Tue 25 Dec 19:27:57 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 2o8q-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-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/2o8q-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-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 ============================================================ Tue 25 Dec 19:28:06 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/2o8q-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.6541 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.90 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: 29.026 4.000 Wilson plot Bfac: 80.46 3635 reflections ( 98.22 % complete ) and 0 restraints for refining 2367 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3238 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3051 (Rfree = 0.000) for 2367 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.06 Search for helices and strands: 0 residues in 0 chains, 2393 seeds are put forward NCS extension: 0 residues added, 2393 seeds are put forward Round 1: 134 peptides, 23 chains. Longest chain 11 peptides. Score 0.368 Round 2: 155 peptides, 19 chains. Longest chain 17 peptides. Score 0.520 Round 3: 166 peptides, 18 chains. Longest chain 33 peptides. Score 0.573 Round 4: 172 peptides, 21 chains. Longest chain 22 peptides. Score 0.547 Round 5: 170 peptides, 20 chains. Longest chain 20 peptides. Score 0.556 Taking the results from Round 3 Chains 19, Residues 148, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4177 restraints for refining 1935 atoms. 3553 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2725 (Rfree = 0.000) for 1935 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.2666 (Rfree = 0.000) for 1883 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.2511 (Rfree = 0.000) for 1854 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 4: After refmac, R = 0.2238 (Rfree = 0.000) for 1825 atoms. Found 4 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2377 (Rfree = 0.000) for 1813 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.08 Search for helices and strands: 0 residues in 0 chains, 1851 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1871 seeds are put forward Round 1: 169 peptides, 24 chains. Longest chain 17 peptides. Score 0.489 Round 2: 166 peptides, 23 chains. Longest chain 19 peptides. Score 0.494 Round 3: 169 peptides, 19 chains. Longest chain 20 peptides. Score 0.568 Round 4: 158 peptides, 20 chains. Longest chain 18 peptides. Score 0.514 Round 5: 163 peptides, 21 chains. Longest chain 14 peptides. Score 0.516 Taking the results from Round 3 Chains 20, Residues 150, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4286 restraints for refining 1936 atoms. 3686 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2728 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2638 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.2613 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2500 (Rfree = 0.000) for 1880 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.2489 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.04 Search for helices and strands: 0 residues in 0 chains, 1909 seeds are put forward NCS extension: 0 residues added, 1909 seeds are put forward Round 1: 140 peptides, 19 chains. Longest chain 13 peptides. Score 0.465 Round 2: 160 peptides, 23 chains. Longest chain 12 peptides. Score 0.472 Round 3: 160 peptides, 20 chains. Longest chain 15 peptides. Score 0.522 Round 4: 159 peptides, 24 chains. Longest chain 14 peptides. Score 0.451 Round 5: 162 peptides, 19 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 5 Chains 19, Residues 143, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4108 restraints for refining 1936 atoms. 3465 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2808 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 12: After refmac, R = 0.2751 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2718 (Rfree = 0.000) for 1867 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 14: After refmac, R = 0.2644 (Rfree = 0.000) for 1848 atoms. Found 8 (8 requested) and removed 30 (4 requested) atoms. Cycle 15: After refmac, R = 0.2329 (Rfree = 0.000) for 1815 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.04 Search for helices and strands: 0 residues in 0 chains, 1852 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1866 seeds are put forward Round 1: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.336 Round 2: 146 peptides, 21 chains. Longest chain 18 peptides. Score 0.453 Round 3: 142 peptides, 20 chains. Longest chain 18 peptides. Score 0.455 Round 4: 144 peptides, 21 chains. Longest chain 20 peptides. Score 0.445 Round 5: 143 peptides, 22 chains. Longest chain 14 peptides. Score 0.423 Taking the results from Round 3 Chains 20, Residues 122, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4350 restraints for refining 1927 atoms. 3869 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2716 (Rfree = 0.000) for 1927 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 17: After refmac, R = 0.2515 (Rfree = 0.000) for 1893 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2606 (Rfree = 0.000) for 1875 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 19: After refmac, R = 0.2556 (Rfree = 0.000) for 1851 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2545 (Rfree = 0.000) for 1828 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.04 Search for helices and strands: 0 residues in 0 chains, 1885 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1902 seeds are put forward Round 1: 133 peptides, 21 chains. Longest chain 12 peptides. Score 0.401 Round 2: 169 peptides, 25 chains. Longest chain 26 peptides. Score 0.472 Round 3: 156 peptides, 20 chains. Longest chain 29 peptides. Score 0.507 Round 4: 159 peptides, 21 chains. Longest chain 16 peptides. Score 0.502 Round 5: 160 peptides, 21 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 3 Chains 20, Residues 136, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 3983 restraints for refining 1936 atoms. 