Mon 24 Dec 07:26:56 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 2eth-2.3-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2eth-2.3-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2eth-2.3-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-2.3-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/2eth-2.3-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-2.3-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 07:27:01 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/2eth-2.3-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-2.3-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 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.5786 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: 0.56 Input MTZ file: 2eth-2.3-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-2.3-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.70 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: 65.143 2.300 Wilson plot Bfac: 44.24 14516 reflections ( 87.11 % complete ) and 0 restraints for refining 2756 atoms. Observations/parameters ratio is 1.32 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2790 (Rfree = 0.000) for 2756 atoms. Found 28 (63 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.72 2.51 NCS extension: 0 residues added, 2752 seeds are put forward Round 1: 166 peptides, 26 chains. Longest chain 13 peptides. Score 0.456 Round 2: 195 peptides, 21 chains. Longest chain 29 peptides. Score 0.636 Round 3: 209 peptides, 17 chains. Longest chain 34 peptides. Score 0.724 Round 4: 208 peptides, 15 chains. Longest chain 29 peptides. Score 0.744 Round 5: 213 peptides, 15 chains. Longest chain 29 peptides. Score 0.755 Taking the results from Round 5 Chains 20, Residues 198, Estimated correctness of the model 91.6 % 6 chains (109 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 121 A 18 chains (200 residues) following loop building 5 chains (112 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3763 restraints for refining 2334 atoms. 2493 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2944 (Rfree = 0.000) for 2334 atoms. Found 34 (53 requested) and removed 32 (26 requested) atoms. Cycle 2: After refmac, R = 0.2816 (Rfree = 0.000) for 2302 atoms. Found 30 (52 requested) and removed 29 (26 requested) atoms. Cycle 3: After refmac, R = 0.2689 (Rfree = 0.000) for 2286 atoms. Found 26 (50 requested) and removed 26 (26 requested) atoms. Cycle 4: After refmac, R = 0.2587 (Rfree = 0.000) for 2274 atoms. Found 17 (49 requested) and removed 27 (26 requested) atoms. Cycle 5: After refmac, R = 0.2568 (Rfree = 0.000) for 2259 atoms. Found 28 (48 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.59 2.39 NCS extension: 45 residues added (10 deleted due to clashes), 2314 seeds are put forward Round 1: 214 peptides, 13 chains. Longest chain 46 peptides. Score 0.779 Round 2: 222 peptides, 16 chains. Longest chain 33 peptides. Score 0.764 Round 3: 216 peptides, 11 chains. Longest chain 36 peptides. Score 0.802 Round 4: 218 peptides, 15 chains. Longest chain 30 peptides. Score 0.766 Round 5: 208 peptides, 13 chains. Longest chain 59 peptides. Score 0.766 Taking the results from Round 3 Chains 12, Residues 205, Estimated correctness of the model 94.3 % 6 chains (160 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 134 A Built loop between residues 111 B and 115 B 10 chains (210 residues) following loop building 4 chains (165 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3255 restraints for refining 2336 atoms. 