Mon 24 Dec 07:26:23 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ifx-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.8-parrot-noncs ############### 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 07:26:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.8-parrot-noncs/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 169 and 0 Target number of residues in the AU: 169 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.54 Input MTZ file: 2ifx-3.8-parrot-noncs.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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 1824 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: 28.919 3.800 Wilson plot Bfac: 80.87 2547 reflections ( 98.61 % complete ) and 0 restraints for refining 2009 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3298 (Rfree = 0.000) for 2009 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 2038 seeds are put forward NCS extension: 0 residues added, 2038 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.320 Round 2: 93 peptides, 12 chains. Longest chain 13 peptides. Score 0.480 Round 3: 110 peptides, 14 chains. Longest chain 16 peptides. Score 0.523 Round 4: 123 peptides, 16 chains. Longest chain 15 peptides. Score 0.543 Round 5: 115 peptides, 13 chains. Longest chain 15 peptides. Score 0.571 Taking the results from Round 5 Chains 13, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3849 restraints for refining 1650 atoms. 3454 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2730 (Rfree = 0.000) for 1650 atoms. Found 7 (9 requested) and removed 30 (4 requested) atoms. Cycle 2: After refmac, R = 0.2673 (Rfree = 0.000) for 1593 atoms. Found 7 (8 requested) and removed 13 (4 requested) atoms. Cycle 3: After refmac, R = 0.2860 (Rfree = 0.000) for 1564 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2558 (Rfree = 0.000) for 1543 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 5: After refmac, R = 0.2701 (Rfree = 0.000) for 1523 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 1586 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1605 seeds are put forward Round 1: 103 peptides, 16 chains. Longest chain 11 peptides. Score 0.434 Round 2: 114 peptides, 15 chains. Longest chain 16 peptides. Score 0.520 Round 3: 100 peptides, 13 chains. Longest chain 15 peptides. Score 0.493 Round 4: 101 peptides, 12 chains. Longest chain 16 peptides. Score 0.524 Round 5: 109 peptides, 13 chains. Longest chain 16 peptides. Score 0.541 Taking the results from Round 5 Chains 13, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3524 restraints for refining 1543 atoms. 3153 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2318 (Rfree = 0.000) for 1543 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 7: After refmac, R = 0.2245 (Rfree = 0.000) for 1523 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2376 (Rfree = 0.000) for 1515 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.2286 (Rfree = 0.000) for 1508 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 10: After refmac, R = 0.2300 (Rfree = 0.000) for 1496 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1555 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 1584 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.343 Round 2: 111 peptides, 15 chains. Longest chain 14 peptides. Score 0.504 Round 3: 113 peptides, 16 chains. Longest chain 17 peptides. Score 0.490 Round 4: 112 peptides, 16 chains. Longest chain 18 peptides. Score 0.485 Round 5: 114 peptides, 15 chains. Longest chain 16 peptides. Score 0.520 Taking the results from Round 5 Chains 16, Residues 99, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3402 restraints for refining 1567 atoms. 2995 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2150 (Rfree = 0.000) for 1567 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.1938 (Rfree = 0.000) for 1552 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2002 (Rfree = 0.000) for 1544 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.1761 (Rfree = 0.000) for 1540 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.1707 (Rfree = 0.000) for 1529 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1597 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1615 seeds are put forward Round 1: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.366 Round 2: 111 peptides, 15 chains. Longest chain 18 peptides. Score 0.504 Round 3: 110 peptides, 14 chains. Longest chain 18 peptides. Score 0.523 Round 4: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.496 Round 5: 113 peptides, 14 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 14, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3646 restraints for refining 1610 atoms. 3264 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2284 (Rfree = 0.000) for 1610 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 17: After refmac, R = 0.2439 (Rfree = 0.000) for 1584 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 18: After refmac, R = 0.2372 (Rfree = 0.000) for 1556 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 19: After refmac, R = 0.2286 (Rfree = 0.000) for 1539 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.2239 (Rfree = 0.000) for 1526 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 1583 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1598 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 10 peptides. Score 0.248 Round 2: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.385 Round 3: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.368 Round 4: 105 peptides, 17 chains. Longest chain 10 peptides. Score 0.419 Round 5: 114 peptides, 20 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 4 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3507 restraints for refining 1542 atoms. 