Sun 23 Dec 22:22:55 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 2oc6-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-3.2-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/2oc6-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-3.2-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 22:23:04 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/2oc6-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-3.2-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6392 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-3.2-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.85 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: 60.653 3.200 Wilson plot Bfac: 70.91 4655 reflections ( 99.66 % complete ) and 0 restraints for refining 2219 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3589 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3108 (Rfree = 0.000) for 2219 atoms. Found 11 (19 requested) and removed 49 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 2237 seeds are put forward NCS extension: 0 residues added, 2237 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.322 Round 2: 131 peptides, 23 chains. Longest chain 11 peptides. Score 0.412 Round 3: 128 peptides, 19 chains. Longest chain 14 peptides. Score 0.489 Round 4: 140 peptides, 22 chains. Longest chain 12 peptides. Score 0.484 Round 5: 128 peptides, 20 chains. Longest chain 10 peptides. Score 0.466 Taking the results from Round 3 Chains 19, Residues 109, Estimated correctness of the model 7.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4021 restraints for refining 1811 atoms. 3604 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2515 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 2: After refmac, R = 0.2388 (Rfree = 0.000) for 1793 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 3: After refmac, R = 0.2392 (Rfree = 0.000) for 1785 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2335 (Rfree = 0.000) for 1776 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2224 (Rfree = 0.000) for 1772 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 1846 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1864 seeds are put forward Round 1: 129 peptides, 23 chains. Longest chain 14 peptides. Score 0.401 Round 2: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.545 Round 3: 141 peptides, 19 chains. Longest chain 16 peptides. Score 0.554 Round 4: 159 peptides, 24 chains. Longest chain 16 peptides. Score 0.535 Round 5: 156 peptides, 24 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 3 Chains 21, Residues 122, Estimated correctness of the model 28.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 3905 restraints for refining 1810 atoms. 3398 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2491 (Rfree = 0.000) for 1810 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 7: After refmac, R = 0.2271 (Rfree = 0.000) for 1816 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 8: After refmac, R = 0.2273 (Rfree = 0.000) for 1806 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2229 (Rfree = 0.000) for 1801 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2188 (Rfree = 0.000) for 1797 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 1861 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1878 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 12 peptides. Score 0.353 Round 2: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.484 Round 3: 140 peptides, 23 chains. Longest chain 13 peptides. Score 0.461 Round 4: 153 peptides, 23 chains. Longest chain 17 peptides. Score 0.527 Round 5: 146 peptides, 22 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 4 Chains 23, Residues 130, Estimated correctness of the model 19.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 3990 restraints for refining 1811 atoms. 3493 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2580 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 12: After refmac, R = 0.2758 (Rfree = 0.000) for 1814 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2328 (Rfree = 0.000) for 1810 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2342 (Rfree = 0.000) for 1802 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2405 (Rfree = 0.000) for 1794 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 1881 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1903 seeds are put forward Round 1: 120 peptides, 20 chains. Longest chain 13 peptides. Score 0.423 Round 2: 131 peptides, 16 chains. Longest chain 24 peptides. Score 0.570 Round 3: 130 peptides, 17 chains. Longest chain 23 peptides. Score 0.544 Round 4: 125 peptides, 17 chains. Longest chain 25 peptides. Score 0.519 Round 5: 131 peptides, 15 chains. Longest chain 23 peptides. Score 0.591 Taking the results from Round 5 Chains 15, Residues 116, Estimated correctness of the model 38.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4012 restraints for refining 1811 atoms. 3563 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2464 (Rfree = 0.000) for 1811 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 17: After refmac, R = 0.2713 (Rfree = 0.000) for 1815 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.2300 (Rfree = 0.000) for 1814 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2368 (Rfree = 0.000) for 1809 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2241 (Rfree = 0.000) for 1802 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 1865 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 1899 seeds are put forward Round 1: 116 peptides, 20 chains. Longest chain 14 peptides. Score 0.400 Round 2: 124 peptides, 18 chains. Longest chain 12 peptides. Score 0.492 Round 3: 130 peptides, 16 chains. Longest chain 18 peptides. Score 0.565 Round 4: 124 peptides, 16 chains. Longest chain 13 peptides. Score 0.537 Round 5: 118 peptides, 18 chains. Longest chain 17 peptides. Score 0.460 Taking the results from Round 3 Chains 16, Residues 114, Estimated correctness of the model 31.