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 2oyo-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-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/2oyo-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-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/2oyo-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-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 270 and 0 Target number of residues in the AU: 270 Target solvent content: 0.6507 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-3.6-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3136 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: 83.295 3.600 Wilson plot Bfac: 78.05 4986 reflections ( 99.82 % complete ) and 0 restraints for refining 3492 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3216 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2817 (Rfree = 0.000) for 3492 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 3577 seeds are put forward NCS extension: 0 residues added, 3577 seeds are put forward Round 1: 153 peptides, 32 chains. Longest chain 10 peptides. Score 0.279 Round 2: 196 peptides, 31 chains. Longest chain 18 peptides. Score 0.464 Round 3: 205 peptides, 30 chains. Longest chain 19 peptides. Score 0.510 Round 4: 217 peptides, 30 chains. Longest chain 21 peptides. Score 0.549 Round 5: 208 peptides, 28 chains. Longest chain 17 peptides. Score 0.548 Taking the results from Round 4 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6187 restraints for refining 2843 atoms. 5391 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2435 (Rfree = 0.000) for 2843 atoms. Found 17 (18 requested) and removed 20 (9 requested) atoms. Cycle 2: After refmac, R = 0.2324 (Rfree = 0.000) for 2804 atoms. Found 10 (18 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2201 (Rfree = 0.000) for 2789 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.2088 (Rfree = 0.000) for 2779 atoms. Found 12 (17 requested) and removed 19 (8 requested) atoms. Cycle 5: After refmac, R = 0.2028 (Rfree = 0.000) for 2753 atoms. Found 8 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 2896 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2913 seeds are put forward Round 1: 185 peptides, 31 chains. Longest chain 12 peptides. Score 0.424 Round 2: 203 peptides, 28 chains. Longest chain 22 peptides. Score 0.532 Round 3: 211 peptides, 25 chains. Longest chain 19 peptides. Score 0.598 Round 4: 213 peptides, 28 chains. Longest chain 23 peptides. Score 0.564 Round 5: 219 peptides, 30 chains. Longest chain 21 peptides. Score 0.555 Taking the results from Round 3 Chains 26, Residues 186, Estimated correctness of the model 13.9 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6055 restraints for refining 2843 atoms. 5219 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2179 (Rfree = 0.000) for 2843 atoms. Found 6 (18 requested) and removed 19 (9 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 2807 atoms. Found 6 (18 requested) and removed 23 (9 requested) atoms. Cycle 8: After refmac, R = 0.2064 (Rfree = 0.000) for 2779 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.1998 (Rfree = 0.000) for 2771 atoms. Found 8 (17 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.1863 (Rfree = 0.000) for 2761 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 2913 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2931 seeds are put forward Round 1: 185 peptides, 31 chains. Longest chain 18 peptides. Score 0.424 Round 2: 205 peptides, 27 chains. Longest chain 17 peptides. Score 0.553 Round 3: 201 peptides, 30 chains. Longest chain 18 peptides. Score 0.496 Round 4: 191 peptides, 27 chains. Longest chain 16 peptides. Score 0.507 Round 5: 199 peptides, 28 chains. Longest chain 14 peptides. Score 0.519 Taking the results from Round 2 Chains 28, Residues 178, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6271 restraints for refining 2841 atoms. 5481 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2047 (Rfree = 0.000) for 2841 atoms. Found 12 (18 requested) and removed 16 (9 requested) atoms. Cycle 12: After refmac, R = 0.1946 (Rfree = 0.000) for 2829 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.1938 (Rfree = 0.000) for 2817 atoms. Found 14 (18 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.1839 (Rfree = 0.000) for 2815 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. Cycle 15: After refmac, R = 0.1811 (Rfree = 0.000) for 2800 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 2908 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2928 seeds are put forward Round 1: 169 peptides, 31 chains. Longest chain 12 peptides. Score 0.363 Round 2: 202 peptides, 33 chains. Longest chain 18 peptides. Score 0.455 Round 3: 197 peptides, 33 chains. Longest chain 18 peptides. Score 0.437 Round 4: 198 peptides, 28 chains. Longest chain 18 peptides. Score 0.516 Round 5: 185 peptides, 28 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 4 Chains 28, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6489 restraints for refining 2843 atoms. 5837 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2034 (Rfree = 0.000) for 2843 atoms. Found 10 (18 requested) and removed 16 (9 requested) atoms. Cycle 17: After refmac, R = 0.2075 (Rfree = 0.000) for 2827 atoms. Found 16 (18 requested) and removed 20 (9 requested) atoms. Cycle 18: After refmac, R = 0.1861 (Rfree = 0.000) for 2812 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2010 (Rfree = 0.000) for 2803 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. Cycle 20: After refmac, R = 0.1907 (Rfree = 0.000) for 2790 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2930 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2945 seeds are put forward Round 1: 151 peptides, 30 chains. Longest chain 12 peptides. Score 0.306 Round 2: 175 peptides, 27 chains. Longest chain 17 peptides. Score 0.451 Round 3: 176 peptides, 25 chains. Longest chain 13 peptides. Score 0.487 Round 4: 173 peptides, 23 chains. Longest chain 17 peptides. Score 0.507 Round 5: 175 peptides, 27 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 4 Chains 23, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6689 restraints for refining 2843 atoms. 