1719 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2583 (Rfree = 0.000) for 2336 atoms. Found 29 (48 requested) and removed 34 (26 requested) atoms. Cycle 7: After refmac, R = 0.2453 (Rfree = 0.000) for 2317 atoms. Found 16 (47 requested) and removed 27 (26 requested) atoms. Cycle 8: After refmac, R = 0.2382 (Rfree = 0.000) for 2301 atoms. Found 18 (46 requested) and removed 28 (26 requested) atoms. Cycle 9: After refmac, R = 0.2309 (Rfree = 0.000) for 2283 atoms. Found 21 (44 requested) and removed 30 (26 requested) atoms. Cycle 10: After refmac, R = 0.2309 (Rfree = 0.000) for 2270 atoms. Found 22 (43 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.59 2.39 NCS extension: 12 residues added (2 deleted due to clashes), 2287 seeds are put forward Round 1: 223 peptides, 8 chains. Longest chain 52 peptides. Score 0.841 Round 2: 226 peptides, 15 chains. Longest chain 45 peptides. Score 0.782 Round 3: 221 peptides, 13 chains. Longest chain 38 peptides. Score 0.792 Round 4: 219 peptides, 11 chains. Longest chain 44 peptides. Score 0.808 Round 5: 224 peptides, 11 chains. Longest chain 41 peptides. Score 0.816 Taking the results from Round 1 Chains 8, Residues 215, Estimated correctness of the model 96.2 % 5 chains (167 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 110 B and 114 B 7 chains (218 residues) following loop building 4 chains (170 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3079 restraints for refining 2314 atoms. 1486 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2339 (Rfree = 0.000) for 2314 atoms. Found 27 (42 requested) and removed 29 (26 requested) atoms. Cycle 12: After refmac, R = 0.2192 (Rfree = 0.000) for 2307 atoms. Found 18 (41 requested) and removed 26 (26 requested) atoms. Cycle 13: After refmac, R = 0.2126 (Rfree = 0.000) for 2297 atoms. Found 14 (40 requested) and removed 26 (26 requested) atoms. Cycle 14: After refmac, R = 0.2108 (Rfree = 0.000) for 2279 atoms. Found 22 (38 requested) and removed 26 (26 requested) atoms. Cycle 15: After refmac, R = 0.2118 (Rfree = 0.000) for 2273 atoms. Found 19 (37 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.59 2.39 NCS extension: 11 residues added (4 deleted due to clashes), 2278 seeds are put forward Round 1: 223 peptides, 10 chains. Longest chain 53 peptides. Score 0.824 Round 2: 233 peptides, 11 chains. Longest chain 66 peptides. Score 0.831 Round 3: 228 peptides, 16 chains. Longest chain 31 peptides. Score 0.776 Round 4: 226 peptides, 16 chains. Longest chain 46 peptides. Score 0.772 Round 5: 232 peptides, 12 chains. Longest chain 38 peptides. Score 0.820 Taking the results from Round 2 Chains 13, Residues 222, Estimated correctness of the model 95.7 % 4 chains (156 residues) have been docked in sequence Building loops using Loopy2018 13 chains (222 residues) following loop building 4 chains (156 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3210 restraints for refining 2337 atoms. 1666 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2291 (Rfree = 0.000) for 2337 atoms. Found 17 (37 requested) and removed 30 (26 requested) atoms. Cycle 17: After refmac, R = 0.2143 (Rfree = 0.000) for 2317 atoms. Found 13 (36 requested) and removed 26 (26 requested) atoms. Cycle 18: After refmac, R = 0.2111 (Rfree = 0.000) for 2300 atoms. Found 10 (34 requested) and removed 26 (26 requested) atoms. Cycle 19: After refmac, R = 0.2115 (Rfree = 0.000) for 2284 atoms. Found 10 (33 requested) and removed 26 (26 requested) atoms. Cycle 20: After refmac, R = 0.2106 (Rfree = 0.000) for 2267 atoms. Found 9 (32 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.57 2.37 NCS extension: 10 residues added (1 deleted due to clashes), 2264 seeds are put forward Round 1: 221 peptides, 8 chains. Longest chain 55 peptides. Score 0.838 Round 2: 228 peptides, 9 chains. Longest chain 69 peptides. Score 0.840 Round 3: 225 peptides, 11 chains. Longest chain 56 peptides. Score 0.818 Round 4: 229 peptides, 11 chains. Longest chain 45 peptides. Score 0.824 Round 5: 233 peptides, 10 chains. Longest chain 56 peptides. Score 0.839 Taking the results from Round 2 Chains 9, Residues 219, Estimated correctness of the model 96.1 % 5 chains (175 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 77 A Built loop between residues 113 B and 116 B 7 chains (230 residues) following loop building 3 chains (186 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2974 restraints for refining 2337 atoms. 