Sun 23 Dec 22:22:56 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 2pw4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.8-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/2pw4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.8-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 22:23:05 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/2pw4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.8-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 133 and 0 Target number of residues in the AU: 133 Target solvent content: 0.6557 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 188 Adjusted target solvent content: 0.51 Input MTZ file: 2pw4-3.8-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: 5 Cell parameters: 77.750 59.670 57.820 90.000 128.790 90.000 Input sequence file: 2pw4-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1504 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 Loops will be built when appropriate and at the last cycle Resolution range: 25.783 3.800 Wilson plot Bfac: 80.87 2037 reflections ( 97.14 % complete ) and 0 restraints for refining 1675 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3232 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2618 (Rfree = 0.000) for 1675 atoms. Found 6 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 1701 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.317 Round 2: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.437 Round 3: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.466 Round 4: 89 peptides, 14 chains. Longest chain 8 peptides. Score 0.447 Round 5: 91 peptides, 13 chains. Longest chain 11 peptides. Score 0.493 Taking the results from Round 5 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3178 restraints for refining 1360 atoms. 2879 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2218 (Rfree = 0.000) for 1360 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.1930 (Rfree = 0.000) for 1352 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.1928 (Rfree = 0.000) for 1338 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.2233 (Rfree = 0.000) for 1332 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.1965 (Rfree = 0.000) for 1328 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.358 Round 2: 105 peptides, 15 chains. Longest chain 14 peptides. Score 0.527 Round 3: 105 peptides, 13 chains. Longest chain 17 peptides. Score 0.583 Round 4: 106 peptides, 14 chains. Longest chain 17 peptides. Score 0.561 Round 5: 107 peptides, 13 chains. Longest chain 17 peptides. Score 0.594 Taking the results from Round 5 Chains 13, Residues 94, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 2814 restraints for refining 1302 atoms. 2422 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 1302 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 7: After refmac, R = 0.2664 (Rfree = 0.000) for 1274 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.2260 (Rfree = 0.000) for 1267 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 9: After refmac, R = 0.2040 (Rfree = 0.000) for 1251 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2167 (Rfree = 0.000) for 1247 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 1302 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 10 peptides. Score 0.328 Round 2: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.463 Round 3: 109 peptides, 16 chains. Longest chain 11 peptides. Score 0.524 Round 4: 116 peptides, 17 chains. Longest chain 11 peptides. Score 0.541 Round 5: 105 peptides, 14 chains. Longest chain 12 peptides. Score 0.555 Taking the results from Round 5 Chains 14, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3189 restraints for refining 1360 atoms. 2839 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2302 (Rfree = 0.000) for 1360 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 12: After refmac, R = 0.2207 (Rfree = 0.000) for 1345 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2115 (Rfree = 0.000) for 1339 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.1794 (Rfree = 0.000) for 1337 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.1875 (Rfree = 0.000) for 1335 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 1412 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.323 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.397 Round 3: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.402 Round 4: 83 peptides, 12 chains. Longest chain 13 peptides. Score 0.468 Round 5: 87 peptides, 10 chains. Longest chain 30 peptides. Score 0.557 Taking the results from Round 5 Chains 10, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3135 restraints for refining 1360 atoms. 2837 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2292 (Rfree = 0.000) for 1360 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.1828 (Rfree = 0.000) for 1351 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.1524 (Rfree = 0.000) for 1350 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.1589 (Rfree = 0.000) for 1351 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1554 (Rfree = 0.000) for 1353 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 1414 seeds are put forward Round 1: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.357 Round 2: 80 peptides, 12 chains. Longest chain 18 peptides. Score 0.446 Round 3: 85 peptides, 13 chains. Longest chain 13 peptides. Score 0.450 Round 4: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.417 Round 5: 77 peptides, 11 chains. Longest chain 14 peptides. Score 0.457 Taking the results from Round 5 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3243 restraints for refining 1360 atoms. 2990 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1868 (Rfree = 0.000) for 1360 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1638 (Rfree = 0.000) for 1352 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.1577 (Rfree = 0.000) for 1353 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.1394 (Rfree = 0.000) for 1355 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1367 (Rfree = 0.000) for 1355 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.342 Round 2: 88 peptides, 14 chains. Longest chain 12 peptides. Score 0.440 Round 3: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.334 Round 4: 89 peptides, 15 chains. Longest chain 12 peptides. Score 0.415 Round 5: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 2 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3211 restraints for refining 1360 atoms. 2929 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1692 (Rfree = 0.000) for 1360 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.1554 (Rfree = 0.000) for 1354 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.1526 (Rfree = 0.000) for 1343 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.1408 (Rfree = 0.000) for 1343 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1394 (Rfree = 0.000) for 1337 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 1380 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.266 Round 2: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.360 Round 3: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.417 Round 4: 88 peptides, 14 chains. Longest chain 14 peptides. Score 0.440 Round 5: 87 peptides, 13 chains. Longest chain 18 peptides. Score 0.464 Taking the results from Round 5 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3161 restraints for refining 1360 atoms. 2878 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1989 (Rfree = 0.000) for 1360 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.1865 (Rfree = 0.000) for 1352 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.1510 (Rfree = 0.000) for 1352 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.1620 (Rfree = 0.000) for 1344 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1569 (Rfree = 0.000) for 1344 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.302 Round 2: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.379 Round 3: 62 peptides, 10 chains. Longest chain 9 peptides. Score 0.374 Round 4: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.379 Round 5: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.346 Taking the results from Round 4 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3271 restraints for refining 1359 atoms. 3058 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1754 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 37: After refmac, R = 0.1529 (Rfree = 0.000) for 1362 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.1584 (Rfree = 0.000) for 1356 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1363 (Rfree = 0.000) for 1352 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.1462 (Rfree = 0.000) for 1346 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.63 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.323 Round 2: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.300 Round 3: 48 peptides, 8 chains. Longest chain 11 peptides. Score 0.331 Round 4: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.318 Round 5: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.349 Taking the results from Round 5 Chains 10, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2037 reflections ( 97.14 % complete ) and 3285 restraints for refining 1360 atoms. 3099 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1746 (Rfree = 0.000) for 1360 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.1776 (Rfree = 0.000) for 1355 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.1469 (Rfree = 0.000) for 1350 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.1365 (Rfree = 0.000) for 1347 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1532 (Rfree = 0.000) for 1345 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 1410 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 8 peptides. Score 0.230 Round 2: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.379 Round 3: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.268 Round 4: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.314 Round 5: 56 peptides, 10 chains. Longest chain 12 peptides. Score 0.323 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 49, 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 2pw4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2037 reflections ( 97.14 % complete ) and 3292 restraints for refining 1360 atoms. 3105 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1548 (Rfree = 0.000) for 1360 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1521 (Rfree = 0.000) for 1355 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1412 (Rfree = 0.000) for 1352 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1340 (Rfree = 0.000) for 1349 atoms. TimeTaking 27.52