Sun 23 Dec 22:22:52 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 2od4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.4-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/2od4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.4-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 22:23:02 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/2od4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.4-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 146 and 0 Target number of residues in the AU: 146 Target solvent content: 0.6274 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: 2od4-3.4-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: 2od4-3.4-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 3.401 Wilson plot Bfac: 64.82 2870 reflections ( 98.39 % complete ) and 0 restraints for refining 1788 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3093 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2657 (Rfree = 0.000) for 1788 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 0 residues added, 1838 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.240 Round 2: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.341 Round 3: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.310 Round 4: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.442 Round 5: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.387 Taking the results from Round 4 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3351 restraints for refining 1469 atoms. 3017 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2170 (Rfree = 0.000) for 1469 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.1976 (Rfree = 0.000) for 1455 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2223 (Rfree = 0.000) for 1449 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2193 (Rfree = 0.000) for 1450 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.1723 (Rfree = 0.000) for 1451 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 1525 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.387 Round 2: 90 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Round 3: 99 peptides, 14 chains. Longest chain 15 peptides. Score 0.513 Round 4: 101 peptides, 14 chains. Longest chain 16 peptides. Score 0.526 Round 5: 105 peptides, 16 chains. Longest chain 15 peptides. Score 0.494 Taking the results from Round 4 Chains 14, Residues 87, Estimated correctness of the model 2.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3349 restraints for refining 1469 atoms. 3015 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2002 (Rfree = 0.000) for 1469 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 7: After refmac, R = 0.2068 (Rfree = 0.000) for 1461 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 8: After refmac, R = 0.1971 (Rfree = 0.000) for 1457 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2122 (Rfree = 0.000) for 1457 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.1873 (Rfree = 0.000) for 1452 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1518 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.282 Round 2: 91 peptides, 15 chains. Longest chain 12 peptides. Score 0.427 Round 3: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.497 Round 4: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.448 Round 5: 96 peptides, 14 chains. Longest chain 11 peptides. Score 0.493 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 ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3306 restraints for refining 1469 atoms. 2977 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1904 (Rfree = 0.000) for 1469 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.1810 (Rfree = 0.000) for 1464 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2036 (Rfree = 0.000) for 1460 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.1838 (Rfree = 0.000) for 1456 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1922 (Rfree = 0.000) for 1461 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 1519 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1545 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.405 Round 2: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.469 Round 3: 118 peptides, 19 chains. Longest chain 11 peptides. Score 0.494 Round 4: 113 peptides, 17 chains. Longest chain 15 peptides. Score 0.518 Round 5: 120 peptides, 18 chains. Longest chain 11 peptides. Score 0.535 Taking the results from Round 5 Chains 18, Residues 102, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3274 restraints for refining 1469 atoms. 2884 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1877 (Rfree = 0.000) for 1469 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.1763 (Rfree = 0.000) for 1458 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.1717 (Rfree = 0.000) for 1453 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.1689 (Rfree = 0.000) for 1449 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1661 (Rfree = 0.000) for 1444 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1488 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1502 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.311 Round 2: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.442 Round 3: 117 peptides, 20 chains. Longest chain 15 peptides. Score 0.459 Round 4: 94 peptides, 14 chains. Longest chain 14 peptides. Score 0.479 Round 5: 100 peptides, 17 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 4 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3386 restraints for refining 1469 atoms. 3080 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1867 (Rfree = 0.000) for 1469 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 22: After refmac, R = 0.1853 (Rfree = 0.000) for 1463 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.1858 (Rfree = 0.000) for 1466 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.1807 (Rfree = 0.000) for 1466 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1835 (Rfree = 0.000) for 1470 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1517 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1543 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 13 peptides. Score 0.352 Round 2: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.434 Round 3: 106 peptides, 15 chains. Longest chain 13 peptides. Score 0.530 Round 4: 90 peptides, 15 chains. Longest chain 12 peptides. Score 0.419 Round 5: 95 peptides, 14 chains. Longest chain 12 peptides. Score 0.486 Taking the results from Round 3 Chains 15, Residues 91, Estimated correctness of the model 4.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3246 restraints for refining 1469 atoms. 2897 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1810 (Rfree = 0.000) for 1469 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.1877 (Rfree = 0.000) for 1464 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1975 (Rfree = 0.000) for 1459 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.1573 (Rfree = 0.000) for 1454 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.1757 (Rfree = 0.000) for 1450 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1519 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.319 Round 2: 103 peptides, 18 chains. Longest chain 13 peptides. Score 0.420 Round 3: 112 peptides, 16 chains. Longest chain 13 peptides. Score 0.539 Round 4: 115 peptides, 17 chains. Longest chain 16 peptides. Score 0.531 Round 5: 114 peptides, 17 chains. Longest chain 12 peptides. Score 0.524 Taking the results from Round 3 Chains 16, Residues 96, Estimated correctness of the model 7.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3253 restraints for refining 1469 atoms. 2885 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1771 (Rfree = 0.000) for 1469 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.1747 (Rfree = 0.000) for 1464 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.1826 (Rfree = 0.000) for 1462 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1729 (Rfree = 0.000) for 1464 atoms. Found 7 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1701 (Rfree = 0.000) for 1465 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 1508 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1526 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.317 Round 2: 92 peptides, 15 chains. Longest chain 9 peptides. Score 0.434 Round 3: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.462 Round 4: 94 peptides, 15 chains. Longest chain 13 peptides. Score 0.448 Round 5: 91 peptides, 13 chains. Longest chain 9 peptides. Score 0.489 Taking the results from Round 5 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3412 restraints for refining 1469 atoms. 3113 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2054 (Rfree = 0.000) for 1469 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.1974 (Rfree = 0.000) for 1472 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.1845 (Rfree = 0.000) for 1474 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1859 (Rfree = 0.000) for 1469 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.1699 (Rfree = 0.000) for 1469 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 1519 seeds are put forward NCS extension: 0 residues added, 1519 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.322 Round 2: 78 peptides, 14 chains. Longest chain 9 peptides. Score 0.360 Round 3: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.389 Round 4: 85 peptides, 14 chains. Longest chain 9 peptides. Score 0.414 Round 5: 83 peptides, 12 chains. Longest chain 14 peptides. Score 0.464 Taking the results from Round 5 Chains 12, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3460 restraints for refining 1468 atoms. 3188 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1973 (Rfree = 0.000) for 1468 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.1791 (Rfree = 0.000) for 1463 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1793 (Rfree = 0.000) for 1462 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1586 (Rfree = 0.000) for 1466 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1795 (Rfree = 0.000) for 1466 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 1507 seeds are put forward NCS extension: 0 residues added, 1507 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 9 peptides. Score 0.259 Round 2: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.363 Round 3: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.420 Round 4: 84 peptides, 12 chains. Longest chain 13 peptides. Score 0.471 Round 5: 83 peptides, 11 chains. Longest chain 12 peptides. Score 0.496 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 72, 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. 2870 reflections ( 98.39 % complete ) and 3375 restraints for refining 1468 atoms. 3098 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1771 (Rfree = 0.000) for 1468 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1768 (Rfree = 0.000) for 1452 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1426 (Rfree = 0.000) for 1446 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1340 (Rfree = 0.000) for 1440 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. TimeTaking 27.95