Sun 23 Dec 22:23:01 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 2od4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.8-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/2od4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.8-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 22:23:11 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/2od4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.8-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 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-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.8-parrot-hancs.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 1781 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3260 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2971 (Rfree = 0.000) for 1781 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 1799 seeds are put forward NCS extension: 0 residues added, 1799 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 10 peptides. Score 0.274 Round 2: 70 peptides, 13 chains. Longest chain 12 peptides. Score 0.330 Round 3: 81 peptides, 13 chains. Longest chain 17 peptides. Score 0.417 Round 4: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.399 Round 5: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.434 Taking the results from Round 5 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3548 restraints for refining 1462 atoms. 3255 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2356 (Rfree = 0.000) for 1462 atoms. Found 7 (8 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.2331 (Rfree = 0.000) for 1442 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 3: After refmac, R = 0.2171 (Rfree = 0.000) for 1434 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 4: After refmac, R = 0.2218 (Rfree = 0.000) for 1420 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.1926 (Rfree = 0.000) for 1417 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1502 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.338 Round 2: 101 peptides, 17 chains. Longest chain 15 peptides. Score 0.436 Round 3: 101 peptides, 15 chains. Longest chain 15 peptides. Score 0.497 Round 4: 92 peptides, 13 chains. Longest chain 22 peptides. Score 0.496 Round 5: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 3 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3311 restraints for refining 1429 atoms. 2982 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1917 (Rfree = 0.000) for 1429 atoms. Found 6 (7 requested) and removed 15 (3 requested) atoms. Cycle 7: After refmac, R = 0.1861 (Rfree = 0.000) for 1409 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 8: After refmac, R = 0.1842 (Rfree = 0.000) for 1397 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 9: After refmac, R = 0.1676 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1726 (Rfree = 0.000) for 1389 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1451 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1472 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 12 peptides. Score 0.296 Round 2: 99 peptides, 16 chains. Longest chain 14 peptides. Score 0.453 Round 3: 110 peptides, 17 chains. Longest chain 13 peptides. Score 0.498 Round 4: 106 peptides, 15 chains. Longest chain 15 peptides. Score 0.530 Round 5: 97 peptides, 15 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 4 Chains 15, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3393 restraints for refining 1462 atoms. 3044 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1822 (Rfree = 0.000) for 1462 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.1757 (Rfree = 0.000) for 1455 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. Cycle 13: After refmac, R = 0.1705 (Rfree = 0.000) for 1444 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.1699 (Rfree = 0.000) for 1437 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.1785 (Rfree = 0.000) for 1428 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 1456 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1485 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.352 Round 2: 103 peptides, 17 chains. Longest chain 19 peptides. Score 0.451 Round 3: 110 peptides, 20 chains. Longest chain 13 peptides. Score 0.409 Round 4: 111 peptides, 18 chains. Longest chain 20 peptides. Score 0.476 Round 5: 99 peptides, 18 chains. Longest chain 16 peptides. Score 0.390 Taking the results from Round 4 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3181 restraints for refining 1462 atoms. 2768 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2095 (Rfree = 0.000) for 1462 atoms. Found 7 (8 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.2164 (Rfree = 0.000) for 1439 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2026 (Rfree = 0.000) for 1429 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 1423 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.1965 (Rfree = 0.000) for 1420 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 1521 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 10 peptides. Score 0.287 Round 2: 77 peptides, 14 chains. Longest chain 12 peptides. Score 0.352 Round 3: 81 peptides, 13 chains. Longest chain 13 peptides. Score 0.417 Round 4: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.419 Round 5: 83 peptides, 13 chains. Longest chain 10 peptides. Score 0.432 Taking the results from Round 5 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3354 restraints for refining 1462 atoms. 3087 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2318 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 22: After refmac, R = 0.2010 (Rfree = 0.000) for 1449 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.1942 (Rfree = 0.000) for 1445 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.1919 (Rfree = 0.000) for 1440 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.1715 (Rfree = 0.000) for 1440 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1497 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 8 peptides. Score 0.257 Round 2: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.316 Round 3: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.397 Round 4: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.434 Round 5: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.422 Taking the results from Round 4 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3270 restraints for refining 1434 atoms. 2977 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2214 (Rfree = 0.000) for 1434 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 27: After refmac, R = 0.1895 (Rfree = 0.000) for 1421 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.1850 (Rfree = 0.000) for 1418 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 29: After refmac, R = 0.1674 (Rfree = 0.000) for 1410 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.1713 (Rfree = 0.000) for 1408 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1470 seeds are put forward NCS extension: 0 residues added, 1470 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 7 peptides. Score 0.212 Round 2: 93 peptides, 18 chains. Longest chain 7 peptides. Score 0.344 Round 3: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.352 Round 4: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.412 Round 5: 91 peptides, 15 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 5 Chains 15, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3478 restraints for refining 1462 atoms. 3189 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1936 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.1800 (Rfree = 0.000) for 1458 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.1870 (Rfree = 0.000) for 1451 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.1785 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1796 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1504 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1515 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 9 peptides. Score 0.258 Round 2: 87 peptides, 17 chains. Longest chain 11 peptides. Score 0.330 Round 3: 88 peptides, 18 chains. Longest chain 9 peptides. Score 0.304 Round 4: 94 peptides, 18 chains. Longest chain 13 peptides. Score 0.352 Round 5: 97 peptides, 18 chains. Longest chain 14 peptides. Score 0.375 Taking the results from Round 5 Chains 18, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3468 restraints for refining 1462 atoms. 3170 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1686 (Rfree = 0.000) for 1462 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 37: After refmac, R = 0.1655 (Rfree = 0.000) for 1452 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.1770 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.1662 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1174 (Rfree = 0.000) for 1446 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1498 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1516 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 8 peptides. Score 0.252 Round 2: 76 peptides, 13 chains. Longest chain 11 peptides. Score 0.379 Round 3: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.399 Round 4: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.333 Round 5: 68 peptides, 11 chains. Longest chain 9 peptides. Score 0.385 Taking the results from Round 3 Chains 14, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2075 reflections ( 98.25 % complete ) and 3359 restraints for refining 1462 atoms. 3097 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1680 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 42: After refmac, R = 0.1737 (Rfree = 0.000) for 1453 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.1681 (Rfree = 0.000) for 1451 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.1657 (Rfree = 0.000) for 1446 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.1604 (Rfree = 0.000) for 1444 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 1500 seeds are put forward NCS extension: 0 residues added, 1500 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 6 peptides. Score 0.214 Round 2: 80 peptides, 15 chains. Longest chain 7 peptides. Score 0.342 Round 3: 86 peptides, 16 chains. Longest chain 7 peptides. Score 0.356 Round 4: 91 peptides, 16 chains. Longest chain 8 peptides. Score 0.394 Round 5: 84 peptides, 15 chains. Longest chain 7 peptides. Score 0.374 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 75, 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 3207 restraints for refining 1440 atoms. 2923 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1853 (Rfree = 0.000) for 1440 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1854 (Rfree = 0.000) for 1433 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1840 (Rfree = 0.000) for 1427 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1657 (Rfree = 0.000) for 1419 atoms. TimeTaking 27.8