Sun 23 Dec 22:22:59 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 2od4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-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/2od4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-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 22:23:09 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/2od4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-3.2-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6198 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: 2od4-3.2-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: 2od4-3.2-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 3.200 Wilson plot Bfac: 61.23 3433 reflections ( 98.54 % complete ) and 0 restraints for refining 1786 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2626 (Rfree = 0.000) for 1786 atoms. Found 14 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward NCS extension: 0 residues added, 1809 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.360 Round 2: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.492 Round 3: 111 peptides, 19 chains. Longest chain 15 peptides. Score 0.447 Round 4: 109 peptides, 16 chains. Longest chain 15 peptides. Score 0.520 Round 5: 117 peptides, 17 chains. Longest chain 17 peptides. Score 0.543 Taking the results from Round 5 Chains 17, Residues 100, Estimated correctness of the model 24.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3317 restraints for refining 1476 atoms. 2934 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2333 (Rfree = 0.000) for 1476 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.2178 (Rfree = 0.000) for 1463 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 3: After refmac, R = 0.2125 (Rfree = 0.000) for 1457 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2085 (Rfree = 0.000) for 1450 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2100 (Rfree = 0.000) for 1446 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 1511 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1530 seeds are put forward Round 1: 102 peptides, 15 chains. Longest chain 16 peptides. Score 0.503 Round 2: 103 peptides, 15 chains. Longest chain 21 peptides. Score 0.510 Round 3: 108 peptides, 12 chains. Longest chain 21 peptides. Score 0.622 Round 4: 114 peptides, 14 chains. Longest chain 16 peptides. Score 0.604 Round 5: 120 peptides, 13 chains. Longest chain 21 peptides. Score 0.660 Taking the results from Round 5 Chains 13, Residues 107, Estimated correctness of the model 56.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3270 restraints for refining 1476 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2278 (Rfree = 0.000) for 1476 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.2062 (Rfree = 0.000) for 1465 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.1964 (Rfree = 0.000) for 1462 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.1916 (Rfree = 0.000) for 1457 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.1894 (Rfree = 0.000) for 1450 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 1500 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 1527 seeds are put forward Round 1: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.505 Round 2: 119 peptides, 17 chains. Longest chain 18 peptides. Score 0.555 Round 3: 125 peptides, 15 chains. Longest chain 21 peptides. Score 0.639 Round 4: 123 peptides, 18 chains. Longest chain 14 peptides. Score 0.553 Round 5: 124 peptides, 16 chains. Longest chain 19 peptides. Score 0.610 Taking the results from Round 3 Chains 15, Residues 110, Estimated correctness of the model 51.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3251 restraints for refining 1476 atoms. 2826 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2271 (Rfree = 0.000) for 1476 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 1475 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.1868 (Rfree = 0.000) for 1474 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.1901 (Rfree = 0.000) for 1473 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1897 (Rfree = 0.000) for 1471 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 1513 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 1554 seeds are put forward Round 1: 109 peptides, 16 chains. Longest chain 21 peptides. Score 0.520 Round 2: 121 peptides, 16 chains. Longest chain 21 peptides. Score 0.593 Round 3: 120 peptides, 14 chains. Longest chain 21 peptides. Score 0.637 Round 4: 114 peptides, 16 chains. Longest chain 14 peptides. Score 0.552 Round 5: 112 peptides, 14 chains. Longest chain 20 peptides. Score 0.593 Taking the results from Round 3 Chains 14, Residues 106, Estimated correctness of the model 50.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3316 restraints for refining 1476 atoms. 2906 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2013 (Rfree = 0.000) for 1476 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.1897 (Rfree = 0.000) for 1474 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.1856 (Rfree = 0.000) for 1467 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1820 (Rfree = 0.000) for 1466 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1805 (Rfree = 0.000) for 1463 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 1495 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 1531 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 14 peptides. Score 0.364 Round 2: 99 peptides, 17 chains. Longest chain 15 peptides. Score 0.422 Round 3: 96 peptides, 15 chains. Longest chain 16 peptides. Score 0.462 Round 4: 93 peptides, 13 chains. Longest chain 17 peptides. Score 0.503 Round 5: 99 peptides, 16 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 4 Chains 13, Residues 80, Estimated correctness of the model 12.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3510 restraints for refining 1476 atoms. 