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4113 restraints for refining 1811 atoms. 3673 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2313 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 22: After refmac, R = 0.2169 (Rfree = 0.000) for 1812 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2164 (Rfree = 0.000) for 1805 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2105 (Rfree = 0.000) for 1801 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2170 (Rfree = 0.000) for 1794 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 1837 seeds are put forward NCS extension: 0 residues added, 1837 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 14 peptides. Score 0.351 Round 2: 124 peptides, 18 chains. Longest chain 14 peptides. Score 0.492 Round 3: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.519 Round 4: 126 peptides, 17 chains. Longest chain 15 peptides. Score 0.524 Round 5: 124 peptides, 18 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 4 Chains 17, Residues 109, Estimated correctness of the model 19.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4066 restraints for refining 1811 atoms. 3647 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2331 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 27: After refmac, R = 0.2256 (Rfree = 0.000) for 1811 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2719 (Rfree = 0.000) for 1806 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2527 (Rfree = 0.000) for 1814 atoms. Found 13 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2135 (Rfree = 0.000) for 1818 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 1890 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1906 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.394 Round 2: 121 peptides, 19 chains. Longest chain 13 peptides. Score 0.452 Round 3: 120 peptides, 19 chains. Longest chain 14 peptides. Score 0.447 Round 4: 127 peptides, 20 chains. Longest chain 14 peptides. Score 0.461 Round 5: 128 peptides, 19 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 5 Chains 19, Residues 109, Estimated correctness of the model 7.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4111 restraints for refining 1811 atoms. 3694 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2339 (Rfree = 0.000) for 1811 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 32: After refmac, R = 0.2288 (Rfree = 0.000) for 1809 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.2277 (Rfree = 0.000) for 1802 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2381 (Rfree = 0.000) for 1797 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2344 (Rfree = 0.000) for 1792 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 1859 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1877 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 11 peptides. Score 0.291 Round 2: 111 peptides, 20 chains. Longest chain 11 peptides. Score 0.370 Round 3: 116 peptides, 18 chains. Longest chain 13 peptides. Score 0.449 Round 4: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.443 Round 5: 110 peptides, 16 chains. Longest chain 12 peptides. Score 0.464 Taking the results from Round 5 Chains 16, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4207 restraints for refining 1811 atoms. 3847 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2371 (Rfree = 0.000) for 1811 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.2653 (Rfree = 0.000) for 1809 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2246 (Rfree = 0.000) for 1815 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2229 (Rfree = 0.000) for 1807 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2235 (Rfree = 0.000) for 1803 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 1860 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1874 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 11 peptides. Score 0.291 Round 2: 101 peptides, 15 chains. Longest chain 12 peptides. Score 0.439 Round 3: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.411 Round 4: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.380 Round 5: 103 peptides, 16 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 2 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4655 reflections ( 99.66 % complete ) and 4274 restraints for refining 1811 atoms. 3945 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2165 (Rfree = 0.000) for 1811 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2091 (Rfree = 0.000) for 1814 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2156 (Rfree = 0.000) for 1806 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2231 (Rfree = 0.000) for 1813 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2100 (Rfree = 0.000) for 1814 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 1872 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1875 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 10 peptides. Score 0.301 Round 2: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.402 Round 3: 99 peptides, 17 chains. Longest chain 8 peptides. Score 0.376 Round 4: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.439 Round 5: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 86, 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 2oc6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4655 reflections ( 99.66 % complete ) and 4132 restraints for refining 1811 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2196 (Rfree = 0.000) for 1811 atoms. Found 0 (16 requested) and removed 5 (8 requested) atoms. Cycle 47: After refmac, R = 0.2435 (Rfree = 0.000) for 1802 atoms. Found 0 (16 requested) and removed 4 (8 requested) atoms. Cycle 48: After refmac, R = 0.2081 (Rfree = 0.000) for 1796 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.2082 (Rfree = 0.000) for 1792 atoms. TimeTaking 31.17