Mon 24 Dec 00:51:11 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 2eth-2.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-2.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-2.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-2.3-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/2eth-2.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-2.3-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 ============================================================ Mon 24 Dec 00:51:15 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/2eth-2.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-2.3-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 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-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-2.3-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.65 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 2729 atoms. Observations/parameters ratio is 1.33 ------------------------------------------------------ Starting model: R = 0.3265 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2733 (Rfree = 0.000) for 2729 atoms. Found 44 (62 requested) and removed 33 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.66 2.45 NCS extension: 0 residues added, 2740 seeds are put forward Round 1: 175 peptides, 24 chains. Longest chain 13 peptides. Score 0.524 Round 2: 201 peptides, 18 chains. Longest chain 25 peptides. Score 0.692 Round 3: 213 peptides, 15 chains. Longest chain 40 peptides. Score 0.755 Round 4: 219 peptides, 12 chains. Longest chain 36 peptides. Score 0.798 Round 5: 220 peptides, 16 chains. Longest chain 31 peptides. Score 0.760 Taking the results from Round 4 Chains 12, Residues 207, Estimated correctness of the model 94.1 % 5 chains (132 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 B and 134 B 11 chains (209 residues) following loop building 4 chains (134 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3502 restraints for refining 2337 atoms. 2097 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2927 (Rfree = 0.000) for 2337 atoms. Found 45 (53 requested) and removed 40 (26 requested) atoms. Cycle 2: After refmac, R = 0.2782 (Rfree = 0.000) for 2312 atoms. Found 31 (52 requested) and removed 35 (26 requested) atoms. Cycle 3: After refmac, R = 0.2639 (Rfree = 0.000) for 2287 atoms. Found 29 (51 requested) and removed 34 (26 requested) atoms. Cycle 4: After refmac, R = 0.2499 (Rfree = 0.000) for 2267 atoms. Found 13 (49 requested) and removed 26 (26 requested) atoms. Cycle 5: After refmac, R = 0.2384 (Rfree = 0.000) for 2242 atoms. Found 13 (47 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.58 2.38 NCS extension: 67 residues added (8 deleted due to clashes), 2303 seeds are put forward Round 1: 219 peptides, 10 chains. Longest chain 54 peptides. Score 0.817 Round 2: 226 peptides, 10 chains. Longest chain 65 peptides. Score 0.828 Round 3: 228 peptides, 9 chains. Longest chain 81 peptides. Score 0.840 Round 4: 229 peptides, 9 chains. Longest chain 68 peptides. Score 0.841 Round 5: 231 peptides, 9 chains. Longest chain 70 peptides. Score 0.844 Taking the results from Round 5 Chains 9, Residues 222, Estimated correctness of the model 96.3 % 4 chains (165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 B and 134 B 8 chains (224 residues) following loop building 3 chains (167 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3239 restraints for refining 2337 atoms. 