null Sun 23 Dec 22:22:53 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.8-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 22:23:03 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.8-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 150 and 0 Target number of residues in the AU: 150 Target solvent content: 0.6569 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-3.8-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-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2000 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 Loops will be built when appropriate and at the last cycle Resolution range: 24.534 3.800 Wilson plot Bfac: 81.99 2258 reflections ( 99.60 % complete ) and 0 restraints for refining 2211 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3339 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3548 (Rfree = 0.000) for 2211 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 4.11 Search for helices and strands: 0 residues in 0 chains, 2229 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.223 Round 2: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.327 Round 3: 59 peptides, 12 chains. Longest chain 6 peptides. Score 0.264 Round 4: 67 peptides, 11 chains. Longest chain 11 peptides. Score 0.361 Round 5: 71 peptides, 11 chains. Longest chain 10 peptides. Score 0.390 Taking the results from Round 5 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 4556 restraints for refining 1808 atoms. 4327 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2918 (Rfree = 0.000) for 1808 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 2: After refmac, R = 0.2743 (Rfree = 0.000) for 1770 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2563 (Rfree = 0.000) for 1761 atoms. Found 8 (9 requested) and removed 19 (4 requested) atoms. Cycle 4: After refmac, R = 0.2023 (Rfree = 0.000) for 1735 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2290 (Rfree = 0.000) for 1727 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 1772 seeds are put forward Round 1: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.330 Round 2: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.384 Round 3: 83 peptides, 13 chains. Longest chain 9 peptides. Score 0.412 Round 4: 88 peptides, 15 chains. Longest chain 13 peptides. Score 0.386 Round 5: 89 peptides, 13 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 5 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 4114 restraints for refining 1683 atoms. 3800 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2365 (Rfree = 0.000) for 1683 atoms. Found 9 (9 requested) and removed 30 (4 requested) atoms. Cycle 7: After refmac, R = 0.2298 (Rfree = 0.000) for 1642 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.2089 (Rfree = 0.000) for 1619 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2141 (Rfree = 0.000) for 1608 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2161 (Rfree = 0.000) for 1601 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 1647 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.258 Round 2: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.330 Round 3: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.308 Round 4: 86 peptides, 13 chains. Longest chain 14 peptides. Score 0.432 Round 5: 95 peptides, 13 chains. Longest chain 21 peptides. Score 0.490 Taking the results from Round 5 Chains 13, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3589 restraints for refining 1613 atoms. 3274 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2177 (Rfree = 0.000) for 1613 atoms. Found 7 (8 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2139 (Rfree = 0.000) for 1591 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.2020 (Rfree = 0.000) for 1577 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.1951 (Rfree = 0.000) for 1565 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.1912 (Rfree = 0.000) for 1556 atoms. Found 5 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.87 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.247 Round 2: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.357 Round 3: 83 peptides, 16 chains. Longest chain 7 peptides. Score 0.319 Round 4: 96 peptides, 15 chains. Longest chain 13 peptides. Score 0.440 Round 5: 96 peptides, 14 chains. Longest chain 19 peptides. Score 0.468 Taking the results from Round 5 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3770 restraints for refining 1637 atoms. 3456 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1971 (Rfree = 0.000) for 1637 atoms. Found 7 (9 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.1904 (Rfree = 0.000) for 1624 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.1936 (Rfree = 0.000) for 1618 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 19: After refmac, R = 0.1906 (Rfree = 0.000) for 1611 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2025 (Rfree = 0.000) for 1608 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 1655 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 7 peptides. Score 0.254 Round 2: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.362 Round 3: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.362 Round 4: 75 peptides, 12 chains. Longest chain 13 peptides. Score 0.387 Round 5: 72 peptides, 11 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 5 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3955 restraints for refining 1657 atoms. 3704 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1936 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.1891 (Rfree = 0.000) for 1637 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.1703 (Rfree = 0.000) for 1632 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.1755 (Rfree = 0.000) for 1627 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 25: After refmac, R = 0.1227 (Rfree = 0.000) for 1626 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 7 peptides. Score 0.278 Round 2: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.293 Round 3: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.367 Round 4: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.321 Round 5: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3699 restraints for refining 1614 atoms. 3404 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1922 (Rfree = 0.000) for 1614 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.1778 (Rfree = 0.000) for 1599 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 28: After refmac, R = 0.1757 (Rfree = 0.000) for 1588 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.1686 (Rfree = 0.000) for 1582 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.1639 (Rfree = 0.000) for 1577 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1644 seeds are put forward Round 1: 77 peptides, 18 chains. Longest chain 6 peptides. Score 0.208 Round 2: 84 peptides, 18 chains. Longest chain 8 peptides. Score 0.263 Round 3: 91 peptides, 16 chains. Longest chain 8 peptides. Score 0.377 Round 4: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.386 Round 5: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 5 Chains 18, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3938 restraints for refining 1671 atoms. 3620 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1928 (Rfree = 0.000) for 1671 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.1870 (Rfree = 0.000) for 1654 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 33: After refmac, R = 0.1990 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.1716 (Rfree = 0.000) for 1641 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.1338 (Rfree = 0.000) for 1638 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 1695 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.239 Round 2: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.264 Round 3: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.300 Round 4: 84 peptides, 14 chains. Longest chain 17 peptides. Score 0.388 Round 5: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 4 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3747 restraints for refining 1707 atoms. 3413 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1978 (Rfree = 0.000) for 1707 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 37: After refmac, R = 0.1843 (Rfree = 0.000) for 1686 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.1911 (Rfree = 0.000) for 1676 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1715 (Rfree = 0.000) for 1674 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1647 (Rfree = 0.000) for 1671 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 1729 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 8 peptides. Score 0.244 Round 2: 85 peptides, 16 chains. Longest chain 13 peptides. Score 0.334 Round 3: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.350 Round 4: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.350 Round 5: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 5 Chains 15, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2258 reflections ( 99.60 % complete ) and 3884 restraints for refining 1665 atoms. 3611 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1983 (Rfree = 0.000) for 1665 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.1896 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 43: After refmac, R = 0.1846 (Rfree = 0.000) for 1647 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1823 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 45: After refmac, R = 0.1734 (Rfree = 0.000) for 1638 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 1700 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 7 peptides. Score 0.212 Round 2: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.276 Round 3: 67 peptides, 14 chains. Longest chain 8 peptides. Score 0.261 Round 4: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.312 Round 5: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.305 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 53, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2258 reflections ( 99.60 % complete ) and 3860 restraints for refining 1624 atoms. 3660 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1742 (Rfree = 0.000) for 1624 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1904 (Rfree = 0.000) for 1611 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1675 (Rfree = 0.000) for 1602 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1577 (Rfree = 0.000) for 1598 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:58 GMT 2018 Job finished. TimeTaking 30.09 Used memory is bytes: 5122032