Mon 24 Dec 07:30:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oc6-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oc6-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:30:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oc6-3.8-parrot-noncs/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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6646 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: 2oc6-3.8-parrot-noncs.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: 2oc6-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 1984 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: 60.653 3.802 Wilson plot Bfac: 87.20 2794 reflections ( 99.61 % complete ) and 0 restraints for refining 2190 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3645 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2998 (Rfree = 0.000) for 2190 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 2229 seeds are put forward NCS extension: 0 residues added, 2229 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 6 peptides. Score 0.222 Round 2: 125 peptides, 24 chains. Longest chain 12 peptides. Score 0.353 Round 3: 134 peptides, 25 chains. Longest chain 12 peptides. Score 0.381 Round 4: 136 peptides, 24 chains. Longest chain 13 peptides. Score 0.416 Round 5: 124 peptides, 24 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Chains 24, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4152 restraints for refining 1793 atoms. 3728 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2604 (Rfree = 0.000) for 1793 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 2: After refmac, R = 0.2342 (Rfree = 0.000) for 1771 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.2273 (Rfree = 0.000) for 1767 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 4: After refmac, R = 0.2219 (Rfree = 0.000) for 1765 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2168 (Rfree = 0.000) for 1761 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.64 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: 110 peptides, 21 chains. Longest chain 11 peptides. Score 0.339 Round 2: 121 peptides, 21 chains. Longest chain 9 peptides. Score 0.404 Round 3: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.445 Round 4: 128 peptides, 20 chains. Longest chain 13 peptides. Score 0.466 Round 5: 120 peptides, 19 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 4 Chains 20, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4194 restraints for refining 1794 atoms. 3782 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2514 (Rfree = 0.000) for 1794 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 7: After refmac, R = 0.2271 (Rfree = 0.000) for 1782 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2194 (Rfree = 0.000) for 1777 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2118 (Rfree = 0.000) for 1764 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.2128 (Rfree = 0.000) for 1761 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1844 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.334 Round 2: 116 peptides, 17 chains. Longest chain 16 peptides. Score 0.473 Round 3: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.400 Round 4: 126 peptides, 21 chains. Longest chain 13 peptides. Score 0.432 Round 5: 137 peptides, 24 chains. Longest chain 12 peptides. Score 0.422 Taking the results from Round 2 Chains 17, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4182 restraints for refining 1794 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2256 (Rfree = 0.000) for 1794 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 12: After refmac, R = 0.2133 (Rfree = 0.000) for 1785 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2108 (Rfree = 0.000) for 1781 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2482 (Rfree = 0.000) for 1775 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2205 (Rfree = 0.000) for 1773 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 1832 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 1860 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.309 Round 2: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.394 Round 3: 116 peptides, 18 chains. Longest chain 15 peptides. Score 0.449 Round 4: 119 peptides, 18 chains. Longest chain 12 peptides. Score 0.465 Round 5: 107 peptides, 16 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 4 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4164 restraints for refining 1793 atoms. 3778 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2442 (Rfree = 0.000) for 1793 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 17: After refmac, R = 0.2306 (Rfree = 0.000) for 1790 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.2212 (Rfree = 0.000) for 1789 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2139 (Rfree = 0.000) for 1782 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2118 (Rfree = 0.000) for 1776 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1843 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1858 seeds are put forward Round 1: 116 peptides, 24 chains. Longest chain 10 peptides. Score 0.298 Round 2: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.383 Round 3: 105 peptides, 18 chains. Longest chain 9 peptides. Score 0.386 Round 4: 116 peptides, 17 chains. Longest chain 12 peptides. Score 0.473 Round 5: 118 peptides, 19 chains. Longest chain 10 peptides. Score 0.436 Taking the results from Round 4 Chains 17, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4219 restraints for refining 1794 atoms. 3840 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2444 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.2232 (Rfree = 0.000) for 1793 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2188 (Rfree = 0.000) for 1792 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2099 (Rfree = 0.000) for 1783 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2077 (Rfree = 0.000) for 1783 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 1852 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1868 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 6 peptides. Score 0.230 Round 2: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.284 Round 3: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.346 Round 4: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.360 Round 5: 106 peptides, 18 chains. Longest chain 15 peptides. Score 0.392 Taking the results from Round 5 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4297 restraints for refining 1794 atoms. 3963 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2417 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2196 (Rfree = 0.000) for 1784 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2104 (Rfree = 0.000) for 1783 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2165 (Rfree = 0.000) for 1778 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2178 (Rfree = 0.000) for 1778 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward NCS extension: 0 residues added, 1825 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 7 peptides. Score 0.251 Round 2: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.337 Round 3: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.346 Round 4: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.331 Round 5: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4419 restraints for refining 1794 atoms. 4127 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2310 (Rfree = 0.000) for 1794 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.2052 (Rfree = 0.000) for 1789 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1888 (Rfree = 0.000) for 1784 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.1883 (Rfree = 0.000) for 1781 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1895 (Rfree = 0.000) for 1783 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward NCS extension: 0 residues added, 1839 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 8 peptides. Score 0.257 Round 2: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.346 Round 3: 112 peptides, 21 chains. Longest chain 14 peptides. Score 0.351 Round 4: 109 peptides, 21 chains. Longest chain 8 peptides. Score 0.333 Round 5: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 5 Chains 21, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4184 restraints for refining 1794 atoms. 3825 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2272 (Rfree = 0.000) for 1794 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2052 (Rfree = 0.000) for 1782 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1959 (Rfree = 0.000) for 1783 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1879 (Rfree = 0.000) for 1781 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1869 (Rfree = 0.000) for 1776 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 0 residues added, 1838 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.263 Round 2: 87 peptides, 16 chains. Longest chain 14 peptides. Score 0.328 Round 3: 88 peptides, 15 chains. Longest chain 19 peptides. Score 0.362 Round 4: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 5: 89 peptides, 15 chains. Longest chain 20 peptides. Score 0.368 Taking the results from Round 5 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2794 reflections ( 99.61 % complete ) and 4051 restraints for refining 1794 atoms. 3681 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2328 (Rfree = 0.000) for 1794 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 42: After refmac, R = 0.2122 (Rfree = 0.000) for 1786 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2079 (Rfree = 0.000) for 1783 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2060 (Rfree = 0.000) for 1780 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2033 (Rfree = 0.000) for 1775 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 1828 seeds are put forward NCS extension: 0 residues added, 1828 seeds are put forward Round 1: 72 peptides, 17 chains. Longest chain 6 peptides. Score 0.197 Round 2: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.304 Round 3: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.329 Round 4: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.282 Round 5: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.306 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 81, 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. 2794 reflections ( 99.61 % complete ) and 4281 restraints for refining 1793 atoms. 3976 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2462 (Rfree = 0.000) for 1793 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2217 (Rfree = 0.000) for 1787 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2190 (Rfree = 0.000) for 1781 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2185 (Rfree = 0.000) for 1776 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 23.03