Mon 24 Dec 00:52:45 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 2ifx-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-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/2ifx-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-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 00:52:55 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/2ifx-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-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 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-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.70 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 2027 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3177 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3427 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 2050 seeds are put forward NCS extension: 0 residues added, 2050 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.298 Round 2: 111 peptides, 15 chains. Longest chain 16 peptides. Score 0.504 Round 3: 112 peptides, 12 chains. Longest chain 17 peptides. Score 0.579 Round 4: 112 peptides, 13 chains. Longest chain 17 peptides. Score 0.557 Round 5: 118 peptides, 13 chains. Longest chain 16 peptides. Score 0.586 Taking the results from Round 5 Chains 13, Residues 105, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3726 restraints for refining 1648 atoms. 3286 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2571 (Rfree = 0.000) for 1648 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 2: After refmac, R = 0.2659 (Rfree = 0.000) for 1606 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 3: After refmac, R = 0.2430 (Rfree = 0.000) for 1583 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 4: After refmac, R = 0.2689 (Rfree = 0.000) for 1567 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 5: After refmac, R = 0.2297 (Rfree = 0.000) for 1537 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1603 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1617 seeds are put forward Round 1: 105 peptides, 18 chains. Longest chain 13 peptides. Score 0.393 Round 2: 122 peptides, 16 chains. Longest chain 21 peptides. Score 0.538 Round 3: 123 peptides, 17 chains. Longest chain 17 peptides. Score 0.520 Round 4: 128 peptides, 17 chains. Longest chain 18 peptides. Score 0.545 Round 5: 128 peptides, 16 chains. Longest chain 20 peptides. Score 0.568 Taking the results from Round 5 Chains 16, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3707 restraints for refining 1623 atoms. 3275 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2423 (Rfree = 0.000) for 1623 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 7: After refmac, R = 0.2280 (Rfree = 0.000) for 1596 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 8: After refmac, R = 0.1899 (Rfree = 0.000) for 1575 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.1859 (Rfree = 0.000) for 1567 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2545 (Rfree = 0.000) for 1563 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 1624 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1652 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 12 peptides. Score 0.391 Round 2: 106 peptides, 17 chains. Longest chain 10 peptides. Score 0.425 Round 3: 98 peptides, 13 chains. Longest chain 11 peptides. Score 0.482 Round 4: 107 peptides, 13 chains. Longest chain 17 peptides. Score 0.531 Round 5: 113 peptides, 16 chains. Longest chain 18 peptides. Score 0.490 Taking the results from Round 4 Chains 13, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 2547 reflections ( 98.61 % complete ) and 3643 restraints for refining 1621 atoms. 3280 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2633 (Rfree = 0.000) for 1621 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 12: After refmac, R = 0.2582 (Rfree = 0.000) for 1576 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 13: After refmac, R = 0.2510 (Rfree = 0.000) for 1556 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2562 (Rfree = 0.000) for 1544 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 15: After refmac, R = 0.2628 (Rfree = 0.000) for 1529 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 1604 seeds are put forward NCS extension: 0 residues added, 1604 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 10 peptides. Score 0.268 Round 2: 115 peptides, 19 chains. Longest chain 14 peptides. Score 0.427 Round 3: 120 peptides, 19 chains. Longest chain 15 peptides. Score 0.456 Round 4: 114 peptides, 19 chains. Longest chain 12 peptides. Score 0.421 Round 5: 121 peptides, 16 chains. Longest chain 15 peptides. Score 0.533 Taking the results from Round 5 Chains 18, Residues 105, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3412 restraints for refining 1599 atoms. 2969 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2122 (Rfree = 0.000) for 1599 atoms. Found 3 (8 requested) and removed 22 (4 requested) atoms. Cycle 17: After refmac, R = 0.2001 (Rfree = 0.000) for 1573 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2175 (Rfree = 0.000) for 1560 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.2097 (Rfree = 0.000) for 1552 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 20: After refmac, R = 0.2045 (Rfree = 0.000) for 1542 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1599 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1612 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.327 Round 2: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.395 Round 3: 102 peptides, 14 chains. Longest chain 14 peptides. Score 0.479 Round 4: 104 peptides, 13 chains. Longest chain 14 peptides. Score 0.515 Round 5: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 4 Chains 13, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3548 restraints for refining 1559 atoms. 