1270 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2439 (Rfree = 0.000) for 2337 atoms. Found 32 (32 requested) and removed 32 (26 requested) atoms. Cycle 22: After refmac, R = 0.2193 (Rfree = 0.000) for 2330 atoms. Found 15 (31 requested) and removed 26 (26 requested) atoms. Cycle 23: After refmac, R = 0.2141 (Rfree = 0.000) for 2315 atoms. Found 18 (30 requested) and removed 26 (26 requested) atoms. Cycle 24: After refmac, R = 0.2124 (Rfree = 0.000) for 2305 atoms. Found 13 (29 requested) and removed 28 (26 requested) atoms. Cycle 25: After refmac, R = 0.2110 (Rfree = 0.000) for 2287 atoms. Found 16 (27 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.57 2.37 NCS extension: 141 residues added (17 deleted due to clashes), 2420 seeds are put forward Round 1: 228 peptides, 10 chains. Longest chain 38 peptides. Score 0.832 Round 2: 231 peptides, 9 chains. Longest chain 77 peptides. Score 0.844 Round 3: 230 peptides, 8 chains. Longest chain 67 peptides. Score 0.851 Round 4: 228 peptides, 11 chains. Longest chain 41 peptides. Score 0.823 Round 5: 232 peptides, 8 chains. Longest chain 56 peptides. Score 0.854 Taking the results from Round 5 Chains 10, Residues 224, Estimated correctness of the model 96.7 % 6 chains (188 residues) have been docked in sequence Building loops using Loopy2018 10 chains (224 residues) following loop building 6 chains (188 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2954 restraints for refining 2337 atoms. 1270 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2430 (Rfree = 0.000) for 2337 atoms. Found 26 (26 requested) and removed 31 (26 requested) atoms. Cycle 27: After refmac, R = 0.2289 (Rfree = 0.000) for 2326 atoms. Found 17 (26 requested) and removed 26 (26 requested) atoms. Cycle 28: After refmac, R = 0.2264 (Rfree = 0.000) for 2314 atoms. Found 15 (26 requested) and removed 26 (26 requested) atoms. Cycle 29: After refmac, R = 0.2232 (Rfree = 0.000) for 2302 atoms. Found 16 (26 requested) and removed 26 (26 requested) atoms. Cycle 30: After refmac, R = 0.2237 (Rfree = 0.000) for 2289 atoms. Found 19 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.59 2.39 NCS extension: 9 residues added (2 deleted due to clashes), 2291 seeds are put forward Round 1: 230 peptides, 9 chains. Longest chain 54 peptides. Score 0.843 Round 2: 232 peptides, 7 chains. Longest chain 79 peptides. Score 0.862 Round 3: 227 peptides, 9 chains. Longest chain 47 peptides. Score 0.838 Round 4: 228 peptides, 11 chains. Longest chain 60 peptides. Score 0.823 Round 5: 226 peptides, 9 chains. Longest chain 58 peptides. Score 0.837 Taking the results from Round 2 Chains 7, Residues 225, Estimated correctness of the model 97.0 % 3 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 B and 119 B 6 chains (227 residues) following loop building 2 chains (190 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2989 restraints for refining 2337 atoms. 1293 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2322 (Rfree = 0.000) for 2337 atoms. Found 22 (26 requested) and removed 32 (26 requested) atoms. Cycle 32: After refmac, R = 0.2205 (Rfree = 0.000) for 2323 atoms. Found 18 (26 requested) and removed 26 (26 requested) atoms. Cycle 33: After refmac, R = 0.2209 (Rfree = 0.000) for 2312 atoms. Found 13 (26 requested) and removed 26 (26 requested) atoms. Cycle 34: After refmac, R = 0.2196 (Rfree = 0.000) for 2297 atoms. Found 15 (26 requested) and removed 26 (26 requested) atoms. Cycle 35: After refmac, R = 0.2196 (Rfree = 0.000) for 2283 atoms. Found 17 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.58 2.38 NCS extension: 28 residues added (8 deleted due to clashes), 2304 seeds are put forward Round 1: 232 peptides, 8 chains. Longest chain 54 peptides. Score 0.854 Round 2: 236 peptides, 5 chains. Longest chain 94 peptides. Score 0.882 Round 3: 230 peptides, 9 chains. Longest chain 84 peptides. Score 0.843 Round 4: 230 peptides, 7 chains. Longest chain 58 peptides. Score 0.859 Round 5: 230 peptides, 8 chains. Longest chain 114 peptides. Score 0.851 Taking the results from Round 2 Chains 5, Residues 231, Estimated correctness of the model 97.8 % 4 chains (217 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 134 A Built loop between residues 67 B and 75 B 3 chains (240 residues) following loop building 2 chains (226 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2588 restraints for refining 2337 atoms. 