Sun 23 Dec 22:23:10 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 2i9w-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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/2i9w-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 22:23:18 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/2i9w-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 128 and 0 Target number of residues in the AU: 128 Target solvent content: 0.6350 Checking the provided sequence file Detected sequence length: 184 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 184 Adjusted target solvent content: 0.48 Input MTZ file: 2i9w-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: 19 Cell parameters: 41.450 54.640 83.800 90.000 90.000 90.000 Input sequence file: 2i9w-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1472 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: 45.770 3.400 Wilson plot Bfac: 68.81 2855 reflections ( 99.58 % complete ) and 0 restraints for refining 1634 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3568 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3169 (Rfree = 0.000) for 1634 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1658 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 10 peptides. Score 0.297 Round 2: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.403 Round 3: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.469 Round 4: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.463 Round 5: 94 peptides, 12 chains. Longest chain 18 peptides. Score 0.567 Taking the results from Round 5 Chains 12, Residues 82, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 3162 restraints for refining 1338 atoms. 2846 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2835 (Rfree = 0.000) for 1338 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.2909 (Rfree = 0.000) for 1323 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2756 (Rfree = 0.000) for 1313 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.2808 (Rfree = 0.000) for 1310 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2504 (Rfree = 0.000) for 1307 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 1346 seeds are put forward Round 1: 88 peptides, 14 chains. Longest chain 18 peptides. Score 0.458 Round 2: 99 peptides, 16 chains. Longest chain 13 peptides. Score 0.476 Round 3: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.457 Round 4: 101 peptides, 14 chains. Longest chain 16 peptides. Score 0.553 Round 5: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.411 Taking the results from Round 4 Chains 14, Residues 87, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 3008 restraints for refining 1321 atoms. 2674 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2644 (Rfree = 0.000) for 1321 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 7: After refmac, R = 0.2918 (Rfree = 0.000) for 1313 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2788 (Rfree = 0.000) for 1304 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2813 (Rfree = 0.000) for 1302 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2752 (Rfree = 0.000) for 1299 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 1343 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 7 peptides. Score 0.316 Round 2: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.380 Round 3: 106 peptides, 16 chains. Longest chain 14 peptides. Score 0.527 Round 4: 95 peptides, 15 chains. Longest chain 16 peptides. Score 0.479 Round 5: 96 peptides, 12 chains. Longest chain 16 peptides. Score 0.580 Taking the results from Round 5 Chains 12, Residues 84, Estimated correctness of the model 22.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 2927 restraints for refining 1339 atoms. 2562 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2594 (Rfree = 0.000) for 1339 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.2501 (Rfree = 0.000) for 1329 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2288 (Rfree = 0.000) for 1324 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2404 (Rfree = 0.000) for 1317 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2201 (Rfree = 0.000) for 1312 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 1349 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.243 Round 2: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.403 Round 3: 101 peptides, 22 chains. Longest chain 7 peptides. Score 0.285 Round 4: 95 peptides, 19 chains. Longest chain 9 peptides. Score 0.341 Round 5: 95 peptides, 19 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 2 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 2890 restraints for refining 1301 atoms. 2599 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2225 (Rfree = 0.000) for 1301 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 1295 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.1891 (Rfree = 0.000) for 1291 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2018 (Rfree = 0.000) for 1287 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1906 (Rfree = 0.000) for 1285 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 1317 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.263 Round 2: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.370 Round 3: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.476 Round 4: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.459 Round 5: 100 peptides, 14 chains. Longest chain 14 peptides. Score 0.547 Taking the results from Round 5 Chains 14, Residues 86, Estimated correctness of the model 10.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 2946 restraints for refining 1339 atoms. 2616 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2492 (Rfree = 0.000) for 1339 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2276 (Rfree = 0.000) for 1330 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2132 (Rfree = 0.000) for 1328 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2090 (Rfree = 0.000) for 1320 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2077 (Rfree = 0.000) for 1319 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1339 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.391 Round 2: 95 peptides, 14 chains. Longest chain 15 peptides. Score 0.511 Round 3: 81 peptides, 12 chains. Longest chain 10 peptides. Score 0.472 Round 4: 91 peptides, 12 chains. Longest chain 12 peptides. Score 0.546 Round 5: 88 peptides, 12 chains. Longest chain 14 peptides. Score 0.525 Taking the results from Round 4 Chains 12, Residues 79, Estimated correctness of the model 10.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 3057 restraints for refining 1338 atoms. 2753 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2419 (Rfree = 0.000) for 1338 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.2295 (Rfree = 0.000) for 1338 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2192 (Rfree = 0.000) for 1340 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1911 (Rfree = 0.000) for 1344 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1857 (Rfree = 0.000) for 1341 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 1359 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.332 Round 2: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.402 Round 3: 86 peptides, 12 chains. Longest chain 16 peptides. Score 0.510 Round 4: 83 peptides, 13 chains. Longest chain 10 peptides. Score 0.453 Round 5: 80 peptides, 11 chains. Longest chain 15 peptides. Score 0.499 Taking the results from Round 3 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 3053 restraints for refining 1339 atoms. 2769 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2233 (Rfree = 0.000) for 1339 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 32: After refmac, R = 0.2089 (Rfree = 0.000) for 1332 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.2045 (Rfree = 0.000) for 1329 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2010 (Rfree = 0.000) for 1324 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1973 (Rfree = 0.000) for 1324 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 1350 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.346 Round 2: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.391 Round 3: 84 peptides, 13 chains. Longest chain 12 peptides. Score 0.461 Round 4: 90 peptides, 14 chains. Longest chain 11 peptides. Score 0.474 Round 5: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.517 Taking the results from Round 5 Chains 13, Residues 75, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 2819 restraints for refining 1338 atoms. 2462 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2738 (Rfree = 0.000) for 1338 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2563 (Rfree = 0.000) for 1329 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2172 (Rfree = 0.000) for 1322 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2078 (Rfree = 0.000) for 1324 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2058 (Rfree = 0.000) for 1326 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 1358 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 9 peptides. Score 0.249 Round 2: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.448 Round 3: 80 peptides, 12 chains. Longest chain 14 peptides. Score 0.464 Round 4: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.429 Round 5: 74 peptides, 12 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 3 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2855 reflections ( 99.58 % complete ) and 2955 restraints for refining 1310 atoms. 2695 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2307 (Rfree = 0.000) for 1310 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2039 (Rfree = 0.000) for 1311 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.1994 (Rfree = 0.000) for 1310 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1960 (Rfree = 0.000) for 1307 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1960 (Rfree = 0.000) for 1305 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 1327 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.239 Round 2: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.332 Round 3: 81 peptides, 13 chains. Longest chain 14 peptides. Score 0.437 Round 4: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.339 Round 5: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.456 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 67, 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 2i9w-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2855 reflections ( 99.58 % complete ) and 3062 restraints for refining 1339 atoms. 2806 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2291 (Rfree = 0.000) for 1339 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 1333 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2068 (Rfree = 0.000) for 1324 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2055 (Rfree = 0.000) for 1317 atoms. TimeTaking 26.42