1641 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2637 (Rfree = 0.000) for 2337 atoms. Found 22 (48 requested) and removed 33 (26 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 2318 atoms. Found 19 (47 requested) and removed 27 (26 requested) atoms. Cycle 8: After refmac, R = 0.2322 (Rfree = 0.000) for 2303 atoms. Found 18 (46 requested) and removed 31 (26 requested) atoms. Cycle 9: After refmac, R = 0.2251 (Rfree = 0.000) for 2286 atoms. Found 19 (44 requested) and removed 30 (26 requested) atoms. Cycle 10: After refmac, R = 0.2211 (Rfree = 0.000) for 2272 atoms. Found 10 (43 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.59 2.39 NCS extension: 21 residues added (1 deleted due to clashes), 2279 seeds are put forward Round 1: 229 peptides, 9 chains. Longest chain 83 peptides. Score 0.841 Round 2: 235 peptides, 8 chains. Longest chain 82 peptides. Score 0.858 Round 3: 235 peptides, 9 chains. Longest chain 90 peptides. Score 0.850 Round 4: 230 peptides, 12 chains. Longest chain 69 peptides. Score 0.817 Round 5: 229 peptides, 14 chains. Longest chain 62 peptides. Score 0.797 Taking the results from Round 2 Chains 8, Residues 227, Estimated correctness of the model 96.9 % 3 chains (181 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 71 A 7 chains (231 residues) following loop building 2 chains (185 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 3039 restraints for refining 2337 atoms. 1344 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2503 (Rfree = 0.000) for 2337 atoms. Found 21 (42 requested) and removed 34 (26 requested) atoms. Cycle 12: After refmac, R = 0.2318 (Rfree = 0.000) for 2316 atoms. Found 22 (41 requested) and removed 27 (26 requested) atoms. Cycle 13: After refmac, R = 0.2191 (Rfree = 0.000) for 2310 atoms. Found 14 (40 requested) and removed 29 (26 requested) atoms. Cycle 14: After refmac, R = 0.2154 (Rfree = 0.000) for 2295 atoms. Found 9 (38 requested) and removed 26 (26 requested) atoms. Cycle 15: After refmac, R = 0.2140 (Rfree = 0.000) for 2277 atoms. Found 9 (37 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.59 2.39 NCS extension: 0 residues added, 2263 seeds are put forward Round 1: 239 peptides, 7 chains. Longest chain 83 peptides. Score 0.871 Round 2: 238 peptides, 7 chains. Longest chain 86 peptides. Score 0.870 Round 3: 229 peptides, 6 chains. Longest chain 111 peptides. Score 0.866 Round 4: 228 peptides, 8 chains. Longest chain 76 peptides. Score 0.848 Round 5: 232 peptides, 10 chains. Longest chain 82 peptides. Score 0.838 Taking the results from Round 1 Chains 7, Residues 232, Estimated correctness of the model 97.4 % 4 chains (213 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 70 A Built loop between residues 67 B and 71 B 5 chains (238 residues) following loop building 2 chains (219 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2766 restraints for refining 2337 atoms. 896 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2373 (Rfree = 0.000) for 2337 atoms. Found 34 (37 requested) and removed 29 (26 requested) atoms. Cycle 17: After refmac, R = 0.2177 (Rfree = 0.000) for 2338 atoms. Found 19 (36 requested) and removed 26 (26 requested) atoms. Cycle 18: After refmac, R = 0.2146 (Rfree = 0.000) for 2328 atoms. Found 13 (35 requested) and removed 26 (26 requested) atoms. Cycle 19: After refmac, R = 0.2140 (Rfree = 0.000) for 2312 atoms. Found 19 (34 requested) and removed 26 (26 requested) atoms. Cycle 20: After refmac, R = 0.2150 (Rfree = 0.000) for 2303 atoms. Found 17 (33 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.58 2.38 NCS extension: 3 residues added (6 deleted due to clashes), 2301 seeds are put forward Round 1: 237 peptides, 6 chains. Longest chain 84 peptides. Score 0.876 Round 2: 236 peptides, 5 chains. Longest chain 111 peptides. Score 0.882 Round 3: 235 peptides, 9 chains. Longest chain 78 peptides. Score 0.850 Round 4: 231 peptides, 7 chains. Longest chain 76 peptides. Score 0.860 Round 5: 224 peptides, 11 chains. Longest chain 62 peptides. Score 0.816 Taking the results from Round 2 Chains 7, Residues 231, Estimated correctness of the model 97.8 % 4 chains (205 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 71 A 6 chains (234 residues) following loop building 3 chains (208 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2873 restraints for refining 2336 atoms. 