687 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2255 (Rfree = 0.000) for 2337 atoms. Found 26 (26 requested) and removed 36 (26 requested) atoms. Cycle 37: After refmac, R = 0.2061 (Rfree = 0.000) for 2322 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 38: After refmac, R = 0.1990 (Rfree = 0.000) for 2320 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 39: After refmac, R = 0.1944 (Rfree = 0.000) for 2319 atoms. Found 16 (26 requested) and removed 27 (26 requested) atoms. Cycle 40: After refmac, R = 0.1957 (Rfree = 0.000) for 2307 atoms. Found 19 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.56 2.36 NCS extension: 98 residues added (16 deleted due to clashes), 2403 seeds are put forward Round 1: 239 peptides, 4 chains. Longest chain 115 peptides. Score 0.892 Round 2: 238 peptides, 8 chains. Longest chain 94 peptides. Score 0.862 Round 3: 237 peptides, 7 chains. Longest chain 84 peptides. Score 0.868 Round 4: 233 peptides, 11 chains. Longest chain 41 peptides. Score 0.831 Round 5: 238 peptides, 8 chains. Longest chain 84 peptides. Score 0.862 Taking the results from Round 1 Chains 4, Residues 235, Estimated correctness of the model 98.1 % 3 chains (222 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 74 A 3 chains (241 residues) following loop building 2 chains (228 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2605 restraints for refining 2337 atoms. 690 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2202 (Rfree = 0.000) for 2337 atoms. Found 26 (26 requested) and removed 35 (26 requested) atoms. Cycle 42: After refmac, R = 0.2045 (Rfree = 0.000) for 2325 atoms. Found 24 (26 requested) and removed 26 (26 requested) atoms. Cycle 43: After refmac, R = 0.2014 (Rfree = 0.000) for 2321 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. Cycle 44: After refmac, R = 0.2000 (Rfree = 0.000) for 2308 atoms. Found 16 (26 requested) and removed 27 (26 requested) atoms. Cycle 45: After refmac, R = 0.1982 (Rfree = 0.000) for 2293 atoms. Found 18 (26 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.57 2.37 NCS extension: 91 residues added (24 deleted due to clashes), 2376 seeds are put forward Round 1: 235 peptides, 6 chains. Longest chain 80 peptides. Score 0.873 Round 2: 234 peptides, 8 chains. Longest chain 71 peptides. Score 0.857 Round 3: 235 peptides, 7 chains. Longest chain 84 peptides. Score 0.866 Round 4: 234 peptides, 12 chains. Longest chain 58 peptides. Score 0.824 Round 5: 234 peptides, 8 chains. Longest chain 58 peptides. Score 0.857 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 229, Estimated correctness of the model 97.5 % 5 chains (216 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 117 A and 120 A Built loop between residues 67 B and 75 B Built loop between residues 98 B and 101 B 3 chains (240 residues) following loop building 2 chains (227 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14516 reflections ( 87.11 % complete ) and 1906 restraints for refining 1883 atoms. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2958 (Rfree = 0.000) for 1883 atoms. Found 9 (21 requested) and removed 0 (21 requested) atoms. Cycle 47: After refmac, R = 0.2815 (Rfree = 0.000) for 1883 atoms. Found 4 (21 requested) and removed 2 (21 requested) atoms. Cycle 48: After refmac, R = 0.2804 (Rfree = 0.000) for 1883 atoms. Found 3 (21 requested) and removed 1 (21 requested) atoms. Cycle 49: After refmac, R = 0.2783 (Rfree = 0.000) for 1883 atoms. TimeTaking 39.95