Mon 24 Dec 00:22:30 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 2od4-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.8-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/2od4-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.8-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 00:22:34 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/2od4-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.8-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 137 and 0 Target number of residues in the AU: 137 Target solvent content: 0.6504 Checking the provided sequence file Detected sequence length: 101 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 202 Adjusted target solvent content: 0.48 Input MTZ file: 2od4-3.8-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1616 target number of atoms Had to go as low as 0.65 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: 28.889 3.800 Wilson plot Bfac: 77.74 2075 reflections ( 98.25 % complete ) and 0 restraints for refining 1786 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3152 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2791 (Rfree = 0.000) for 1786 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 1810 seeds are put forward NCS extension: 0 residues added, 1810 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.256 Round 2: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.375 Round 3: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.402 Round 4: 101 peptides, 16 chains. Longest chain 14 peptides. Score 0.467 Round 5: 97 peptides, 13 chains. Longest chain 21 peptides. Score 0.529 Taking the results from Round 5 Chains 13, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3445 restraints for refining 1462 atoms. 3122 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2391 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 2: After refmac, R = 0.2267 (Rfree = 0.000) for 1437 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2381 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2440 (Rfree = 0.000) for 1417 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2280 (Rfree = 0.000) for 1411 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 1499 seeds are put forward NCS extension: 0 residues added, 1499 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 9 peptides. Score 0.292 Round 2: 96 peptides, 16 chains. Longest chain 14 peptides. Score 0.431 Round 3: 89 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Round 4: 87 peptides, 14 chains. Longest chain 18 peptides. Score 0.429 Round 5: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 2 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3166 restraints for refining 1359 atoms. 2862 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2191 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2010 (Rfree = 0.000) for 1341 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.1942 (Rfree = 0.000) for 1327 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.1905 (Rfree = 0.000) for 1324 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1750 (Rfree = 0.000) for 1323 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 1371 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1386 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 7 peptides. Score 0.254 Round 2: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.420 Round 3: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.415 Round 4: 107 peptides, 17 chains. Longest chain 15 peptides. Score 0.478 Round 5: 105 peptides, 17 chains. Longest chain 15 peptides. Score 0.465 Taking the results from Round 4 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3077 restraints for refining 1398 atoms. 2734 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1946 (Rfree = 0.000) for 1398 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2009 (Rfree = 0.000) for 1388 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.1859 (Rfree = 0.000) for 1384 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.1568 (Rfree = 0.000) for 1377 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.1455 (Rfree = 0.000) for 1370 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 1421 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1446 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.299 Round 2: 107 peptides, 18 chains. Longest chain 15 peptides. Score 0.449 Round 3: 103 peptides, 16 chains. Longest chain 17 peptides. Score 0.481 Round 4: 106 peptides, 16 chains. Longest chain 17 peptides. Score 0.501 Round 5: 101 peptides, 16 chains. Longest chain 10 peptides. Score 0.467 Taking the results from Round 4 Chains 16, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3134 restraints for refining 1390 atoms. 2790 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2555 (Rfree = 0.000) for 1390 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2106 (Rfree = 0.000) for 1374 atoms. Found 4 (7 requested) and removed 9 (3 requested) atoms. Cycle 18: After refmac, R = 0.2165 (Rfree = 0.000) for 1365 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.2091 (Rfree = 0.000) for 1358 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 1358 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.60 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 1430 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.269 Round 2: 100 peptides, 16 chains. Longest chain 12 peptides. Score 0.460 Round 3: 105 peptides, 16 chains. Longest chain 12 peptides. Score 0.494 Round 4: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.467 Round 5: 99 peptides, 14 chains. Longest chain 13 peptides. Score 0.513 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 ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3324 restraints for refining 1441 atoms. 2998 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2508 (Rfree = 0.000) for 1441 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 22: After refmac, R = 0.2133 (Rfree = 0.000) for 1430 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.1950 (Rfree = 0.000) for 1428 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1754 (Rfree = 0.000) for 1421 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1767 (Rfree = 0.000) for 1421 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 1478 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1496 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.358 Round 2: 98 peptides, 15 chains. Longest chain 12 peptides. Score 0.476 Round 3: 100 peptides, 16 chains. Longest chain 12 peptides. Score 0.460 Round 4: 102 peptides, 17 chains. Longest chain 12 peptides. Score 0.444 Round 5: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.478 Taking the results from Round 5 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3282 restraints for refining 1461 atoms. 2939 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1783 (Rfree = 0.000) for 1461 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 27: After refmac, R = 0.1766 (Rfree = 0.000) for 1457 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.1405 (Rfree = 0.000) for 1458 atoms. Found 0 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.1423 (Rfree = 0.000) for 1448 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1306 (Rfree = 0.000) for 1447 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.65 Search for helices and strands: 0 residues in 0 chains, 1486 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1500 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.342 Round 2: 84 peptides, 13 chains. Longest chain 12 peptides. Score 0.439 Round 3: 90 peptides, 13 chains. Longest chain 14 peptides. Score 0.482 Round 4: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.444 Round 5: 84 peptides, 10 chains. Longest chain 15 peptides. Score 0.533 Taking the results from Round 5 Chains 10, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3466 restraints for refining 1462 atoms. 3180 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1887 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.1927 (Rfree = 0.000) for 1457 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 33: After refmac, R = 0.1786 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1749 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1273 (Rfree = 0.000) for 1445 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 1489 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1511 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 10 peptides. Score 0.284 Round 2: 76 peptides, 14 chains. Longest chain 11 peptides. Score 0.344 Round 3: 85 peptides, 15 chains. Longest chain 13 peptides. Score 0.381 Round 4: 80 peptides, 12 chains. Longest chain 15 peptides. Score 0.443 Round 5: 79 peptides, 14 chains. Longest chain 13 peptides. Score 0.368 Taking the results from Round 4 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3440 restraints for refining 1462 atoms. 3180 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1874 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2078 (Rfree = 0.000) for 1458 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.1925 (Rfree = 0.000) for 1453 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 1452 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2024 (Rfree = 0.000) for 1451 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 1488 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 1498 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.246 Round 2: 53 peptides, 11 chains. Longest chain 8 peptides. Score 0.256 Round 3: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.214 Round 4: 54 peptides, 10 chains. Longest chain 13 peptides. Score 0.304 Round 5: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.246 Taking the results from Round 4 Chains 10, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3417 restraints for refining 1431 atoms. 3251 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1925 (Rfree = 0.000) for 1431 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.2079 (Rfree = 0.000) for 1425 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.1844 (Rfree = 0.000) for 1421 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.1770 (Rfree = 0.000) for 1419 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1801 (Rfree = 0.000) for 1423 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.59 Search for helices and strands: 0 residues in 0 chains, 1453 seeds are put forward NCS extension: 0 residues added, 1453 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 7 peptides. Score 0.217 Round 2: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.298 Round 3: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.274 Round 4: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.380 Round 5: 67 peptides, 11 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 53, 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 2od4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2075 reflections ( 98.25 % complete ) and 3156 restraints for refining 1378 atoms. 2954 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1730 (Rfree = 0.000) for 1378 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1753 (Rfree = 0.000) for 1373 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1258 (Rfree = 0.000) for 1364 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1237 (Rfree = 0.000) for 1359 atoms. TimeTaking 24.65