null Mon 24 Dec 08:03:16 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 2a9v-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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/2a9v-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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 08:03:21 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/2a9v-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-3.6-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 513 and 0 Target number of residues in the AU: 513 Target solvent content: 0.6220 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-3.6-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.50 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: 137.806 3.600 Wilson plot Bfac: 62.41 9184 reflections ( 99.99 % complete ) and 0 restraints for refining 7507 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3762 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3777 (Rfree = 0.000) for 7507 atoms. Found 48 (48 requested) and removed 323 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.91 Search for helices and strands: 0 residues in 0 chains, 7325 seeds are put forward NCS extension: 0 residues added, 7325 seeds are put forward Round 1: 182 peptides, 41 chains. Longest chain 7 peptides. Score 0.218 Round 2: 243 peptides, 48 chains. Longest chain 14 peptides. Score 0.300 Round 3: 256 peptides, 46 chains. Longest chain 13 peptides. Score 0.352 Round 4: 259 peptides, 48 chains. Longest chain 13 peptides. Score 0.339 Round 5: 256 peptides, 44 chains. Longest chain 11 peptides. Score 0.372 Taking the results from Round 5 Chains 44, Residues 212, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 15157 restraints for refining 6150 atoms. 14333 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2744 (Rfree = 0.000) for 6150 atoms. Found 19 (39 requested) and removed 92 (19 requested) atoms. Cycle 2: After refmac, R = 0.2484 (Rfree = 0.000) for 6009 atoms. Found 19 (38 requested) and removed 60 (19 requested) atoms. Cycle 3: After refmac, R = 0.2071 (Rfree = 0.000) for 5921 atoms. Found 12 (38 requested) and removed 42 (19 requested) atoms. Cycle 4: After refmac, R = 0.1881 (Rfree = 0.000) for 5872 atoms. Found 6 (37 requested) and removed 38 (18 requested) atoms. Cycle 5: After refmac, R = 0.2028 (Rfree = 0.000) for 5827 atoms. Found 8 (37 requested) and removed 42 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 5927 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5941 seeds are put forward Round 1: 246 peptides, 51 chains. Longest chain 10 peptides. Score 0.277 Round 2: 250 peptides, 48 chains. Longest chain 9 peptides. Score 0.317 Round 3: 253 peptides, 46 chains. Longest chain 9 peptides. Score 0.345 Round 4: 264 peptides, 44 chains. Longest chain 17 peptides. Score 0.390 Round 5: 277 peptides, 46 chains. Longest chain 15 peptides. Score 0.400 Taking the results from Round 5 Chains 46, Residues 231, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14139 restraints for refining 5866 atoms. 13222 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2356 (Rfree = 0.000) for 5866 atoms. Found 15 (37 requested) and removed 74 (18 requested) atoms. Cycle 7: After refmac, R = 0.2199 (Rfree = 0.000) for 5772 atoms. Found 15 (37 requested) and removed 52 (18 requested) atoms. Cycle 8: After refmac, R = 0.2219 (Rfree = 0.000) for 5717 atoms. Found 10 (36 requested) and removed 45 (18 requested) atoms. Cycle 9: After refmac, R = 0.2189 (Rfree = 0.000) for 5669 atoms. Found 16 (36 requested) and removed 37 (18 requested) atoms. Cycle 10: After refmac, R = 0.2066 (Rfree = 0.000) for 5638 atoms. Found 12 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.81 Search for helices and strands: 0 residues in 0 chains, 5782 seeds are put forward NCS extension: 0 residues added, 5782 seeds are put forward Round 1: 255 peptides, 54 chains. Longest chain 8 peptides. Score 0.268 Round 2: 313 peptides, 55 chains. Longest chain 12 peptides. Score 0.393 Round 3: 328 peptides, 56 chains. Longest chain 15 peptides. Score 0.416 Round 4: 315 peptides, 53 chains. Longest chain 12 peptides. Score 0.416 Round 5: 314 peptides, 52 chains. Longest chain 14 peptides. Score 0.423 Taking the results from Round 5 Chains 52, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 13915 restraints for refining 5850 atoms. 