null Mon 24 Dec 07:30:23 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p1a-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:30:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-noncs/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 207 and 0 Target number of residues in the AU: 207 Target solvent content: 0.6351 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-3.2-parrot-noncs.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: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.60 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: 29.570 3.200 Wilson plot Bfac: 69.16 5403 reflections ( 99.41 % complete ) and 0 restraints for refining 2757 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3498 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3126 (Rfree = 0.000) for 2757 atoms. Found 16 (24 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.47 Search for helices and strands: 0 residues in 0 chains, 2825 seeds are put forward NCS extension: 0 residues added, 2825 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 9 peptides. Score 0.250 Round 2: 126 peptides, 24 chains. Longest chain 10 peptides. Score 0.344 Round 3: 128 peptides, 24 chains. Longest chain 10 peptides. Score 0.355 Round 4: 136 peptides, 23 chains. Longest chain 13 peptides. Score 0.419 Round 5: 135 peptides, 23 chains. Longest chain 13 peptides. Score 0.414 Taking the results from Round 4 Chains 23, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5289 restraints for refining 2249 atoms. 4860 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2951 (Rfree = 0.000) for 2249 atoms. Found 10 (20 requested) and removed 21 (10 requested) atoms. Cycle 2: After refmac, R = 0.2792 (Rfree = 0.000) for 2206 atoms. Found 15 (20 requested) and removed 14 (10 requested) atoms. Cycle 3: After refmac, R = 0.2552 (Rfree = 0.000) for 2189 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2768 (Rfree = 0.000) for 2179 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 5: After refmac, R = 0.2384 (Rfree = 0.000) for 2174 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.43 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward NCS extension: 0 residues added, 2299 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 6 peptides. Score 0.265 Round 2: 120 peptides, 24 chains. Longest chain 7 peptides. Score 0.311 Round 3: 132 peptides, 27 chains. Longest chain 7 peptides. Score 0.308 Round 4: 132 peptides, 24 chains. Longest chain 10 peptides. Score 0.377 Round 5: 146 peptides, 27 chains. Longest chain 11 peptides. Score 0.383 Taking the results from Round 5 Chains 27, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5008 restraints for refining 2154 atoms. 4559 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2809 (Rfree = 0.000) for 2154 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2433 (Rfree = 0.000) for 2140 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2375 (Rfree = 0.000) for 2137 atoms. Found 10 (19 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.2185 (Rfree = 0.000) for 2133 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. Cycle 10: After refmac, R = 0.2386 (Rfree = 0.000) for 2121 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.44 Search for helices and strands: 0 residues in 0 chains, 2258 seeds are put forward NCS extension: 0 residues added, 2258 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.242 Round 2: 127 peptides, 21 chains. Longest chain 14 peptides. Score 0.418 Round 3: 119 peptides, 21 chains. Longest chain 9 peptides. Score 0.376 Round 4: 117 peptides, 21 chains. Longest chain 11 peptides. Score 0.365 Round 5: 125 peptides, 21 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 2 Chains 21, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5030 restraints for refining 2162 atoms. 4627 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2327 (Rfree = 0.000) for 2162 atoms. Found 9 (19 requested) and removed 15 (9 requested) atoms. Cycle 12: After refmac, R = 0.2263 (Rfree = 0.000) for 2153 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 13: After refmac, R = 0.2223 (Rfree = 0.000) for 2148 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2928 (Rfree = 0.000) for 2135 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.2827 (Rfree = 0.000) for 2139 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 0 residues added, 2248 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.263 Round 2: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.339 Round 3: 105 peptides, 17 chains. Longest chain 13 peptides. Score 0.394 Round 4: 105 peptides, 16 chains. Longest chain 12 peptides. Score 0.418 Round 5: 107 peptides, 16 chains. Longest chain 11 peptides. Score 0.428 Taking the results from Round 5 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5307 restraints for refining 2204 atoms. 4959 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2607 (Rfree = 0.000) for 2204 atoms. Found 19 (19 requested) and removed 45 (9 requested) atoms. Cycle 17: After refmac, R = 0.2648 (Rfree = 0.000) for 2172 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 18: After refmac, R = 0.2357 (Rfree = 0.000) for 2165 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. Cycle 19: After refmac, R = 0.2985 (Rfree = 0.000) for 2162 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2454 (Rfree = 0.000) for 2162 atoms. Found 13 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2295 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 8 peptides. Score 0.266 Round 2: 117 peptides, 23 chains. Longest chain 9 peptides. Score 0.318 Round 3: 124 peptides, 24 chains. Longest chain 10 peptides. Score 0.333 Round 4: 125 peptides, 22 chains. Longest chain 12 peptides. Score 0.385 Round 5: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 5 Chains 21, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5083 restraints for refining 2168 atoms. 