null Sun 23 Dec 22:23:02 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 2gjg-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-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/2gjg-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-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 22:23:12 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/2gjg-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-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 174 and 0 Target number of residues in the AU: 174 Target solvent content: 0.6255 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.47 Input MTZ file: 2gjg-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: 5 Cell parameters: 89.350 48.920 57.630 90.000 93.310 90.000 Input sequence file: 2gjg-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 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: 28.767 3.801 Wilson plot Bfac: 63.92 2507 reflections ( 98.55 % complete ) and 0 restraints for refining 2200 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3041 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3112 (Rfree = 0.000) for 2200 atoms. Found 11 (12 requested) and removed 31 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.59 Search for helices and strands: 0 residues in 0 chains, 2212 seeds are put forward Round 1: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.360 Round 2: 124 peptides, 21 chains. Longest chain 11 peptides. Score 0.440 Round 3: 132 peptides, 21 chains. Longest chain 13 peptides. Score 0.486 Round 4: 140 peptides, 19 chains. Longest chain 14 peptides. Score 0.575 Round 5: 134 peptides, 20 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 4 Chains 19, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4116 restraints for refining 1794 atoms. 3651 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2554 (Rfree = 0.000) for 1794 atoms. Found 3 (9 requested) and removed 21 (4 requested) atoms. Cycle 2: After refmac, R = 0.2056 (Rfree = 0.000) for 1757 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.1878 (Rfree = 0.000) for 1753 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.1878 (Rfree = 0.000) for 1746 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.1395 (Rfree = 0.000) for 1741 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.55 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 14 peptides. Score 0.411 Round 2: 127 peptides, 19 chains. Longest chain 20 peptides. Score 0.507 Round 3: 143 peptides, 19 chains. Longest chain 19 peptides. Score 0.590 Round 4: 140 peptides, 20 chains. Longest chain 12 peptides. Score 0.553 Round 5: 136 peptides, 19 chains. Longest chain 18 peptides. Score 0.555 Taking the results from Round 3 Chains 19, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4092 restraints for refining 1794 atoms. 3615 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2365 (Rfree = 0.000) for 1794 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.2232 (Rfree = 0.000) for 1773 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.1645 (Rfree = 0.000) for 1772 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.1507 (Rfree = 0.000) for 1765 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.1562 (Rfree = 0.000) for 1762 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.55 Search for helices and strands: 0 residues in 0 chains, 1812 seeds are put forward Round 1: 124 peptides, 20 chains. Longest chain 16 peptides. Score 0.465 Round 2: 133 peptides, 19 chains. Longest chain 18 peptides. Score 0.539 Round 3: 130 peptides, 17 chains. Longest chain 19 peptides. Score 0.570 Round 4: 130 peptides, 19 chains. Longest chain 13 peptides. Score 0.523 Round 5: 119 peptides, 17 chains. Longest chain 14 peptides. Score 0.512 Taking the results from Round 3 Chains 17, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4044 restraints for refining 1794 atoms. 3609 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2621 (Rfree = 0.000) for 1794 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.1872 (Rfree = 0.000) for 1785 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.1649 (Rfree = 0.000) for 1773 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.1335 (Rfree = 0.000) for 1770 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.1319 (Rfree = 0.000) for 1761 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.55 Search for helices and strands: 0 residues in 0 chains, 1789 seeds are put forward Round 1: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.394 Round 2: 110 peptides, 18 chains. Longest chain 16 peptides. Score 0.433 Round 3: 139 peptides, 20 chains. Longest chain 17 peptides. Score 0.548 Round 4: 147 peptides, 22 chains. Longest chain 17 peptides. Score 0.544 Round 5: 139 peptides, 18 chains. Longest chain 19 peptides. Score 0.592 Taking the results from Round 5 Chains 20, Residues 121, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 3954 restraints for refining 1794 atoms. 3446 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2367 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 17: After refmac, R = 0.2136 (Rfree = 0.000) for 1773 atoms. Found 9 (9 requested) and removed 28 (4 requested) atoms. Cycle 18: After refmac, R = 0.1668 (Rfree = 0.000) for 1751 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.1766 (Rfree = 0.000) for 1747 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1790 (Rfree = 0.000) for 1742 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.57 Search for helices and strands: 0 residues in 0 chains, 1811 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 10 peptides. Score 0.286 Round 2: 125 peptides, 21 chains. Longest chain 14 peptides. Score 0.446 Round 3: 123 peptides, 20 chains. Longest chain 16 peptides. Score 0.459 Round 4: 122 peptides, 18 chains. Longest chain 15 peptides. Score 0.504 Round 5: 122 peptides, 18 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 5 Chains 18, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4139 restraints for refining 1794 atoms. 