12919 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2199 (Rfree = 0.000) for 5850 atoms. Found 32 (37 requested) and removed 83 (18 requested) atoms. Cycle 12: After refmac, R = 0.1993 (Rfree = 0.000) for 5774 atoms. Found 16 (37 requested) and removed 45 (18 requested) atoms. Cycle 13: After refmac, R = 0.1919 (Rfree = 0.000) for 5731 atoms. Found 13 (36 requested) and removed 36 (18 requested) atoms. Cycle 14: After refmac, R = 0.1892 (Rfree = 0.000) for 5695 atoms. Found 22 (36 requested) and removed 22 (18 requested) atoms. Cycle 15: After refmac, R = 0.1607 (Rfree = 0.000) for 5685 atoms. Found 7 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.86 Search for helices and strands: 0 residues in 0 chains, 5795 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5811 seeds are put forward Round 1: 284 peptides, 59 chains. Longest chain 9 peptides. Score 0.288 Round 2: 318 peptides, 57 chains. Longest chain 12 peptides. Score 0.386 Round 3: 312 peptides, 55 chains. Longest chain 13 peptides. Score 0.391 Round 4: 330 peptides, 54 chains. Longest chain 18 peptides. Score 0.439 Round 5: 325 peptides, 51 chains. Longest chain 14 peptides. Score 0.456 Taking the results from Round 5 Chains 51, Residues 274, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 13591 restraints for refining 5936 atoms. 12483 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2065 (Rfree = 0.000) for 5936 atoms. Found 29 (38 requested) and removed 77 (19 requested) atoms. Cycle 17: After refmac, R = 0.1867 (Rfree = 0.000) for 5874 atoms. Found 25 (37 requested) and removed 46 (18 requested) atoms. Cycle 18: After refmac, R = 0.1776 (Rfree = 0.000) for 5840 atoms. Found 18 (37 requested) and removed 38 (18 requested) atoms. Cycle 19: After refmac, R = 0.1709 (Rfree = 0.000) for 5812 atoms. Found 21 (37 requested) and removed 35 (18 requested) atoms. Cycle 20: After refmac, R = 0.1666 (Rfree = 0.000) for 5796 atoms. Found 19 (37 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.84 Search for helices and strands: 0 residues in 0 chains, 5937 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5958 seeds are put forward Round 1: 275 peptides, 58 chains. Longest chain 9 peptides. Score 0.276 Round 2: 292 peptides, 54 chains. Longest chain 9 peptides. Score 0.356 Round 3: 302 peptides, 53 chains. Longest chain 17 peptides. Score 0.388 Round 4: 301 peptides, 52 chains. Longest chain 16 peptides. Score 0.395 Round 5: 310 peptides, 53 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 5 Chains 53, Residues 257, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14214 restraints for refining 6149 atoms. 13142 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2043 (Rfree = 0.000) for 6149 atoms. Found 27 (39 requested) and removed 77 (19 requested) atoms. Cycle 22: After refmac, R = 0.1910 (Rfree = 0.000) for 6081 atoms. Found 23 (39 requested) and removed 61 (19 requested) atoms. Cycle 23: After refmac, R = 0.1798 (Rfree = 0.000) for 6033 atoms. Found 16 (38 requested) and removed 38 (19 requested) atoms. Cycle 24: After refmac, R = 0.1721 (Rfree = 0.000) for 6005 atoms. Found 16 (38 requested) and removed 40 (19 requested) atoms. Cycle 25: After refmac, R = 0.1687 (Rfree = 0.000) for 5973 atoms. Found 20 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.83 Search for helices and strands: 0 residues in 0 chains, 6107 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6126 seeds are put forward Round 1: 253 peptides, 53 chains. Longest chain 9 peptides. Score 0.273 Round 2: 261 peptides, 52 chains. Longest chain 9 peptides. Score 0.303 Round 3: 267 peptides, 49 chains. Longest chain 11 peptides. Score 0.348 Round 4: 263 peptides, 45 chains. Longest chain 12 peptides. Score 0.378 Round 5: 275 peptides, 50 chains. Longest chain 14 peptides. Score 0.356 Taking the results from Round 4 Chains 45, Residues 218, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14649 restraints for refining 6149 atoms. 13789 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1919 (Rfree = 0.000) for 6149 atoms. Found 22 (39 requested) and removed 67 (19 requested) atoms. Cycle 27: After refmac, R = 0.1853 (Rfree = 0.000) for 6087 atoms. Found 34 (39 requested) and removed 40 (19 requested) atoms. Cycle 28: After refmac, R = 0.1726 (Rfree = 0.000) for 6076 atoms. Found 29 (39 requested) and removed 36 (19 requested) atoms. Cycle 29: After refmac, R = 0.1638 (Rfree = 0.000) for 6059 atoms. Found 24 (38 requested) and removed 32 (19 requested) atoms. Cycle 30: After refmac, R = 0.1596 (Rfree = 0.000) for 6051 atoms. Found 22 (38 requested) and removed 35 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 6142 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6154 seeds are put forward Round 1: 229 peptides, 52 chains. Longest chain 7 peptides. Score 0.223 Round 2: 247 peptides, 47 chains. Longest chain 9 peptides. Score 0.321 Round 3: 264 peptides, 45 chains. Longest chain 11 peptides. Score 0.380 Round 4: 251 peptides, 46 chains. Longest chain 10 peptides. Score 0.340 Round 5: 256 peptides, 45 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 3 Chains 45, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14463 restraints for refining 6129 atoms. 