null Sun 23 Dec 22:22:41 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 2fg9-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.4-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/2fg9-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.4-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 22:22:50 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/2fg9-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-3.4-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 129 and 0 Target number of residues in the AU: 129 Target solvent content: 0.6518 Checking the provided sequence file Detected sequence length: 178 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 178 Adjusted target solvent content: 0.52 Input MTZ file: 2fg9-3.4-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: 211 Cell parameters: 134.000 134.000 134.000 90.000 90.000 90.000 Input sequence file: 2fg9-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1424 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 Loops will be built when appropriate and at the last cycle Resolution range: 94.752 3.401 Wilson plot Bfac: 77.97 3046 reflections ( 99.61 % complete ) and 0 restraints for refining 1573 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3369 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2659 (Rfree = 0.000) for 1573 atoms. Found 1 (11 requested) and removed 21 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1586 seeds are put forward Round 1: 116 peptides, 18 chains. Longest chain 11 peptides. Score 0.524 Round 2: 126 peptides, 17 chains. Longest chain 21 peptides. Score 0.613 Round 3: 138 peptides, 14 chains. Longest chain 22 peptides. Score 0.737 Round 4: 135 peptides, 14 chains. Longest chain 23 peptides. Score 0.725 Round 5: 136 peptides, 12 chains. Longest chain 22 peptides. Score 0.767 Taking the results from Round 5 Chains 12, Residues 124, Estimated correctness of the model 73.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2698 restraints for refining 1294 atoms. 2214 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2913 (Rfree = 0.000) for 1294 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.2583 (Rfree = 0.000) for 1275 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.2528 (Rfree = 0.000) for 1262 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.2288 (Rfree = 0.000) for 1253 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2191 (Rfree = 0.000) for 1251 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1282 seeds are put forward Round 1: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.537 Round 2: 116 peptides, 14 chains. Longest chain 14 peptides. Score 0.632 Round 3: 124 peptides, 14 chains. Longest chain 18 peptides. Score 0.674 Round 4: 133 peptides, 14 chains. Longest chain 18 peptides. Score 0.716 Round 5: 124 peptides, 13 chains. Longest chain 20 peptides. Score 0.696 Taking the results from Round 4 Chains 14, Residues 119, Estimated correctness of the model 61.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2744 restraints for refining 1295 atoms. 2282 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2639 (Rfree = 0.000) for 1295 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 7: After refmac, R = 0.2488 (Rfree = 0.000) for 1288 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2405 (Rfree = 0.000) for 1282 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2330 (Rfree = 0.000) for 1279 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2248 (Rfree = 0.000) for 1270 atoms. Found 1 (7 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward Round 1: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.567 Round 2: 121 peptides, 15 chains. Longest chain 15 peptides. Score 0.634 Round 3: 121 peptides, 13 chains. Longest chain 19 peptides. Score 0.682 Round 4: 124 peptides, 15 chains. Longest chain 16 peptides. Score 0.651 Round 5: 126 peptides, 15 chains. Longest chain 22 peptides. Score 0.661 Taking the results from Round 3 Chains 13, Residues 108, Estimated correctness of the model 53.1 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2780 restraints for refining 1295 atoms. 2345 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2461 (Rfree = 0.000) for 1295 atoms. Found 5 (7 requested) and removed 6 (4 requested) atoms. Cycle 12: After refmac, R = 0.2278 (Rfree = 0.000) for 1284 atoms. Found 4 (7 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2247 (Rfree = 0.000) for 1276 atoms. Found 3 (7 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.2110 (Rfree = 0.000) for 1272 atoms. Found 4 (7 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2092 (Rfree = 0.000) for 1267 atoms. Found 4 (7 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1299 seeds are put forward Round 1: 112 peptides, 17 chains. Longest chain 17 peptides. Score 0.526 Round 2: 117 peptides, 14 chains. Longest chain 21 peptides. Score 0.637 Round 3: 127 peptides, 18 chains. Longest chain 16 peptides. Score 0.593 Round 4: 119 peptides, 17 chains. Longest chain 15 peptides. Score 0.571 Round 5: 129 peptides, 14 chains. Longest chain 18 peptides. Score 0.698 Taking the results from Round 5 Chains 14, Residues 115, Estimated correctness of the model 57.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2771 restraints for refining 1295 atoms. 2325 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2496 (Rfree = 0.000) for 1295 atoms. Found 5 (7 requested) and removed 8 (4 requested) atoms. Cycle 17: After refmac, R = 0.2331 (Rfree = 0.000) for 1284 atoms. Found 4 (7 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.2411 (Rfree = 0.000) for 1274 atoms. Found 3 (7 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2214 (Rfree = 0.000) for 1267 atoms. Found 2 (7 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2286 (Rfree = 0.000) for 1257 atoms. Found 3 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 1301 seeds are put forward Round 1: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.519 Round 2: 130 peptides, 16 chains. Longest chain 18 peptides. Score 0.658 Round 3: 135 peptides, 15 chains. Longest chain 29 peptides. Score 0.704 Round 4: 123 peptides, 14 chains. Longest chain 25 peptides. Score 0.669 Round 5: 120 peptides, 14 chains. Longest chain 18 peptides. Score 0.653 Taking the results from Round 3 Chains 15, Residues 120, Estimated correctness of the model 58.