3344 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2744 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 22: After refmac, R = 0.2717 (Rfree = 0.000) for 1898 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2674 (Rfree = 0.000) for 1887 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2612 (Rfree = 0.000) for 1859 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 25: After refmac, R = 0.2667 (Rfree = 0.000) for 1832 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 1860 seeds are put forward NCS extension: 57 residues added (0 deleted due to clashes), 1917 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 14 peptides. Score 0.346 Round 2: 158 peptides, 23 chains. Longest chain 15 peptides. Score 0.465 Round 3: 147 peptides, 18 chains. Longest chain 17 peptides. Score 0.508 Round 4: 144 peptides, 17 chains. Longest chain 16 peptides. Score 0.514 Round 5: 147 peptides, 19 chains. Longest chain 17 peptides. Score 0.491 Taking the results from Round 4 Chains 18, Residues 127, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3635 reflections ( 98.22 % complete ) and 4192 restraints for refining 1936 atoms. 3656 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2610 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2629 (Rfree = 0.000) for 1912 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2473 (Rfree = 0.000) for 1890 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2515 (Rfree = 0.000) for 1875 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2326 (Rfree = 0.000) for 1869 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 2.99 Search for helices and strands: 0 residues in 0 chains, 1933 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1953 seeds are put forward Round 1: 119 peptides, 24 chains. Longest chain 16 peptides. Score 0.281 Round 2: 151 peptides, 23 chains. Longest chain 16 peptides. Score 0.437 Round 3: 150 peptides, 22 chains. Longest chain 18 peptides. Score 0.451 Round 4: 153 peptides, 23 chains. Longest chain 17 peptides. Score 0.445 Round 5: 157 peptides, 23 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 5 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4181 restraints for refining 1936 atoms. 3644 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2705 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2480 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 33: After refmac, R = 0.2584 (Rfree = 0.000) for 1888 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 34: After refmac, R = 0.2071 (Rfree = 0.000) for 1875 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2475 (Rfree = 0.000) for 1861 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.05 Search for helices and strands: 0 residues in 0 chains, 1920 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1934 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 10 peptides. Score 0.296 Round 2: 128 peptides, 18 chains. Longest chain 16 peptides. Score 0.435 Round 3: 123 peptides, 18 chains. Longest chain 14 peptides. Score 0.415 Round 4: 140 peptides, 21 chains. Longest chain 13 peptides. Score 0.429 Round 5: 138 peptides, 20 chains. Longest chain 15 peptides. Score 0.439 Taking the results from Round 5 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4322 restraints for refining 1936 atoms. 3846 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2693 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 37: After refmac, R = 0.2639 (Rfree = 0.000) for 1911 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2569 (Rfree = 0.000) for 1897 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2068 (Rfree = 0.000) for 1887 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2232 (Rfree = 0.000) for 1885 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.10 Search for helices and strands: 0 residues in 0 chains, 1920 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1944 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.280 Round 2: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.325 Round 3: 122 peptides, 20 chains. Longest chain 13 peptides. Score 0.373 Round 4: 119 peptides, 19 chains. Longest chain 13 peptides. Score 0.379 Round 5: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3635 reflections ( 98.22 % complete ) and 4368 restraints for refining 1936 atoms. 3913 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2754 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2793 (Rfree = 0.000) for 1913 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 43: After refmac, R = 0.2721 (Rfree = 0.000) for 1895 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2712 (Rfree = 0.000) for 1875 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.2670 (Rfree = 0.000) for 1857 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.05 Search for helices and strands: 0 residues in 0 chains, 1896 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1915 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.258 Round 2: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.363 Round 3: 134 peptides, 21 chains. Longest chain 20 peptides. Score 0.405 Round 4: 121 peptides, 20 chains. Longest chain 12 peptides. Score 0.369 Round 5: 137 peptides, 25 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 113, 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 2o8q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 3635 reflections ( 98.22 % complete ) and 4321 restraints for refining 1892 atoms. 3890 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2813 (Rfree = 0.000) for 1892 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2826 (Rfree = 0.000) for 1872 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2753 (Rfree = 0.000) for 1856 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2605 (Rfree = 0.000) for 1832 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:12:03 GMT 2018 TimeTaking 44.1