4704 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2487 (Rfree = 0.000) for 2168 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. Cycle 22: After refmac, R = 0.2454 (Rfree = 0.000) for 2163 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 23: After refmac, R = 0.2295 (Rfree = 0.000) for 2164 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2372 (Rfree = 0.000) for 2163 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 25: After refmac, R = 0.2293 (Rfree = 0.000) for 2149 atoms. Found 16 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 2246 seeds are put forward NCS extension: 0 residues added, 2246 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 9 peptides. Score 0.273 Round 2: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.304 Round 3: 108 peptides, 20 chains. Longest chain 13 peptides. Score 0.339 Round 4: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.319 Round 5: 122 peptides, 21 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5007 restraints for refining 2198 atoms. 4624 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2518 (Rfree = 0.000) for 2198 atoms. Found 18 (19 requested) and removed 18 (9 requested) atoms. Cycle 27: After refmac, R = 0.2555 (Rfree = 0.000) for 2190 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2357 (Rfree = 0.000) for 2181 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 29: After refmac, R = 0.2302 (Rfree = 0.000) for 2176 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.2226 (Rfree = 0.000) for 2177 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 2269 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2295 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 8 peptides. Score 0.216 Round 2: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.265 Round 3: 85 peptides, 17 chains. Longest chain 11 peptides. Score 0.279 Round 4: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.291 Round 5: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.259 Taking the results from Round 4 Chains 17, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5421 restraints for refining 2219 atoms. 5158 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2424 (Rfree = 0.000) for 2219 atoms. Found 15 (19 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.2327 (Rfree = 0.000) for 2219 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2460 (Rfree = 0.000) for 2213 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.2254 (Rfree = 0.000) for 2217 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.2251 (Rfree = 0.000) for 2206 atoms. Found 15 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.35 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward NCS extension: 0 residues added, 2304 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.221 Round 2: 98 peptides, 21 chains. Longest chain 11 peptides. Score 0.256 Round 3: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.319 Round 4: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.285 Round 5: 89 peptides, 17 chains. Longest chain 8 peptides. Score 0.303 Taking the results from Round 3 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5341 restraints for refining 2210 atoms. 5047 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2303 (Rfree = 0.000) for 2210 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2236 (Rfree = 0.000) for 2209 atoms. Found 13 (19 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2278 (Rfree = 0.000) for 2211 atoms. Found 15 (19 requested) and removed 20 (9 requested) atoms. Cycle 39: After refmac, R = 0.2271 (Rfree = 0.000) for 2199 atoms. Found 16 (19 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.2221 (Rfree = 0.000) for 2203 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.35 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward NCS extension: 0 residues added, 2274 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.252 Round 2: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.301 Round 3: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.323 Round 4: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 5: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.313 Taking the results from Round 3 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5317 restraints for refining 2210 atoms. 5045 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2258 (Rfree = 0.000) for 2210 atoms. Found 12 (19 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.2364 (Rfree = 0.000) for 2212 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2225 (Rfree = 0.000) for 2211 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.2265 (Rfree = 0.000) for 2206 atoms. Found 18 (19 requested) and removed 12 (9 requested) atoms. Cycle 45: After refmac, R = 0.2213 (Rfree = 0.000) for 2211 atoms. Found 15 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.36 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward NCS extension: 0 residues added, 2304 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.202 Round 2: 74 peptides, 14 chains. Longest chain 7 peptides. Score 0.291 Round 3: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.274 Round 4: 74 peptides, 15 chains. Longest chain 6 peptides. Score 0.263 Round 5: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 66, 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 2p1a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5403 reflections ( 99.41 % complete ) and 5402 restraints for refining 2226 atoms. 5153 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2240 (Rfree = 0.000) for 2226 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2361 (Rfree = 0.000) for 2213 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2141 (Rfree = 0.000) for 2200 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2311 (Rfree = 0.000) for 2186 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:01:54 GMT 2018 Job finished. TimeTaking 31.51 Used memory is bytes: 18035040