1076 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2339 (Rfree = 0.000) for 2336 atoms. Found 21 (32 requested) and removed 29 (26 requested) atoms. Cycle 22: After refmac, R = 0.2208 (Rfree = 0.000) for 2322 atoms. Found 17 (31 requested) and removed 26 (26 requested) atoms. Cycle 23: After refmac, R = 0.2155 (Rfree = 0.000) for 2309 atoms. Found 12 (30 requested) and removed 26 (26 requested) atoms. Cycle 24: After refmac, R = 0.2164 (Rfree = 0.000) for 2291 atoms. Found 10 (28 requested) and removed 26 (26 requested) atoms. Cycle 25: After refmac, R = 0.2161 (Rfree = 0.000) for 2272 atoms. Found 15 (27 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.58 2.38 NCS extension: 59 residues added (52 deleted due to clashes), 2322 seeds are put forward Round 1: 232 peptides, 5 chains. Longest chain 82 peptides. Score 0.877 Round 2: 235 peptides, 6 chains. Longest chain 83 peptides. Score 0.873 Round 3: 236 peptides, 7 chains. Longest chain 74 peptides. Score 0.867 Round 4: 236 peptides, 7 chains. Longest chain 114 peptides. Score 0.867 Round 5: 235 peptides, 9 chains. Longest chain 58 peptides. Score 0.850 Taking the results from Round 1 Chains 6, Residues 227, Estimated correctness of the model 97.6 % 4 chains (212 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 71 A Built loop between residues 66 B and 71 B 3 chains (235 residues) following loop building 2 chains (221 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2691 restraints for refining 2337 atoms. 827 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2291 (Rfree = 0.000) for 2337 atoms. Found 26 (26 requested) and removed 28 (26 requested) atoms. Cycle 27: After refmac, R = 0.2151 (Rfree = 0.000) for 2327 atoms. Found 18 (26 requested) and removed 27 (26 requested) atoms. Cycle 28: After refmac, R = 0.2115 (Rfree = 0.000) for 2315 atoms. Found 14 (26 requested) and removed 27 (26 requested) atoms. Cycle 29: After refmac, R = 0.2118 (Rfree = 0.000) for 2298 atoms. Found 11 (26 requested) and removed 27 (26 requested) atoms. Cycle 30: After refmac, R = 0.2113 (Rfree = 0.000) for 2280 atoms. Found 12 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.57 2.37 NCS extension: 0 residues added, 2266 seeds are put forward Round 1: 234 peptides, 5 chains. Longest chain 83 peptides. Score 0.879 Round 2: 237 peptides, 7 chains. Longest chain 85 peptides. Score 0.868 Round 3: 234 peptides, 8 chains. Longest chain 61 peptides. Score 0.857 Round 4: 233 peptides, 10 chains. Longest chain 61 peptides. Score 0.839 Round 5: 234 peptides, 8 chains. Longest chain 69 peptides. Score 0.857 Taking the results from Round 1 Chains 5, Residues 229, Estimated correctness of the model 97.7 % 4 chains (215 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 70 A Built loop between residues 67 B and 72 B 3 chains (236 residues) following loop building 2 chains (222 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2676 restraints for refining 2337 atoms. 806 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2242 (Rfree = 0.000) for 2337 atoms. Found 26 (26 requested) and removed 28 (26 requested) atoms. Cycle 32: After refmac, R = 0.2149 (Rfree = 0.000) for 2332 atoms. Found 17 (26 requested) and removed 26 (26 requested) atoms. Cycle 33: After refmac, R = 0.2086 (Rfree = 0.000) for 2320 atoms. Found 16 (26 requested) and removed 26 (26 requested) atoms. Cycle 34: After refmac, R = 0.2047 (Rfree = 0.000) for 2309 atoms. Found 13 (26 requested) and removed 27 (26 requested) atoms. Cycle 35: After refmac, R = 0.2037 (Rfree = 0.000) for 2291 atoms. Found 18 (26 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.57 2.37 NCS extension: 0 residues added, 2282 seeds are put forward Round 1: 234 peptides, 6 chains. Longest chain 81 peptides. Score 0.872 Round 2: 233 peptides, 6 chains. Longest chain 91 peptides. Score 0.871 Round 3: 234 peptides, 10 chains. Longest chain 62 peptides. Score 0.841 Round 4: 230 peptides, 8 chains. Longest chain 91 peptides. Score 0.851 Round 5: 233 peptides, 8 chains. Longest chain 83 peptides. Score 0.855 Taking the results from Round 1 Chains 6, Residues 228, Estimated correctness of the model 97.4 % 5 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 69 A Built loop between residues 67 B and 71 B 4 chains (234 residues) following loop building 3 chains (220 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2689 restraints for refining 2337 atoms. 