3197 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2022 (Rfree = 0.000) for 1559 atoms. Found 6 (8 requested) and removed 15 (4 requested) atoms. Cycle 22: After refmac, R = 0.2169 (Rfree = 0.000) for 1535 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 23: After refmac, R = 0.2291 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 24: After refmac, R = 0.2088 (Rfree = 0.000) for 1514 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 25: After refmac, R = 0.2182 (Rfree = 0.000) for 1509 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 1566 seeds are put forward NCS extension: 0 residues added, 1566 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 13 peptides. Score 0.305 Round 2: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.448 Round 3: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.410 Round 4: 103 peptides, 16 chains. Longest chain 14 peptides. Score 0.434 Round 5: 104 peptides, 16 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 2 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3414 restraints for refining 1551 atoms. 3042 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2084 (Rfree = 0.000) for 1551 atoms. Found 5 (8 requested) and removed 19 (4 requested) atoms. Cycle 27: After refmac, R = 0.1982 (Rfree = 0.000) for 1524 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2003 (Rfree = 0.000) for 1516 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.1905 (Rfree = 0.000) for 1510 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 30: After refmac, R = 0.1987 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1539 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 1554 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 7 peptides. Score 0.212 Round 2: 95 peptides, 19 chains. Longest chain 10 peptides. Score 0.302 Round 3: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.345 Round 4: 97 peptides, 18 chains. Longest chain 11 peptides. Score 0.343 Round 5: 104 peptides, 18 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 5 Chains 18, Residues 86, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3517 restraints for refining 1562 atoms. 3172 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2204 (Rfree = 0.000) for 1562 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 32: After refmac, R = 0.2050 (Rfree = 0.000) for 1544 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2190 (Rfree = 0.000) for 1536 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2054 (Rfree = 0.000) for 1529 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 35: After refmac, R = 0.2187 (Rfree = 0.000) for 1519 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1584 seeds are put forward NCS extension: 0 residues added, 1584 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 10 peptides. Score 0.301 Round 2: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.311 Round 3: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.338 Round 4: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.371 Round 5: 94 peptides, 15 chains. Longest chain 9 peptides. Score 0.406 Taking the results from Round 5 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3478 restraints for refining 1581 atoms. 3149 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2024 (Rfree = 0.000) for 1581 atoms. Found 4 (8 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.1738 (Rfree = 0.000) for 1558 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2027 (Rfree = 0.000) for 1546 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2154 (Rfree = 0.000) for 1538 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2129 (Rfree = 0.000) for 1530 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1590 seeds are put forward NCS extension: 0 residues added, 1590 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.270 Round 2: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.347 Round 3: 79 peptides, 16 chains. Longest chain 7 peptides. Score 0.279 Round 4: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.366 Round 5: 82 peptides, 13 chains. Longest chain 9 peptides. Score 0.386 Taking the results from Round 5 Chains 13, Residues 69, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3501 restraints for refining 1549 atoms. 3208 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2137 (Rfree = 0.000) for 1549 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.2218 (Rfree = 0.000) for 1531 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2328 (Rfree = 0.000) for 1530 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.2056 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.2358 (Rfree = 0.000) for 1522 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 1555 seeds are put forward NCS extension: 0 residues added, 1555 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.226 Round 2: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.252 Round 3: 70 peptides, 15 chains. Longest chain 6 peptides. Score 0.244 Round 4: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.290 Round 5: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.270 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 58, 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 3362 restraints for refining 1505 atoms. 3144 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1826 (Rfree = 0.000) for 1505 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1986 (Rfree = 0.000) for 1493 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1856 (Rfree = 0.000) for 1484 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1962 (Rfree = 0.000) for 1479 atoms. TimeTaking 28.63