Mon 24 Dec 00:00:43 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 2pg4-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-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/2pg4-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-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 00:00:47 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/2pg4-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-4.0-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6705 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-4.0-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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1520 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 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: 77.669 4.000 Wilson plot Bfac: 92.45 2116 reflections ( 99.39 % complete ) and 0 restraints for refining 1675 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3856 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3698 (Rfree = 0.000) for 1675 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.99 3.78 Search for helices and strands: 0 residues in 0 chains, 1705 seeds are put forward NCS extension: 0 residues added, 1705 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.322 Round 2: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.341 Round 3: 83 peptides, 13 chains. Longest chain 11 peptides. Score 0.424 Round 4: 82 peptides, 13 chains. Longest chain 14 peptides. Score 0.416 Round 5: 99 peptides, 14 chains. Longest chain 13 peptides. Score 0.502 Taking the results from Round 5 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3277 restraints for refining 1373 atoms. 2951 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3002 (Rfree = 0.000) for 1373 atoms. Found 0 (6 requested) and removed 10 (3 requested) atoms. Cycle 2: After refmac, R = 0.2544 (Rfree = 0.000) for 1338 atoms. Found 0 (6 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2413 (Rfree = 0.000) for 1322 atoms. Found 3 (6 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.2557 (Rfree = 0.000) for 1305 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2189 (Rfree = 0.000) for 1296 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 1363 seeds are put forward NCS extension: 0 residues added, 1363 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.325 Round 2: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.445 Round 3: 86 peptides, 12 chains. Longest chain 16 peptides. Score 0.476 Round 4: 89 peptides, 11 chains. Longest chain 19 peptides. Score 0.525 Round 5: 87 peptides, 11 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 4 Chains 11, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3235 restraints for refining 1373 atoms. 2934 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3230 (Rfree = 0.000) for 1373 atoms. Found 4 (6 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.2723 (Rfree = 0.000) for 1356 atoms. Found 1 (6 requested) and removed 18 (3 requested) atoms. Cycle 8: After refmac, R = 0.2159 (Rfree = 0.000) for 1337 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.2710 (Rfree = 0.000) for 1330 atoms. Found 1 (6 requested) and removed 23 (3 requested) atoms. Cycle 10: After refmac, R = 0.2951 (Rfree = 0.000) for 1306 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 1363 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 1395 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 9 peptides. Score 0.301 Round 2: 97 peptides, 16 chains. Longest chain 11 peptides. Score 0.430 Round 3: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.425 Round 4: 89 peptides, 13 chains. Longest chain 16 peptides. Score 0.466 Round 5: 89 peptides, 13 chains. Longest chain 14 peptides. Score 0.466 Taking the results from Round 5 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3264 restraints for refining 1373 atoms. 2973 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2443 (Rfree = 0.000) for 1373 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 12: After refmac, R = 0.2700 (Rfree = 0.000) for 1360 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2270 (Rfree = 0.000) for 1352 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2061 (Rfree = 0.000) for 1346 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2226 (Rfree = 0.000) for 1341 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 3.66 Search for helices and strands: 0 residues in 0 chains, 1391 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1409 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.290 Round 2: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.356 Round 3: 71 peptides, 12 chains. Longest chain 9 peptides. Score 0.367 Round 4: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.372 Round 5: 75 peptides, 11 chains. Longest chain 14 peptides. Score 0.430 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3386 restraints for refining 1373 atoms. 3141 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2755 (Rfree = 0.000) for 1373 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2410 (Rfree = 0.000) for 1364 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2643 (Rfree = 0.000) for 1360 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2302 (Rfree = 0.000) for 1353 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2154 (Rfree = 0.000) for 1350 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 1407 seeds are put forward NCS extension: 0 residues added, 1407 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.290 Round 2: 84 peptides, 14 chains. Longest chain 12 peptides. Score 0.399 Round 3: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.416 Round 4: 83 peptides, 11 chains. Longest chain 14 peptides. Score 0.486 Round 5: 83 peptides, 14 chains. Longest chain 8 peptides. Score 0.392 Taking the results from Round 4 Chains 11, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3339 restraints for refining 1373 atoms. 3062 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2523 (Rfree = 0.000) for 1373 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 1359 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2144 (Rfree = 0.000) for 1348 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.1907 (Rfree = 0.000) for 1342 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2491 (Rfree = 0.000) for 1339 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 3.65 Search for helices and strands: 0 residues in 0 chains, 1394 seeds are put forward NCS extension: 0 residues added, 1394 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 11 peptides. Score 0.336 Round 2: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.362 Round 3: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.372 Round 4: 79 peptides, 14 chains. Longest chain 14 peptides. Score 0.362 Round 5: 79 peptides, 12 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 5 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3221 restraints for refining 1372 atoms. 2965 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2504 (Rfree = 0.000) for 1372 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2284 (Rfree = 0.000) for 1363 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.1927 (Rfree = 0.000) for 1353 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2419 (Rfree = 0.000) for 1344 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 1341 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward NCS extension: 0 residues added, 1397 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.245 Round 2: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.387 Round 3: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.352 Round 4: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.374 Round 5: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 2 Chains 13, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3244 restraints for refining 1373 atoms. 2997 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2774 (Rfree = 0.000) for 1373 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2286 (Rfree = 0.000) for 1367 atoms. Found 2 (6 requested) and removed 11 (3 requested) atoms. Cycle 33: After refmac, R = 0.2057 (Rfree = 0.000) for 1355 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1830 (Rfree = 0.000) for 1350 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2022 (Rfree = 0.000) for 1346 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward NCS extension: 0 residues added, 1408 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.255 Round 2: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.395 Round 3: 75 peptides, 11 chains. Longest chain 13 peptides. Score 0.430 Round 4: 76 peptides, 10 chains. Longest chain 14 peptides. Score 0.470 Round 5: 82 peptides, 12 chains. Longest chain 13 peptides. Score 0.448 Taking the results from Round 4 Chains 10, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3260 restraints for refining 1373 atoms. 3006 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2378 (Rfree = 0.000) for 1373 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2152 (Rfree = 0.000) for 1364 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.1729 (Rfree = 0.000) for 1359 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.1887 (Rfree = 0.000) for 1354 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1909 (Rfree = 0.000) for 1350 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 1414 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1427 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.255 Round 2: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.331 Round 3: 80 peptides, 14 chains. Longest chain 8 peptides. Score 0.369 Round 4: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.364 Round 5: 75 peptides, 11 chains. Longest chain 16 peptides. Score 0.430 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2116 reflections ( 99.39 % complete ) and 3373 restraints for refining 1373 atoms. 3128 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2416 (Rfree = 0.000) for 1373 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.1979 (Rfree = 0.000) for 1364 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2149 (Rfree = 0.000) for 1357 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.2464 (Rfree = 0.000) for 1350 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2254 (Rfree = 0.000) for 1347 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward NCS extension: 0 residues added, 1401 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.255 Round 2: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.280 Round 3: 66 peptides, 12 chains. Longest chain 9 peptides. Score 0.327 Round 4: 69 peptides, 9 chains. Longest chain 17 peptides. Score 0.453 Round 5: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.351 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 60, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2pg4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2116 reflections ( 99.39 % complete ) and 3095 restraints for refining 1372 atoms. 2808 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2096 (Rfree = 0.000) for 1372 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2146 (Rfree = 0.000) for 1357 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1925 (Rfree = 0.000) for 1350 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2123 (Rfree = 0.000) for 1346 atoms. TimeTaking 22.6