 0.517 Taking the results from Round 4 Chains 20, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5034 restraints for refining 2211 atoms. 4462 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2513 (Rfree = 0.000) for 2211 atoms. Found 9 (10 requested) and removed 16 (5 requested) atoms. Cycle 17: After refmac, R = 0.2351 (Rfree = 0.000) for 2193 atoms. Found 3 (10 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2261 (Rfree = 0.000) for 2180 atoms. Found 2 (10 requested) and removed 12 (5 requested) atoms. Cycle 19: After refmac, R = 0.2274 (Rfree = 0.000) for 2164 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2217 (Rfree = 0.000) for 2157 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.33 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2269 seeds are put forward Round 1: 149 peptides, 25 chains. Longest chain 14 peptides. Score 0.394 Round 2: 165 peptides, 25 chains. Longest chain 12 peptides. Score 0.458 Round 3: 167 peptides, 24 chains. Longest chain 14 peptides. Score 0.482 Round 4: 160 peptides, 22 chains. Longest chain 18 peptides. Score 0.489 Round 5: 172 peptides, 23 chains. Longest chain 13 peptides. Score 0.516 Taking the results from Round 5 Chains 23, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5026 restraints for refining 2211 atoms. 4453 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2680 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 22: After refmac, R = 0.2482 (Rfree = 0.000) for 2205 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2393 (Rfree = 0.000) for 2195 atoms. Found 2 (10 requested) and removed 15 (5 requested) atoms. Cycle 24: After refmac, R = 0.2333 (Rfree = 0.000) for 2180 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2295 (Rfree = 0.000) for 2177 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2281 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2293 seeds are put forward Round 1: 137 peptides, 26 chains. Longest chain 9 peptides. Score 0.325 Round 2: 150 peptides, 21 chains. Longest chain 16 peptides. Score 0.469 Round 3: 147 peptides, 22 chains. Longest chain 17 peptides. Score 0.440 Round 4: 162 peptides, 25 chains. Longest chain 15 peptides. Score 0.446 Round 5: 157 peptides, 20 chains. Longest chain 19 peptides. Score 0.512 Taking the results from Round 5 Chains 20, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5043 restraints for refining 2206 atoms. 4515 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3040 (Rfree = 0.000) for 2206 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.2328 (Rfree = 0.000) for 2186 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2229 (Rfree = 0.000) for 2172 atoms. Found 0 (10 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.2207 (Rfree = 0.000) for 2158 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2091 (Rfree = 0.000) for 2154 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.28 Search for helices and strands: 0 residues in 0 chains, 2247 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2274 seeds are put forward Round 1: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.293 Round 2: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.336 Round 3: 136 peptides, 23 chains. Longest chain 13 peptides. Score 0.377 Round 4: 126 peptides, 17 chains. Longest chain 24 peptides. Score 0.446 Round 5: 131 peptides, 20 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 4 Chains 17, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5271 restraints for refining 2211 atoms. 4852 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2326 (Rfree = 0.000) for 2211 atoms. Found 5 (10 requested) and removed 13 (5 requested) atoms. Cycle 32: After refmac, R = 0.2194 (Rfree = 0.000) for 2197 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2147 (Rfree = 0.000) for 2185 atoms. Found 2 (10 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2193 (Rfree = 0.000) for 2173 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.2093 (Rfree = 0.000) for 2170 atoms. Found 0 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.27 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2296 seeds are put forward Round 1: 116 peptides, 24 chains. Longest chain 10 peptides. Score 0.267 Round 2: 134 peptides, 23 chains. Longest chain 12 peptides. Score 0.368 Round 3: 135 peptides, 24 chains. Longest chain 15 peptides. Score 0.354 Round 4: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.363 Round 5: 137 peptides, 23 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5212 restraints for refining 2210 atoms. 4779 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2526 (Rfree = 0.000) for 2210 atoms. Found 6 (10 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.2324 (Rfree = 0.000) for 2195 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2262 (Rfree = 0.000) for 2188 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2210 (Rfree = 0.000) for 2183 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2197 (Rfree = 0.000) for 2178 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.31 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2253 seeds are put forward Round 1: 107 peptides, 24 chains. Longest chain 6 peptides. Score 0.224 Round 2: 128 peptides, 24 chains. Longest chain 9 peptides. Score 0.323 Round 3: 135 peptides, 24 chains. Longest chain 14 peptides. Score 0.354 Round 4: 138 peptides, 25 chains. Longest chain 13 peptides. Score 0.348 Round 5: 130 peptides, 22 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 5 Chains 22, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3639 reflections ( 99.62 % complete ) and 5210 restraints for refining 2211 atoms. 4800 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2624 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2460 (Rfree = 0.000) for 2200 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2404 (Rfree = 0.000) for 2194 atoms. Found 0 (10 requested) and removed 13 (5 requested) atoms. Cycle 44: After refmac, R = 0.2495 (Rfree = 0.000) for 2180 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.2420 (Rfree = 0.000) for 2170 atoms. Found 5 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward NCS extension: 0 residues added, 2232 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 11 peptides. Score 0.267 Round 2: 110 peptides, 21 chains. Longest chain 10 peptides. Score 0.299 Round 3: 122 peptides, 19 chains. Longest chain 11 peptides. Score 0.392 Round 4: 121 peptides, 18 chains. Longest chain 24 peptides. Score 0.407 Round 5: 114 peptides, 20 chains. Longest chain 11 peptides. Score 0.338 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 103, 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 2glz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3639 reflections ( 99.62 % complete ) and 5188 restraints for refining 2211 atoms. 4794 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2674 (Rfree = 0.000) for 2211 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2686 (Rfree = 0.000) for 2202 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2767 (Rfree = 0.000) for 2195 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 49: After refmac, R = 0.2980 (Rfree = 0.000) for 2188 atoms. TimeTaking 32.72