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2712 restraints for refining 1294 atoms. 2247 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2466 (Rfree = 0.000) for 1294 atoms. Found 7 (7 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.2395 (Rfree = 0.000) for 1290 atoms. Found 7 (7 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2351 (Rfree = 0.000) for 1292 atoms. Found 7 (7 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2315 (Rfree = 0.000) for 1290 atoms. Found 3 (7 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2140 (Rfree = 0.000) for 1286 atoms. Found 4 (6 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1324 seeds are put forward Round 1: 97 peptides, 15 chains. Longest chain 20 peptides. Score 0.482 Round 2: 112 peptides, 13 chains. Longest chain 30 peptides. Score 0.635 Round 3: 112 peptides, 13 chains. Longest chain 31 peptides. Score 0.635 Round 4: 112 peptides, 13 chains. Longest chain 28 peptides. Score 0.635 Round 5: 120 peptides, 10 chains. Longest chain 36 peptides. Score 0.742 Taking the results from Round 5 Chains 13, Residues 110, Estimated correctness of the model 68.0 % 2 chains (40 residues) have been docked in sequence Building loops using Loopy2018 13 chains (110 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2328 restraints for refining 1295 atoms. 1726 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2687 (Rfree = 0.000) for 1295 atoms. Found 6 (6 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.2547 (Rfree = 0.000) for 1284 atoms. Found 4 (6 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2456 (Rfree = 0.000) for 1278 atoms. Found 0 (6 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2299 (Rfree = 0.000) for 1270 atoms. Found 1 (6 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.2291 (Rfree = 0.000) for 1258 atoms. Found 2 (6 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1294 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 18 peptides. Score 0.456 Round 2: 102 peptides, 13 chains. Longest chain 26 peptides. Score 0.576 Round 3: 100 peptides, 13 chains. Longest chain 16 peptides. Score 0.563 Round 4: 100 peptides, 12 chains. Longest chain 22 peptides. Score 0.592 Round 5: 107 peptides, 13 chains. Longest chain 35 peptides. Score 0.606 Taking the results from Round 5 Chains 15, Residues 94, Estimated correctness of the model 30.6 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2689 restraints for refining 1295 atoms. 2241 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2454 (Rfree = 0.000) for 1295 atoms. Found 5 (5 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2278 (Rfree = 0.000) for 1292 atoms. Found 5 (5 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2219 (Rfree = 0.000) for 1287 atoms. Found 5 (5 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2188 (Rfree = 0.000) for 1284 atoms. Found 4 (5 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.2202 (Rfree = 0.000) for 1278 atoms. Found 3 (5 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1313 seeds are put forward Round 1: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.465 Round 2: 101 peptides, 14 chains. Longest chain 21 peptides. Score 0.540 Round 3: 104 peptides, 13 chains. Longest chain 25 peptides. Score 0.588 Round 4: 99 peptides, 14 chains. Longest chain 23 peptides. Score 0.527 Round 5: 114 peptides, 16 chains. Longest chain 22 peptides. Score 0.567 Taking the results from Round 3 Chains 13, Residues 91, Estimated correctness of the model 24.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2830 restraints for refining 1295 atoms. 2461 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2379 (Rfree = 0.000) for 1295 atoms. Found 5 (5 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2284 (Rfree = 0.000) for 1290 atoms. Found 5 (5 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.2220 (Rfree = 0.000) for 1288 atoms. Found 3 (5 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.2211 (Rfree = 0.000) for 1285 atoms. Found 1 (5 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2170 (Rfree = 0.000) for 1279 atoms. Found 5 (5 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.315 Round 2: 93 peptides, 14 chains. Longest chain 18 peptides. Score 0.485 Round 3: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.460 Round 4: 104 peptides, 16 chains. Longest chain 13 peptides. Score 0.501 Round 5: 105 peptides, 13 chains. Longest chain 21 peptides. Score 0.594 Taking the results from Round 5 Chains 13, Residues 92, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3046 reflections ( 99.61 % complete ) and 2873 restraints for refining 1295 atoms. 2518 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2376 (Rfree = 0.000) for 1295 atoms. Found 5 (5 requested) and removed 4 (4 requested) atoms. Cycle 42: After refmac, R = 0.2248 (Rfree = 0.000) for 1292 atoms. Found 3 (5 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2235 (Rfree = 0.000) for 1286 atoms. Found 2 (5 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2203 (Rfree = 0.000) for 1283 atoms. Found 0 (5 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2174 (Rfree = 0.000) for 1276 atoms. Found 2 (5 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1305 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.311 Round 2: 96 peptides, 13 chains. Longest chain 15 peptides. Score 0.537 Round 3: 93 peptides, 14 chains. Longest chain 15 peptides. Score 0.485 Round 4: 96 peptides, 14 chains. Longest chain 15 peptides. Score 0.506 Round 5: 94 peptides, 14 chains. Longest chain 19 peptides. Score 0.492 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 83, Estimated correctness of the model 6.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fg9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3046 reflections ( 99.61 % complete ) and 2754 restraints for refining 1262 atoms. 2435 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2312 (Rfree = 0.000) for 1262 atoms. Found 0 (5 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2201 (Rfree = 0.000) for 1253 atoms. Found 0 (5 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2263 (Rfree = 0.000) for 1246 atoms. Found 0 (5 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2197 (Rfree = 0.000) for 1240 atoms. Found 0 (5 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:18 GMT 2018 Job finished. TimeTaking 49.63 Used memory is bytes: 8358016