null 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 2etj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-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/2etj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-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 22:23:08 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/2etj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-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 147 and 0 Target number of residues in the AU: 147 Target solvent content: 0.6637 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 250 Adjusted target solvent content: 0.43 Input MTZ file: 2etj-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: 144 Cell parameters: 51.821 51.821 76.293 90.000 90.000 120.000 Input sequence file: 2etj-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2000 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 Loops will be built when appropriate and at the last cycle Resolution range: 24.534 4.000 Wilson plot Bfac: 87.18 1930 reflections ( 99.54 % complete ) and 0 restraints for refining 2212 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3482 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3227 (Rfree = 0.000) for 2212 atoms. Found 7 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 2235 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.243 Round 2: 69 peptides, 15 chains. Longest chain 8 peptides. Score 0.243 Round 3: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.269 Round 4: 72 peptides, 14 chains. Longest chain 9 peptides. Score 0.300 Round 5: 75 peptides, 13 chains. Longest chain 13 peptides. Score 0.355 Taking the results from Round 5 Chains 13, Residues 62, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 4356 restraints for refining 1723 atoms. 4109 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2617 (Rfree = 0.000) for 1723 atoms. Found 3 (8 requested) and removed 16 (4 requested) atoms. Cycle 2: After refmac, R = 0.2180 (Rfree = 0.000) for 1687 atoms. Found 7 (8 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.2123 (Rfree = 0.000) for 1673 atoms. Found 3 (7 requested) and removed 9 (3 requested) atoms. Cycle 4: After refmac, R = 0.1983 (Rfree = 0.000) for 1658 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.1956 (Rfree = 0.000) for 1652 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 4.09 Search for helices and strands: 0 residues in 0 chains, 1694 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.262 Round 2: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.325 Round 3: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.348 Round 4: 64 peptides, 12 chains. Longest chain 7 peptides. Score 0.305 Round 5: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 5 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 3948 restraints for refining 1575 atoms. 3735 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1986 (Rfree = 0.000) for 1575 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 7: After refmac, R = 0.1801 (Rfree = 0.000) for 1572 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.1693 (Rfree = 0.000) for 1564 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.1630 (Rfree = 0.000) for 1559 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.1579 (Rfree = 0.000) for 1553 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 4.10 Search for helices and strands: 0 residues in 0 chains, 1602 seeds are put forward Round 1: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.306 Round 2: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.315 Round 3: 64 peptides, 10 chains. Longest chain 12 peptides. Score 0.372 Round 4: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.339 Round 5: 73 peptides, 11 chains. Longest chain 10 peptides. Score 0.405 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 3981 restraints for refining 1622 atoms. 3744 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1858 (Rfree = 0.000) for 1622 atoms. Found 4 (7 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.1673 (Rfree = 0.000) for 1603 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.1524 (Rfree = 0.000) for 1595 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 14: After refmac, R = 0.1586 (Rfree = 0.000) for 1593 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 15: After refmac, R = 0.1400 (Rfree = 0.000) for 1587 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 1616 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.289 Round 2: 62 peptides, 10 chains. Longest chain 12 peptides. Score 0.357 Round 3: 65 peptides, 11 chains. Longest chain 15 peptides. Score 0.346 Round 4: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.362 Round 5: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.373 Taking the results from Round 5 Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 3994 restraints for refining 1640 atoms. 3762 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1946 (Rfree = 0.000) for 1640 atoms. Found 5 (7 requested) and removed 16 (3 requested) atoms. Cycle 17: After refmac, R = 0.1632 (Rfree = 0.000) for 1622 atoms. Found 2 (7 requested) and removed 11 (3 requested) atoms. Cycle 18: After refmac, R = 0.1547 (Rfree = 0.000) for 1609 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.1323 (Rfree = 0.000) for 1605 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1364 (Rfree = 0.000) for 1604 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 1671 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.261 Round 2: 73 peptides, 12 chains. Longest chain 9 peptides. Score 0.373 Round 3: 75 peptides, 12 chains. Longest chain 13 peptides. Score 0.387 Round 4: 79 peptides, 11 chains. Longest chain 13 peptides. Score 0.446 Round 5: 79 peptides, 12 chains. Longest chain 13 peptides. Score 0.415 Taking the results from Round 4 Chains 12, Residues 68, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 3921 restraints for refining 1654 atoms. 