null Sun 23 Dec 22:23:08 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 2pw4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.6-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/2pw4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.6-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/2pw4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.6-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 138 and 0 Target number of residues in the AU: 138 Target solvent content: 0.6428 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: 2pw4-3.6-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: 2pw4-3.6-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 3.601 Wilson plot Bfac: 72.41 2378 reflections ( 97.34 % complete ) and 0 restraints for refining 1666 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3170 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2883 (Rfree = 0.000) for 1666 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 1704 seeds are put forward Round 1: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.346 Round 2: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.449 Round 3: 89 peptides, 13 chains. Longest chain 15 peptides. Score 0.479 Round 4: 92 peptides, 15 chains. Longest chain 14 peptides. Score 0.437 Round 5: 96 peptides, 15 chains. Longest chain 11 peptides. Score 0.466 Taking the results from Round 3 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 3144 restraints for refining 1362 atoms. 2823 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2333 (Rfree = 0.000) for 1362 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.2297 (Rfree = 0.000) for 1342 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2112 (Rfree = 0.000) for 1330 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2054 (Rfree = 0.000) for 1323 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.1867 (Rfree = 0.000) for 1321 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 1370 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 7 peptides. Score 0.330 Round 2: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.402 Round 3: 89 peptides, 15 chains. Longest chain 10 peptides. Score 0.415 Round 4: 81 peptides, 13 chains. Longest chain 10 peptides. Score 0.420 Round 5: 103 peptides, 13 chains. Longest chain 17 peptides. Score 0.571 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 2.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 2897 restraints for refining 1363 atoms. 2493 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2016 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.1782 (Rfree = 0.000) for 1355 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 8: After refmac, R = 0.1652 (Rfree = 0.000) for 1353 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.1599 (Rfree = 0.000) for 1345 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.1538 (Rfree = 0.000) for 1341 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 1380 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.334 Round 2: 87 peptides, 13 chains. Longest chain 12 peptides. Score 0.464 Round 3: 98 peptides, 14 chains. Longest chain 11 peptides. Score 0.510 Round 4: 99 peptides, 14 chains. Longest chain 13 peptides. Score 0.517 Round 5: 102 peptides, 11 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 5 Chains 12, Residues 91, Estimated correctness of the model 21.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 2828 restraints for refining 1363 atoms. 2424 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2387 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.1997 (Rfree = 0.000) for 1350 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2050 (Rfree = 0.000) for 1338 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 14: After refmac, R = 0.1842 (Rfree = 0.000) for 1341 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.1771 (Rfree = 0.000) for 1336 atoms. Found 4 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 1379 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.327 Round 2: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.427 Round 3: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.442 Round 4: 94 peptides, 14 chains. Longest chain 13 peptides. Score 0.483 Round 5: 91 peptides, 12 chains. Longest chain 14 peptides. Score 0.523 Taking the results from Round 5 Chains 12, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 3089 restraints for refining 1363 atoms. 2785 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2172 (Rfree = 0.000) for 1363 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.1749 (Rfree = 0.000) for 1357 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.1883 (Rfree = 0.000) for 1351 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.1813 (Rfree = 0.000) for 1348 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1697 (Rfree = 0.000) for 1346 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 1393 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.382 Round 2: 88 peptides, 13 chains. Longest chain 18 peptides. Score 0.471 Round 3: 84 peptides, 12 chains. Longest chain 12 peptides. Score 0.475 Round 4: 84 peptides, 13 chains. Longest chain 16 peptides. Score 0.442 Round 5: 86 peptides, 14 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 3 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 3177 restraints for refining 1363 atoms. 2901 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2103 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.1865 (Rfree = 0.000) for 1364 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.1694 (Rfree = 0.000) for 1359 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.1863 (Rfree = 0.000) for 1357 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1743 (Rfree = 0.000) for 1358 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.317 Round 2: 82 peptides, 12 chains. Longest chain 18 peptides. Score 0.460 Round 3: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.435 Round 4: 82 peptides, 14 chains. Longest chain 12 peptides. Score 0.394 Round 5: 87 peptides, 13 chains. Longest chain 14 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 ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 3160 restraints for refining 1363 atoms. 2877 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2314 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.1991 (Rfree = 0.000) for 1359 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.1912 (Rfree = 0.000) for 1357 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 29: After refmac, R = 0.1847 (Rfree = 0.000) for 1354 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.1520 (Rfree = 0.000) for 1354 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 1396 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 12 peptides. Score 0.340 Round 2: 85 peptides, 12 chains. Longest chain 13 peptides. Score 0.482 Round 3: 86 peptides, 14 chains. Longest chain 13 peptides. Score 0.425 Round 4: 79 peptides, 14 chains. Longest chain 13 peptides. Score 0.370 Round 5: 85 peptides, 12 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 5 Chains 12, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 3170 restraints for refining 1362 atoms. 2890 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2339 (Rfree = 0.000) for 1362 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.1884 (Rfree = 0.000) for 1358 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.1912 (Rfree = 0.000) for 1355 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.1815 (Rfree = 0.000) for 1353 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1743 (Rfree = 0.000) for 1354 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.334 Round 2: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.392 Round 3: 80 peptides, 13 chains. Longest chain 12 peptides. Score 0.412 Round 4: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.389 Round 5: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 5 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 3167 restraints for refining 1363 atoms. 2904 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1753 (Rfree = 0.000) for 1363 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 37: After refmac, R = 0.1594 (Rfree = 0.000) for 1356 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1554 (Rfree = 0.000) for 1350 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1513 (Rfree = 0.000) for 1348 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1447 (Rfree = 0.000) for 1347 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 1386 seeds are put forward Round 1: 78 peptides, 13 chains. Longest chain 13 peptides. Score 0.397 Round 2: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.450 Round 3: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.419 Round 4: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.431 Round 5: 86 peptides, 10 chains. Longest chain 19 peptides. Score 0.550 Taking the results from Round 5 Chains 10, Residues 76, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2378 reflections ( 97.34 % complete ) and 2958 restraints for refining 1363 atoms. 2595 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2300 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.1996 (Rfree = 0.000) for 1359 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1679 (Rfree = 0.000) for 1355 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.1670 (Rfree = 0.000) for 1356 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1708 (Rfree = 0.000) for 1355 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.271 Round 2: 66 peptides, 10 chains. Longest chain 11 peptides. Score 0.407 Round 3: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.351 Round 4: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.368 Round 5: 74 peptides, 11 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 63, 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. 2378 reflections ( 97.34 % complete ) and 3258 restraints for refining 1363 atoms. 3017 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2405 (Rfree = 0.000) for 1363 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2280 (Rfree = 0.000) for 1355 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1921 (Rfree = 0.000) for 1350 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2214 (Rfree = 0.000) for 1346 atoms. Found 0 (8 requested) and removed 1 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:55 GMT 2018 Job finished. TimeTaking 27.78 Used memory is bytes: 14391696