3203 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2090 (Rfree = 0.000) for 1476 atoms. Found 12 (13 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.1898 (Rfree = 0.000) for 1482 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.1819 (Rfree = 0.000) for 1478 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1805 (Rfree = 0.000) for 1473 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1816 (Rfree = 0.000) for 1469 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1530 seeds are put forward Round 1: 117 peptides, 19 chains. Longest chain 19 peptides. Score 0.488 Round 2: 115 peptides, 17 chains. Longest chain 17 peptides. Score 0.531 Round 3: 115 peptides, 14 chains. Longest chain 19 peptides. Score 0.610 Round 4: 123 peptides, 18 chains. Longest chain 19 peptides. Score 0.553 Round 5: 119 peptides, 17 chains. Longest chain 17 peptides. Score 0.555 Taking the results from Round 3 Chains 14, Residues 101, Estimated correctness of the model 43.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3323 restraints for refining 1476 atoms. 2933 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2018 (Rfree = 0.000) for 1476 atoms. Found 12 (13 requested) and removed 6 (6 requested) atoms. Cycle 27: After refmac, R = 0.1882 (Rfree = 0.000) for 1479 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.1886 (Rfree = 0.000) for 1472 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1796 (Rfree = 0.000) for 1471 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1698 (Rfree = 0.000) for 1464 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.17 Search for helices and strands: 0 residues in 0 chains, 1509 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1533 seeds are put forward Round 1: 89 peptides, 16 chains. Longest chain 14 peptides. Score 0.379 Round 2: 115 peptides, 16 chains. Longest chain 21 peptides. Score 0.558 Round 3: 103 peptides, 16 chains. Longest chain 18 peptides. Score 0.481 Round 4: 108 peptides, 16 chains. Longest chain 16 peptides. Score 0.514 Round 5: 108 peptides, 16 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 2 Chains 16, Residues 99, Estimated correctness of the model 29.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3254 restraints for refining 1476 atoms. 2874 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1867 (Rfree = 0.000) for 1476 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.1809 (Rfree = 0.000) for 1480 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1661 (Rfree = 0.000) for 1475 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1536 (Rfree = 0.000) for 1476 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1459 (Rfree = 0.000) for 1470 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 1505 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 1543 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 17 peptides. Score 0.404 Round 2: 110 peptides, 15 chains. Longest chain 20 peptides. Score 0.554 Round 3: 105 peptides, 15 chains. Longest chain 22 peptides. Score 0.523 Round 4: 107 peptides, 17 chains. Longest chain 19 peptides. Score 0.478 Round 5: 108 peptides, 15 chains. Longest chain 17 peptides. Score 0.542 Taking the results from Round 2 Chains 15, Residues 95, Estimated correctness of the model 28.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3276 restraints for refining 1475 atoms. 2911 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1585 (Rfree = 0.000) for 1475 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.1552 (Rfree = 0.000) for 1470 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1644 (Rfree = 0.000) for 1469 atoms. Found 11 (13 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.1650 (Rfree = 0.000) for 1473 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1606 (Rfree = 0.000) for 1477 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1532 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 1565 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.392 Round 2: 108 peptides, 18 chains. Longest chain 17 peptides. Score 0.456 Round 3: 114 peptides, 17 chains. Longest chain 18 peptides. Score 0.524 Round 4: 113 peptides, 18 chains. Longest chain 18 peptides. Score 0.490 Round 5: 112 peptides, 18 chains. Longest chain 14 peptides. Score 0.483 Taking the results from Round 3 Chains 17, Residues 97, Estimated correctness of the model 19.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3433 reflections ( 98.54 % complete ) and 3308 restraints for refining 1476 atoms. 2937 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1698 (Rfree = 0.000) for 1476 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.1483 (Rfree = 0.000) for 1482 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1437 (Rfree = 0.000) for 1478 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1425 (Rfree = 0.000) for 1472 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1599 (Rfree = 0.000) for 1467 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.18 Search for helices and strands: 0 residues in 0 chains, 1505 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1525 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 16 peptides. Score 0.374 Round 2: 100 peptides, 15 chains. Longest chain 18 peptides. Score 0.490 Round 3: 87 peptides, 13 chains. Longest chain 13 peptides. Score 0.461 Round 4: 88 peptides, 14 chains. Longest chain 13 peptides. Score 0.437 Round 5: 88 peptides, 11 chains. Longest chain 24 peptides. Score 0.529 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 77, Estimated correctness of the model 20.5 % 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. 3433 reflections ( 98.54 % complete ) and 3402 restraints for refining 1476 atoms. 3105 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1585 (Rfree = 0.000) for 1476 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1798 (Rfree = 0.000) for 1470 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1421 (Rfree = 0.000) for 1464 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1380 (Rfree = 0.000) for 1458 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 27.97