Mon 24 Dec 00:27:42 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 2od4-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.4-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/2od4-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.4-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 00:27:46 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/2od4-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-3.4-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 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-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-3.4-parrot-mrncs.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 1783 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3055 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2797 (Rfree = 0.000) for 1783 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 1831 seeds are put forward NCS extension: 0 residues added, 1831 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.304 Round 2: 123 peptides, 21 chains. Longest chain 14 peptides. Score 0.470 Round 3: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.467 Round 4: 106 peptides, 17 chains. Longest chain 13 peptides. Score 0.472 Round 5: 108 peptides, 17 chains. Longest chain 12 peptides. Score 0.485 Taking the results from Round 5 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3312 restraints for refining 1469 atoms. 2940 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2141 (Rfree = 0.000) for 1469 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2072 (Rfree = 0.000) for 1458 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.1912 (Rfree = 0.000) for 1458 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.1931 (Rfree = 0.000) for 1452 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.1699 (Rfree = 0.000) for 1451 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1545 seeds are put forward Round 1: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.465 Round 2: 124 peptides, 20 chains. Longest chain 16 peptides. Score 0.505 Round 3: 114 peptides, 15 chains. Longest chain 16 peptides. Score 0.578 Round 4: 125 peptides, 18 chains. Longest chain 18 peptides. Score 0.565 Round 5: 125 peptides, 15 chains. Longest chain 15 peptides. Score 0.639 Taking the results from Round 5 Chains 15, Residues 110, Estimated correctness of the model 40.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3271 restraints for refining 1469 atoms. 2846 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2080 (Rfree = 0.000) for 1469 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.1762 (Rfree = 0.000) for 1469 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.1679 (Rfree = 0.000) for 1459 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.1673 (Rfree = 0.000) for 1457 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.1647 (Rfree = 0.000) for 1455 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 1509 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1527 seeds are put forward Round 1: 98 peptides, 15 chains. Longest chain 14 peptides. Score 0.476 Round 2: 105 peptides, 14 chains. Longest chain 17 peptides. Score 0.551 Round 3: 108 peptides, 15 chains. Longest chain 18 peptides. Score 0.542 Round 4: 108 peptides, 16 chains. Longest chain 16 peptides. Score 0.514 Round 5: 114 peptides, 17 chains. Longest chain 13 peptides. Score 0.524 Taking the results from Round 2 Chains 14, Residues 91, Estimated correctness of the model 11.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3364 restraints for refining 1469 atoms. 3014 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1748 (Rfree = 0.000) for 1469 atoms. Found 7 (11 requested) and removed 5 (5 requested) atoms. Cycle 12: After refmac, R = 0.1565 (Rfree = 0.000) for 1464 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.1509 (Rfree = 0.000) for 1458 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.1508 (Rfree = 0.000) for 1454 atoms. Found 0 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.1509 (Rfree = 0.000) for 1448 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1495 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1509 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 14 peptides. Score 0.394 Round 2: 100 peptides, 14 chains. Longest chain 14 peptides. Score 0.519 Round 3: 90 peptides, 12 chains. Longest chain 15 peptides. Score 0.513 Round 4: 93 peptides, 14 chains. Longest chain 13 peptides. Score 0.472 Round 5: 110 peptides, 16 chains. Longest chain 14 peptides. Score 0.527 Taking the results from Round 5 Chains 16, Residues 94, Estimated correctness of the model 3.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3382 restraints for refining 1468 atoms. 3022 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1881 (Rfree = 0.000) for 1468 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 17: After refmac, R = 0.1664 (Rfree = 0.000) for 1464 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.1565 (Rfree = 0.000) for 1463 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.1527 (Rfree = 0.000) for 1462 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1493 (Rfree = 0.000) for 1456 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1529 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.338 Round 2: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.429 Round 3: 88 peptides, 13 chains. Longest chain 15 peptides. Score 0.468 Round 4: 103 peptides, 16 chains. Longest chain 15 peptides. Score 0.481 Round 5: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.497 Taking the results from Round 5 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 3335 restraints for refining 1469 atoms. 3006 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1737 (Rfree = 0.000) for 1469 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.1694 (Rfree = 0.000) for 1465 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.1666 (Rfree = 0.000) for 1460 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.1585 (Rfree = 0.000) for 1456 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1519 (Rfree = 0.000) for 1452 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 1506 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.387 Round 2: 87 peptides, 12 chains. Longest chain 13 peptides. Score 0.492 Round 3: 100 peptides, 15 chains. Longest chain 14 peptides. Score 0.490 Round 4: 99 peptides, 15 chains. Longest chain 14 peptides. Score 0.483 Round 5: 108 peptides, 15 chains. Longest chain 14 peptides. Score 0.542 Taking the results from Round 5 Chains 15, Residues 93, Estimated correctness of the model 8.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3370 restraints for refining 1468 atoms. 3013 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1767 (Rfree = 0.000) for 1468 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.1748 (Rfree = 0.000) for 1466 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1645 (Rfree = 0.000) for 1462 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1567 (Rfree = 0.000) for 1460 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.1587 (Rfree = 0.000) for 1455 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 1494 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1512 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.358 Round 2: 90 peptides, 13 chains. Longest chain 13 peptides. Score 0.482 Round 3: 88 peptides, 14 chains. Longest chain 13 peptides. Score 0.437 Round 4: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.441 Round 5: 94 peptides, 15 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 2 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3490 restraints for refining 1468 atoms. 3195 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1686 (Rfree = 0.000) for 1468 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.1568 (Rfree = 0.000) for 1466 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.1490 (Rfree = 0.000) for 1463 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1460 (Rfree = 0.000) for 1459 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1442 (Rfree = 0.000) for 1456 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1481 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1496 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 10 peptides. Score 0.356 Round 2: 90 peptides, 14 chains. Longest chain 10 peptides. Score 0.451 Round 3: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.476 Round 4: 103 peptides, 16 chains. Longest chain 10 peptides. Score 0.481 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 1.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2870 reflections ( 98.39 % complete ) and 3441 restraints for refining 1469 atoms. 3096 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1847 (Rfree = 0.000) for 1469 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.1734 (Rfree = 0.000) for 1465 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1712 (Rfree = 0.000) for 1463 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1580 (Rfree = 0.000) for 1459 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1604 (Rfree = 0.000) for 1455 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1531 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.356 Round 2: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.453 Round 3: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.418 Round 4: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.497 Round 5: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.434 Taking the results from Round 4 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 3457 restraints for refining 1469 atoms. 3128 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1958 (Rfree = 0.000) for 1469 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.1758 (Rfree = 0.000) for 1465 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.1713 (Rfree = 0.000) for 1463 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1719 (Rfree = 0.000) for 1460 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1662 (Rfree = 0.000) for 1455 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 1491 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1508 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.326 Round 2: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.447 Round 3: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.404 Round 4: 82 peptides, 12 chains. Longest chain 14 peptides. Score 0.457 Round 5: 89 peptides, 15 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 70, 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 3496 restraints for refining 1469 atoms. 3228 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1918 (Rfree = 0.000) for 1469 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1803 (Rfree = 0.000) for 1463 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2438 (Rfree = 0.000) for 1455 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2060 (Rfree = 0.000) for 1448 atoms. TimeTaking 22.63