3172 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2133 (Rfree = 0.000) for 1542 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.2365 (Rfree = 0.000) for 1528 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 23: After refmac, R = 0.2348 (Rfree = 0.000) for 1518 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2526 (Rfree = 0.000) for 1507 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 25: After refmac, R = 0.2467 (Rfree = 0.000) for 1503 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1540 seeds are put forward NCS extension: 0 residues added, 1540 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.249 Round 2: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.342 Round 3: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.351 Round 4: 81 peptides, 15 chains. Longest chain 7 peptides. Score 0.322 Round 5: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 3 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3584 restraints for refining 1546 atoms. 3330 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 1546 atoms. Found 6 (8 requested) and removed 14 (4 requested) atoms. Cycle 27: After refmac, R = 0.2243 (Rfree = 0.000) for 1528 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2306 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2319 (Rfree = 0.000) for 1519 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 30: After refmac, R = 0.2247 (Rfree = 0.000) for 1512 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1573 seeds are put forward NCS extension: 0 residues added, 1573 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 9 peptides. Score 0.265 Round 2: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.342 Round 3: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.387 Round 4: 87 peptides, 13 chains. Longest chain 17 peptides. Score 0.418 Round 5: 92 peptides, 14 chains. Longest chain 19 peptides. Score 0.421 Taking the results from Round 5 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3466 restraints for refining 1535 atoms. 3168 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2459 (Rfree = 0.000) for 1535 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 32: After refmac, R = 0.2384 (Rfree = 0.000) for 1512 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 33: After refmac, R = 0.2246 (Rfree = 0.000) for 1508 atoms. Found 5 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.2552 (Rfree = 0.000) for 1496 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2109 (Rfree = 0.000) for 1488 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 1534 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 1568 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.254 Round 2: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.328 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.353 Round 4: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.351 Round 5: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.345 Taking the results from Round 3 Chains 16, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3323 restraints for refining 1508 atoms. 3043 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2260 (Rfree = 0.000) for 1508 atoms. Found 4 (8 requested) and removed 14 (4 requested) atoms. Cycle 37: After refmac, R = 0.1919 (Rfree = 0.000) for 1487 atoms. Found 1 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.1705 (Rfree = 0.000) for 1474 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1679 (Rfree = 0.000) for 1471 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1943 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward NCS extension: 0 residues added, 1512 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 6 peptides. Score 0.234 Round 2: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.353 Round 3: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.371 Round 4: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.313 Round 5: 91 peptides, 14 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 5 Chains 14, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3281 restraints for refining 1526 atoms. 2987 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2344 (Rfree = 0.000) for 1526 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 42: After refmac, R = 0.2247 (Rfree = 0.000) for 1507 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2260 (Rfree = 0.000) for 1497 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.1818 (Rfree = 0.000) for 1488 atoms. Found 2 (8 requested) and removed 12 (4 requested) atoms. Cycle 45: After refmac, R = 0.1877 (Rfree = 0.000) for 1473 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.39 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: 76 peptides, 16 chains. Longest chain 9 peptides. Score 0.258 Round 2: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.291 Round 3: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.349 Round 4: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.329 Round 5: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.400 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 78, 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 2ifx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2547 reflections ( 98.61 % complete ) and 3179 restraints for refining 1514 atoms. 2882 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2329 (Rfree = 0.000) for 1514 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2036 (Rfree = 0.000) for 1507 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1995 (Rfree = 0.000) for 1497 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1659 (Rfree = 0.000) for 1489 atoms. TimeTaking 21.73