3741 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1868 (Rfree = 0.000) for 1794 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.1834 (Rfree = 0.000) for 1781 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.1875 (Rfree = 0.000) for 1775 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.1667 (Rfree = 0.000) for 1768 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 25: After refmac, R = 0.1886 (Rfree = 0.000) for 1759 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.54 Search for helices and strands: 0 residues in 0 chains, 1798 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 9 peptides. Score 0.298 Round 2: 121 peptides, 18 chains. Longest chain 19 peptides. Score 0.498 Round 3: 110 peptides, 17 chains. Longest chain 12 peptides. Score 0.460 Round 4: 106 peptides, 16 chains. Longest chain 19 peptides. Score 0.462 Round 5: 106 peptides, 15 chains. Longest chain 21 peptides. Score 0.488 Taking the results from Round 2 Chains 18, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4047 restraints for refining 1793 atoms. 3653 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2111 (Rfree = 0.000) for 1793 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.1983 (Rfree = 0.000) for 1781 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.1469 (Rfree = 0.000) for 1774 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.1323 (Rfree = 0.000) for 1761 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1266 (Rfree = 0.000) for 1755 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.59 Search for helices and strands: 0 residues in 0 chains, 1791 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.314 Round 2: 95 peptides, 15 chains. Longest chain 17 peptides. Score 0.422 Round 3: 98 peptides, 15 chains. Longest chain 20 peptides. Score 0.440 Round 4: 94 peptides, 13 chains. Longest chain 18 peptides. Score 0.471 Round 5: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.423 Taking the results from Round 4 Chains 13, Residues 81, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4044 restraints for refining 1794 atoms. 3653 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2287 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.1913 (Rfree = 0.000) for 1782 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.1975 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.1511 (Rfree = 0.000) for 1779 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.1787 (Rfree = 0.000) for 1774 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.57 Search for helices and strands: 0 residues in 0 chains, 1803 seeds are put forward Round 1: 100 peptides, 18 chains. Longest chain 18 peptides. Score 0.370 Round 2: 116 peptides, 19 chains. Longest chain 14 peptides. Score 0.444 Round 3: 111 peptides, 17 chains. Longest chain 18 peptides. Score 0.466 Round 4: 106 peptides, 17 chains. Longest chain 16 peptides. Score 0.436 Round 5: 108 peptides, 17 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 3 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4127 restraints for refining 1793 atoms. 3768 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2123 (Rfree = 0.000) for 1793 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.1895 (Rfree = 0.000) for 1778 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.1390 (Rfree = 0.000) for 1775 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1259 (Rfree = 0.000) for 1768 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1218 (Rfree = 0.000) for 1767 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.58 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.340 Round 2: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.404 Round 3: 97 peptides, 13 chains. Longest chain 17 peptides. Score 0.488 Round 4: 100 peptides, 16 chains. Longest chain 8 peptides. Score 0.426 Round 5: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.336 Taking the results from Round 3 Chains 13, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2507 reflections ( 98.55 % complete ) and 4187 restraints for refining 1794 atoms. 3864 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1882 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.1786 (Rfree = 0.000) for 1789 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1324 (Rfree = 0.000) for 1788 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1186 (Rfree = 0.000) for 1782 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1103 (Rfree = 0.000) for 1779 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.56 Search for helices and strands: 0 residues in 0 chains, 1804 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 7 peptides. Score 0.260 Round 2: 84 peptides, 13 chains. Longest chain 13 peptides. Score 0.408 Round 3: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.298 Round 4: 78 peptides, 12 chains. Longest chain 10 peptides. Score 0.398 Round 5: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 71, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2gjg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2507 reflections ( 98.55 % complete ) and 4198 restraints for refining 1791 atoms. 3892 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1640 (Rfree = 0.000) for 1791 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2256 (Rfree = 0.000) for 1783 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1199 (Rfree = 0.000) for 1776 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1132 (Rfree = 0.000) for 1769 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:56 GMT 2018 Job finished. TimeTaking 30.91 Used memory is bytes: 5641504