6112 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1876 (Rfree = 0.000) for 2843 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.1864 (Rfree = 0.000) for 2831 atoms. Found 6 (18 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.1822 (Rfree = 0.000) for 2818 atoms. Found 12 (18 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.1823 (Rfree = 0.000) for 2814 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1780 (Rfree = 0.000) for 2809 atoms. Found 6 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 2901 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2923 seeds are put forward Round 1: 157 peptides, 29 chains. Longest chain 12 peptides. Score 0.349 Round 2: 185 peptides, 32 chains. Longest chain 14 peptides. Score 0.408 Round 3: 183 peptides, 29 chains. Longest chain 15 peptides. Score 0.449 Round 4: 177 peptides, 27 chains. Longest chain 14 peptides. Score 0.459 Round 5: 183 peptides, 27 chains. Longest chain 13 peptides. Score 0.480 Taking the results from Round 5 Chains 27, Residues 156, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6508 restraints for refining 2843 atoms. 5890 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1994 (Rfree = 0.000) for 2843 atoms. Found 8 (18 requested) and removed 18 (9 requested) atoms. Cycle 27: After refmac, R = 0.2015 (Rfree = 0.000) for 2823 atoms. Found 11 (18 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.1881 (Rfree = 0.000) for 2819 atoms. Found 11 (18 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.1872 (Rfree = 0.000) for 2816 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1787 (Rfree = 0.000) for 2813 atoms. Found 9 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2956 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 9 peptides. Score 0.245 Round 2: 168 peptides, 32 chains. Longest chain 11 peptides. Score 0.342 Round 3: 162 peptides, 27 chains. Longest chain 12 peptides. Score 0.403 Round 4: 167 peptides, 30 chains. Longest chain 10 peptides. Score 0.372 Round 5: 171 peptides, 25 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 5 Chains 25, Residues 146, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6456 restraints for refining 2843 atoms. 5836 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2079 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 32: After refmac, R = 0.1948 (Rfree = 0.000) for 2835 atoms. Found 2 (18 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.1949 (Rfree = 0.000) for 2815 atoms. Found 3 (18 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 2801 atoms. Found 7 (17 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.2006 (Rfree = 0.000) for 2795 atoms. Found 15 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 2936 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2949 seeds are put forward Round 1: 149 peptides, 27 chains. Longest chain 10 peptides. Score 0.351 Round 2: 173 peptides, 25 chains. Longest chain 20 peptides. Score 0.476 Round 3: 164 peptides, 25 chains. Longest chain 17 peptides. Score 0.444 Round 4: 172 peptides, 26 chains. Longest chain 14 peptides. Score 0.457 Round 5: 167 peptides, 24 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 2 Chains 26, Residues 148, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6346 restraints for refining 2843 atoms. 5742 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1809 (Rfree = 0.000) for 2843 atoms. Found 7 (18 requested) and removed 18 (9 requested) atoms. Cycle 37: After refmac, R = 0.1739 (Rfree = 0.000) for 2829 atoms. Found 4 (18 requested) and removed 15 (9 requested) atoms. Cycle 38: After refmac, R = 0.2070 (Rfree = 0.000) for 2816 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.1660 (Rfree = 0.000) for 2815 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. Cycle 40: After refmac, R = 0.1603 (Rfree = 0.000) for 2807 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2946 seeds are put forward Round 1: 148 peptides, 29 chains. Longest chain 13 peptides. Score 0.311 Round 2: 160 peptides, 29 chains. Longest chain 10 peptides. Score 0.361 Round 3: 160 peptides, 26 chains. Longest chain 16 peptides. Score 0.412 Round 4: 166 peptides, 26 chains. Longest chain 16 peptides. Score 0.435 Round 5: 156 peptides, 26 chains. Longest chain 16 peptides. Score 0.396 Taking the results from Round 4 Chains 27, Residues 140, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6448 restraints for refining 2843 atoms. 5879 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1828 (Rfree = 0.000) for 2843 atoms. Found 12 (18 requested) and removed 13 (9 requested) atoms. Cycle 42: After refmac, R = 0.1743 (Rfree = 0.000) for 2830 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2411 (Rfree = 0.000) for 2832 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 44: After refmac, R = 0.1834 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 45: After refmac, R = 0.1631 (Rfree = 0.000) for 2818 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2960 seeds are put forward Round 1: 136 peptides, 26 chains. Longest chain 16 peptides. Score 0.315 Round 2: 143 peptides, 26 chains. Longest chain 11 peptides. Score 0.344 Round 3: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.377 Round 4: 139 peptides, 25 chains. Longest chain 11 peptides. Score 0.345 Round 5: 146 peptides, 26 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 115, 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 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4986 reflections ( 99.82 % complete ) and 6837 restraints for refining 2843 atoms. 6400 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1886 (Rfree = 0.000) for 2843 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1911 (Rfree = 0.000) for 2828 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1806 (Rfree = 0.000) for 2815 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1808 (Rfree = 0.000) for 2806 atoms. TimeTaking 55.08