3642 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1873 (Rfree = 0.000) for 1654 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 22: After refmac, R = 0.1579 (Rfree = 0.000) for 1647 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 23: After refmac, R = 0.1469 (Rfree = 0.000) for 1641 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1479 (Rfree = 0.000) for 1632 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1434 (Rfree = 0.000) for 1627 atoms. Found 0 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 4.05 Search for helices and strands: 0 residues in 0 chains, 1674 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.252 Round 2: 75 peptides, 13 chains. Longest chain 13 peptides. Score 0.355 Round 3: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.374 Round 4: 68 peptides, 11 chains. Longest chain 13 peptides. Score 0.369 Round 5: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 5 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 4109 restraints for refining 1695 atoms. 3860 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1613 (Rfree = 0.000) for 1695 atoms. Found 1 (8 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.1552 (Rfree = 0.000) for 1681 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.1495 (Rfree = 0.000) for 1673 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1422 (Rfree = 0.000) for 1668 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1454 (Rfree = 0.000) for 1662 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 4.10 Search for helices and strands: 0 residues in 0 chains, 1705 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.229 Round 2: 55 peptides, 9 chains. Longest chain 14 peptides. Score 0.338 Round 3: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.299 Round 4: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.291 Round 5: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.299 Taking the results from Round 2 Chains 9, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 4237 restraints for refining 1687 atoms. 4062 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1539 (Rfree = 0.000) for 1687 atoms. Found 1 (8 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.1543 (Rfree = 0.000) for 1675 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.1352 (Rfree = 0.000) for 1671 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1386 (Rfree = 0.000) for 1668 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1308 (Rfree = 0.000) for 1663 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 4.13 Search for helices and strands: 0 residues in 0 chains, 1707 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.236 Round 2: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.284 Round 3: 81 peptides, 15 chains. Longest chain 15 peptides. Score 0.336 Round 4: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.328 Round 5: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.367 Taking the results from Round 5 Chains 14, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 4215 restraints for refining 1726 atoms. 3961 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1648 (Rfree = 0.000) for 1726 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 37: After refmac, R = 0.1575 (Rfree = 0.000) for 1708 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.1517 (Rfree = 0.000) for 1699 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 39: After refmac, R = 0.1392 (Rfree = 0.000) for 1691 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1314 (Rfree = 0.000) for 1686 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 4.10 Search for helices and strands: 0 residues in 0 chains, 1718 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 8 peptides. Score 0.229 Round 2: 58 peptides, 12 chains. Longest chain 10 peptides. Score 0.256 Round 3: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.289 Round 4: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.289 Round 5: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 99.54 % complete ) and 4131 restraints for refining 1705 atoms. 3922 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1545 (Rfree = 0.000) for 1705 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.1394 (Rfree = 0.000) for 1700 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.1356 (Rfree = 0.000) for 1694 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.1344 (Rfree = 0.000) for 1689 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1314 (Rfree = 0.000) for 1686 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 4.12 Search for helices and strands: 0 residues in 0 chains, 1727 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 9 peptides. Score 0.269 Round 2: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.390 Round 3: 74 peptides, 13 chains. Longest chain 13 peptides. Score 0.348 Round 4: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.318 Round 5: 67 peptides, 12 chains. Longest chain 13 peptides. Score 0.328 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 60, 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 2etj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1930 reflections ( 99.54 % complete ) and 4145 restraints for refining 1707 atoms. 3916 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1607 (Rfree = 0.000) for 1707 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1452 (Rfree = 0.000) for 1698 atoms. Found 0 (8 requested) and removed 3 (4 requested) atoms. Cycle 48: After refmac, R = 0.1402 (Rfree = 0.000) for 1691 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1527 (Rfree = 0.000) for 1686 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:55 GMT 2018 Job finished. TimeTaking 28.93 Used memory is bytes: 13339344