Sun 23 Dec 22:23:07 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 2od4-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.6-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/2od4-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.6-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 22:23:16 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/2od4-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.6-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6402 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: 2od4-3.6-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.6-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 3.600 Wilson plot Bfac: 70.75 2426 reflections ( 98.42 % complete ) and 0 restraints for refining 1783 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3145 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2864 (Rfree = 0.000) for 1783 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 0 residues added, 1823 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.286 Round 2: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.441 Round 3: 101 peptides, 16 chains. Longest chain 15 peptides. Score 0.467 Round 4: 105 peptides, 15 chains. Longest chain 17 peptides. Score 0.523 Round 5: 105 peptides, 15 chains. Longest chain 14 peptides. Score 0.523 Taking the results from Round 5 Chains 15, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3353 restraints for refining 1464 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2405 (Rfree = 0.000) for 1464 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 2: After refmac, R = 0.2290 (Rfree = 0.000) for 1450 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2339 (Rfree = 0.000) for 1443 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.2197 (Rfree = 0.000) for 1435 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.1841 (Rfree = 0.000) for 1431 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 1489 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 1508 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 11 peptides. Score 0.272 Round 2: 91 peptides, 17 chains. Longest chain 13 peptides. Score 0.362 Round 3: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.404 Round 4: 82 peptides, 13 chains. Longest chain 12 peptides. Score 0.425 Round 5: 94 peptides, 15 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 5 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3435 restraints for refining 1441 atoms. 3134 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2103 (Rfree = 0.000) for 1441 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.1724 (Rfree = 0.000) for 1429 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.1555 (Rfree = 0.000) for 1418 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.1531 (Rfree = 0.000) for 1411 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.1536 (Rfree = 0.000) for 1405 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 1451 seeds are put forward NCS extension: 0 residues added, 1451 seeds are put forward Round 1: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.402 Round 2: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.394 Round 3: 98 peptides, 15 chains. Longest chain 13 peptides. Score 0.476 Round 4: 105 peptides, 13 chains. Longest chain 16 peptides. Score 0.578 Round 5: 101 peptides, 13 chains. Longest chain 15 peptides. Score 0.554 Taking the results from Round 4 Chains 13, Residues 92, Estimated correctness of the model 5.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3313 restraints for refining 1451 atoms. 2958 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2128 (Rfree = 0.000) for 1451 atoms. Found 7 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2148 (Rfree = 0.000) for 1440 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2216 (Rfree = 0.000) for 1435 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2095 (Rfree = 0.000) for 1433 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.1977 (Rfree = 0.000) for 1430 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.53 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: 84 peptides, 17 chains. Longest chain 10 peptides. Score 0.306 Round 2: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.418 Round 3: 97 peptides, 15 chains. Longest chain 18 peptides. Score 0.470 Round 4: 106 peptides, 17 chains. Longest chain 14 peptides. Score 0.472 Round 5: 100 peptides, 16 chains. Longest chain 18 peptides. Score 0.460 Taking the results from Round 4 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3359 restraints for refining 1464 atoms. 3020 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2212 (Rfree = 0.000) for 1464 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 17: After refmac, R = 0.2041 (Rfree = 0.000) for 1457 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.2044 (Rfree = 0.000) for 1451 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.1899 (Rfree = 0.000) for 1451 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.1997 (Rfree = 0.000) for 1444 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 1521 seeds are put forward NCS extension: 0 residues added, 1521 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 8 peptides. Score 0.254 Round 2: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.326 Round 3: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.405 Round 4: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.436 Round 5: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.472 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3397 restraints for refining 1465 atoms. 3095 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2021 (Rfree = 0.000) for 1465 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 22: After refmac, R = 0.1798 (Rfree = 0.000) for 1459 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.1865 (Rfree = 0.000) for 1453 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.1661 (Rfree = 0.000) for 1448 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1593 (Rfree = 0.000) for 1444 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward NCS extension: 0 residues added, 1491 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.262 Round 2: 101 peptides, 17 chains. Longest chain 13 peptides. Score 0.436 Round 3: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.434 Round 4: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.398 Round 5: 105 peptides, 19 chains. Longest chain 9 peptides. Score 0.404 Taking the results from Round 2 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3380 restraints for refining 1465 atoms. 3061 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2066 (Rfree = 0.000) for 1465 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.1916 (Rfree = 0.000) for 1463 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.1930 (Rfree = 0.000) for 1462 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.1799 (Rfree = 0.000) for 1460 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1703 (Rfree = 0.000) for 1463 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 1510 seeds are put forward NCS extension: 0 residues added, 1510 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.316 Round 2: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.422 Round 3: 98 peptides, 15 chains. Longest chain 13 peptides. Score 0.476 Round 4: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.439 Round 5: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.424 Taking the results from Round 3 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3442 restraints for refining 1465 atoms. 3125 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1872 (Rfree = 0.000) for 1465 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.1665 (Rfree = 0.000) for 1460 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1594 (Rfree = 0.000) for 1455 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.1560 (Rfree = 0.000) for 1453 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1557 (Rfree = 0.000) for 1446 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 1474 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1492 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.288 Round 2: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.352 Round 3: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.415 Round 4: 102 peptides, 17 chains. Longest chain 13 peptides. Score 0.444 Round 5: 103 peptides, 17 chains. Longest chain 13 peptides. Score 0.451 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3385 restraints for refining 1465 atoms. 3058 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1875 (Rfree = 0.000) for 1465 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.1766 (Rfree = 0.000) for 1461 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.1812 (Rfree = 0.000) for 1460 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1612 (Rfree = 0.000) for 1459 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2022 (Rfree = 0.000) for 1455 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.42 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: 69 peptides, 14 chains. Longest chain 13 peptides. Score 0.286 Round 2: 87 peptides, 16 chains. Longest chain 13 peptides. Score 0.364 Round 3: 81 peptides, 15 chains. Longest chain 13 peptides. Score 0.350 Round 4: 77 peptides, 13 chains. Longest chain 14 peptides. Score 0.386 Round 5: 75 peptides, 14 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 4 Chains 13, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2426 reflections ( 98.42 % complete ) and 3434 restraints for refining 1443 atoms. 3191 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1727 (Rfree = 0.000) for 1443 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.1711 (Rfree = 0.000) for 1444 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.1529 (Rfree = 0.000) for 1445 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1523 (Rfree = 0.000) for 1441 atoms. Found 0 (9 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.1570 (Rfree = 0.000) for 1433 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 1475 seeds are put forward NCS extension: 0 residues added, 1475 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 12 peptides. Score 0.311 Round 2: 83 peptides, 15 chains. Longest chain 12 peptides. Score 0.366 Round 3: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.294 Round 4: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.352 Round 5: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.414 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 71, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2od4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2426 reflections ( 98.42 % complete ) and 3333 restraints for refining 1465 atoms. 3050 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1841 (Rfree = 0.000) for 1465 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1951 (Rfree = 0.000) for 1460 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2153 (Rfree = 0.000) for 1454 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1799 (Rfree = 0.000) for 1444 atoms. TimeTaking 27.62