null Sun 23 Dec 22:23:05 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 2od4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-4.0-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/2od4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-4.0-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 22:23:15 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/2od4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-4.0-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 135 and 0 Target number of residues in the AU: 135 Target solvent content: 0.6555 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: 2od4-4.0-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: 2od4-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1616 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: 28.889 4.000 Wilson plot Bfac: 80.16 1758 reflections ( 98.27 % complete ) and 0 restraints for refining 1784 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3315 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2264 (Rfree = 0.000) for 1784 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 0 residues added, 1816 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 7 peptides. Score 0.239 Round 2: 84 peptides, 13 chains. Longest chain 13 peptides. Score 0.439 Round 3: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.446 Round 4: 79 peptides, 14 chains. Longest chain 13 peptides. Score 0.368 Round 5: 76 peptides, 13 chains. Longest chain 14 peptides. Score 0.379 Taking the results from Round 3 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3564 restraints for refining 1458 atoms. 3315 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2114 (Rfree = 0.000) for 1458 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 2: After refmac, R = 0.1979 (Rfree = 0.000) for 1442 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 3: After refmac, R = 0.1877 (Rfree = 0.000) for 1433 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.1785 (Rfree = 0.000) for 1426 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.1812 (Rfree = 0.000) for 1418 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 1458 seeds are put forward NCS extension: 0 residues added, 1458 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 15 peptides. Score 0.342 Round 2: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.376 Round 3: 92 peptides, 15 chains. Longest chain 16 peptides. Score 0.434 Round 4: 84 peptides, 13 chains. Longest chain 10 peptides. Score 0.439 Round 5: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 4 Chains 13, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3450 restraints for refining 1422 atoms. 3179 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1831 (Rfree = 0.000) for 1422 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.1685 (Rfree = 0.000) for 1412 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.1651 (Rfree = 0.000) for 1400 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.1565 (Rfree = 0.000) for 1395 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1642 (Rfree = 0.000) for 1387 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 1443 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.303 Round 2: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.366 Round 3: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.402 Round 4: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.379 Round 5: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.390 Taking the results from Round 3 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3372 restraints for refining 1429 atoms. 3084 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1827 (Rfree = 0.000) for 1429 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.1655 (Rfree = 0.000) for 1426 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.1650 (Rfree = 0.000) for 1419 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.1504 (Rfree = 0.000) for 1416 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.1557 (Rfree = 0.000) for 1412 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 1463 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 1468 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.301 Round 2: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.472 Round 3: 92 peptides, 15 chains. Longest chain 9 peptides. Score 0.434 Round 4: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.506 Round 5: 98 peptides, 14 chains. Longest chain 13 peptides. Score 0.506 Taking the results from Round 5 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3374 restraints for refining 1459 atoms. 3052 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1837 (Rfree = 0.000) for 1459 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 17: After refmac, R = 0.1617 (Rfree = 0.000) for 1450 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.1625 (Rfree = 0.000) for 1442 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.1488 (Rfree = 0.000) for 1437 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.1493 (Rfree = 0.000) for 1432 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 1449 seeds are put forward NCS extension: 0 residues added, 1449 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.292 Round 2: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.431 Round 3: 70 peptides, 10 chains. Longest chain 10 peptides. Score 0.435 Round 4: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.357 Round 5: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 3 Chains 10, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3555 restraints for refining 1457 atoms. 3325 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1652 (Rfree = 0.000) for 1457 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 22: After refmac, R = 0.1506 (Rfree = 0.000) for 1447 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.1493 (Rfree = 0.000) for 1439 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.1441 (Rfree = 0.000) for 1434 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1426 (Rfree = 0.000) for 1428 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 1459 seeds are put forward NCS extension: 0 residues added, 1459 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.261 Round 2: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.326 Round 3: 73 peptides, 13 chains. Longest chain 9 peptides. Score 0.355 Round 4: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.355 Round 5: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 5 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3396 restraints for refining 1403 atoms. 3165 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1794 (Rfree = 0.000) for 1403 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.1634 (Rfree = 0.000) for 1399 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.1605 (Rfree = 0.000) for 1394 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.1556 (Rfree = 0.000) for 1393 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1972 (Rfree = 0.000) for 1389 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 1434 seeds are put forward NCS extension: 0 residues added, 1434 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.258 Round 2: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.344 Round 3: 69 peptides, 11 chains. Longest chain 9 peptides. Score 0.393 Round 4: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.292 Round 5: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 3 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3337 restraints for refining 1388 atoms. 3116 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1753 (Rfree = 0.000) for 1388 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.1569 (Rfree = 0.000) for 1380 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.1502 (Rfree = 0.000) for 1373 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1433 (Rfree = 0.000) for 1368 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1451 (Rfree = 0.000) for 1364 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward NCS extension: 0 residues added, 1403 seeds are put forward Round 1: 63 peptides, 15 chains. Longest chain 5 peptides. Score 0.195 Round 2: 81 peptides, 14 chains. Longest chain 13 peptides. Score 0.384 Round 3: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.340 Round 4: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.349 Round 5: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.303 Taking the results from Round 2 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3180 restraints for refining 1355 atoms. 2926 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1653 (Rfree = 0.000) for 1355 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.1539 (Rfree = 0.000) for 1352 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.1497 (Rfree = 0.000) for 1348 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1456 (Rfree = 0.000) for 1346 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.1444 (Rfree = 0.000) for 1343 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.70 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 5 residues added (0 deleted due to clashes), 1395 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.286 Round 2: 74 peptides, 16 chains. Longest chain 6 peptides. Score 0.257 Round 3: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.360 Round 4: 79 peptides, 13 chains. Longest chain 15 peptides. Score 0.402 Round 5: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.322 Taking the results from Round 4 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1758 reflections ( 98.27 % complete ) and 3243 restraints for refining 1385 atoms. 2992 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1668 (Rfree = 0.000) for 1385 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 42: After refmac, R = 0.1564 (Rfree = 0.000) for 1383 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.1533 (Rfree = 0.000) for 1381 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 44: After refmac, R = 0.1504 (Rfree = 0.000) for 1377 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.1481 (Rfree = 0.000) for 1374 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 0 residues added, 1399 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.286 Round 2: 70 peptides, 14 chains. Longest chain 10 peptides. Score 0.294 Round 3: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.379 Round 4: 68 peptides, 12 chains. Longest chain 12 peptides. Score 0.349 Round 5: 67 peptides, 13 chains. Longest chain 11 peptides. Score 0.305 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 63, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2od4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1758 reflections ( 98.27 % complete ) and 3230 restraints for refining 1406 atoms. 2976 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1671 (Rfree = 0.000) for 1406 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1642 (Rfree = 0.000) for 1401 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1651 (Rfree = 0.000) for 1397 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1622 (Rfree = 0.000) for 1394 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:19 GMT 2018 Job finished. TimeTaking 26.24 Used memory is bytes: 3389536