831 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2246 (Rfree = 0.000) for 2337 atoms. Found 26 (26 requested) and removed 31 (26 requested) atoms. Cycle 37: After refmac, R = 0.2110 (Rfree = 0.000) for 2326 atoms. Found 23 (26 requested) and removed 26 (26 requested) atoms. Cycle 38: After refmac, R = 0.2052 (Rfree = 0.000) for 2318 atoms. Found 16 (26 requested) and removed 26 (26 requested) atoms. Cycle 39: After refmac, R = 0.2045 (Rfree = 0.000) for 2304 atoms. Found 13 (26 requested) and removed 27 (26 requested) atoms. Cycle 40: After refmac, R = 0.2034 (Rfree = 0.000) for 2286 atoms. Found 18 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.58 2.38 NCS extension: 113 residues added (46 deleted due to clashes), 2393 seeds are put forward Round 1: 235 peptides, 6 chains. Longest chain 81 peptides. Score 0.873 Round 2: 234 peptides, 6 chains. Longest chain 91 peptides. Score 0.872 Round 3: 234 peptides, 7 chains. Longest chain 76 peptides. Score 0.864 Round 4: 232 peptides, 8 chains. Longest chain 92 peptides. Score 0.854 Round 5: 224 peptides, 9 chains. Longest chain 58 peptides. Score 0.834 Taking the results from Round 1 Chains 7, Residues 229, Estimated correctness of the model 97.5 % 5 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 70 A Built loop between residues 118 A and 121 A Built loop between residues 67 B and 71 B 4 chains (237 residues) following loop building 2 chains (222 residues) in sequence following loop building ------------------------------------------------------ 14516 reflections ( 87.11 % complete ) and 2683 restraints for refining 2337 atoms. 807 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2236 (Rfree = 0.000) for 2337 atoms. Found 24 (26 requested) and removed 33 (26 requested) atoms. Cycle 42: After refmac, R = 0.2113 (Rfree = 0.000) for 2319 atoms. Found 14 (26 requested) and removed 26 (26 requested) atoms. Cycle 43: After refmac, R = 0.2059 (Rfree = 0.000) for 2301 atoms. Found 18 (26 requested) and removed 27 (26 requested) atoms. Cycle 44: After refmac, R = 0.2054 (Rfree = 0.000) for 2290 atoms. Found 12 (26 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.2033 (Rfree = 0.000) for 2274 atoms. Found 13 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.57 2.37 NCS extension: 0 residues added, 2263 seeds are put forward Round 1: 231 peptides, 6 chains. Longest chain 80 peptides. Score 0.868 Round 2: 234 peptides, 6 chains. Longest chain 91 peptides. Score 0.872 Round 3: 236 peptides, 7 chains. Longest chain 79 peptides. Score 0.867 Round 4: 231 peptides, 10 chains. Longest chain 71 peptides. Score 0.836 Round 5: 235 peptides, 8 chains. Longest chain 72 peptides. Score 0.858 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 228, Estimated correctness of the model 97.4 % 5 chains (202 residues) have been docked in sequence Sequence coverage is 88 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 67 A and 71 A Built loop between residues 130 B and 134 B 5 chains (233 residues) following loop building 3 chains (208 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14516 reflections ( 87.11 % complete ) and 1794 restraints for refining 1776 atoms. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3262 (Rfree = 0.000) for 1776 atoms. Found 5 (20 requested) and removed 0 (20 requested) atoms. Cycle 47: After refmac, R = 0.3146 (Rfree = 0.000) for 1776 atoms. Found 6 (20 requested) and removed 0 (20 requested) atoms. Cycle 48: After refmac, R = 0.3090 (Rfree = 0.000) for 1776 atoms. Found 5 (20 requested) and removed 0 (20 requested) atoms. Cycle 49: After refmac, R = 0.3053 (Rfree = 0.000) for 1776 atoms. TimeTaking 41.08