13632 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1825 (Rfree = 0.000) for 6129 atoms. Found 35 (39 requested) and removed 58 (19 requested) atoms. Cycle 32: After refmac, R = 0.1688 (Rfree = 0.000) for 6088 atoms. Found 34 (39 requested) and removed 40 (19 requested) atoms. Cycle 33: After refmac, R = 0.1713 (Rfree = 0.000) for 6074 atoms. Found 32 (39 requested) and removed 38 (19 requested) atoms. Cycle 34: After refmac, R = 0.1669 (Rfree = 0.000) for 6064 atoms. Found 35 (38 requested) and removed 31 (19 requested) atoms. Cycle 35: After refmac, R = 0.1301 (Rfree = 0.000) for 6064 atoms. Found 2 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 6171 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6183 seeds are put forward Round 1: 204 peptides, 45 chains. Longest chain 7 peptides. Score 0.233 Round 2: 266 peptides, 50 chains. Longest chain 10 peptides. Score 0.335 Round 3: 257 peptides, 46 chains. Longest chain 13 peptides. Score 0.354 Round 4: 252 peptides, 46 chains. Longest chain 13 peptides. Score 0.343 Round 5: 257 peptides, 45 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Chains 45, Residues 212, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14676 restraints for refining 6150 atoms. 13852 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1875 (Rfree = 0.000) for 6150 atoms. Found 39 (39 requested) and removed 49 (19 requested) atoms. Cycle 37: After refmac, R = 0.1725 (Rfree = 0.000) for 6126 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 38: After refmac, R = 0.1765 (Rfree = 0.000) for 6122 atoms. Found 34 (39 requested) and removed 33 (19 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 6110 atoms. Found 26 (39 requested) and removed 26 (19 requested) atoms. Cycle 40: After refmac, R = 0.1704 (Rfree = 0.000) for 6105 atoms. Found 34 (39 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.88 Search for helices and strands: 0 residues in 0 chains, 6254 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 6267 seeds are put forward Round 1: 176 peptides, 40 chains. Longest chain 7 peptides. Score 0.213 Round 2: 202 peptides, 41 chains. Longest chain 9 peptides. Score 0.272 Round 3: 218 peptides, 42 chains. Longest chain 12 peptides. Score 0.302 Round 4: 215 peptides, 40 chains. Longest chain 12 peptides. Score 0.316 Round 5: 219 peptides, 39 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 5 Chains 39, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9184 reflections ( 99.99 % complete ) and 14877 restraints for refining 6150 atoms. 14196 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1847 (Rfree = 0.000) for 6150 atoms. Found 39 (39 requested) and removed 36 (19 requested) atoms. Cycle 42: After refmac, R = 0.1822 (Rfree = 0.000) for 6143 atoms. Found 39 (39 requested) and removed 27 (19 requested) atoms. Cycle 43: After refmac, R = 0.1826 (Rfree = 0.000) for 6143 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. Cycle 44: After refmac, R = 0.1764 (Rfree = 0.000) for 6137 atoms. Found 30 (39 requested) and removed 28 (19 requested) atoms. Cycle 45: After refmac, R = 0.1808 (Rfree = 0.000) for 6129 atoms. Found 39 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.85 Search for helices and strands: 0 residues in 0 chains, 6255 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6268 seeds are put forward Round 1: 150 peptides, 34 chains. Longest chain 6 peptides. Score 0.210 Round 2: 173 peptides, 39 chains. Longest chain 7 peptides. Score 0.216 Round 3: 183 peptides, 36 chains. Longest chain 13 peptides. Score 0.278 Round 4: 189 peptides, 37 chains. Longest chain 13 peptides. Score 0.283 Round 5: 179 peptides, 34 chains. Longest chain 13 peptides. Score 0.290 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 145, 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 2a9v-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9184 reflections ( 99.99 % complete ) and 14815 restraints for refining 6093 atoms. 14269 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1926 (Rfree = 0.000) for 6093 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1953 (Rfree = 0.000) for 6060 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1918 (Rfree = 0.000) for 6038 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2013 (Rfree = 0.000) for 6017 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:03:12 GMT 2018 Job finished. TimeTaking 59.94 Used memory is bytes: 17896312