null Mon 24 Dec 01:12:37 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gb5-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-parrot-mrncs ############### 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 01:12:42 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-parrot-mrncs/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 394 and 0 Target number of residues in the AU: 394 Target solvent content: 0.6379 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-3.6-parrot-mrncs.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: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.80 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: 49.644 3.600 Wilson plot Bfac: 70.46 7206 reflections ( 99.41 % complete ) and 0 restraints for refining 4772 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3214 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3047 (Rfree = 0.000) for 4772 atoms. Found 19 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 4836 seeds are put forward NCS extension: 0 residues added, 4836 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 12 peptides. Score 0.255 Round 2: 267 peptides, 45 chains. Longest chain 15 peptides. Score 0.426 Round 3: 298 peptides, 47 chains. Longest chain 15 peptides. Score 0.482 Round 4: 314 peptides, 49 chains. Longest chain 23 peptides. Score 0.500 Round 5: 304 peptides, 43 chains. Longest chain 16 peptides. Score 0.537 Taking the results from Round 5 Chains 45, Residues 261, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8919 restraints for refining 3899 atoms. 7890 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2820 (Rfree = 0.000) for 3899 atoms. Found 18 (25 requested) and removed 31 (12 requested) atoms. Cycle 2: After refmac, R = 0.2666 (Rfree = 0.000) for 3817 atoms. Found 20 (24 requested) and removed 24 (12 requested) atoms. Cycle 3: After refmac, R = 0.2705 (Rfree = 0.000) for 3786 atoms. Found 14 (24 requested) and removed 17 (12 requested) atoms. Cycle 4: After refmac, R = 0.2336 (Rfree = 0.000) for 3758 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 5: After refmac, R = 0.2310 (Rfree = 0.000) for 3732 atoms. Found 5 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 3802 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3824 seeds are put forward Round 1: 277 peptides, 48 chains. Longest chain 18 peptides. Score 0.418 Round 2: 301 peptides, 48 chains. Longest chain 15 peptides. Score 0.479 Round 3: 305 peptides, 46 chains. Longest chain 15 peptides. Score 0.509 Round 4: 298 peptides, 43 chains. Longest chain 18 peptides. Score 0.524 Round 5: 291 peptides, 40 chains. Longest chain 20 peptides. Score 0.538 Taking the results from Round 5 Chains 40, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8737 restraints for refining 3825 atoms. 7773 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2476 (Rfree = 0.000) for 3825 atoms. Found 14 (24 requested) and removed 33 (12 requested) atoms. Cycle 7: After refmac, R = 0.2336 (Rfree = 0.000) for 3787 atoms. Found 10 (24 requested) and removed 18 (12 requested) atoms. Cycle 8: After refmac, R = 0.2288 (Rfree = 0.000) for 3770 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 9: After refmac, R = 0.2282 (Rfree = 0.000) for 3760 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2354 (Rfree = 0.000) for 3744 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 3842 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3858 seeds are put forward Round 1: 260 peptides, 44 chains. Longest chain 13 peptides. Score 0.419 Round 2: 302 peptides, 46 chains. Longest chain 17 peptides. Score 0.502 Round 3: 308 peptides, 43 chains. Longest chain 19 peptides. Score 0.546 Round 4: 303 peptides, 43 chains. Longest chain 16 peptides. Score 0.535 Round 5: 302 peptides, 43 chains. Longest chain 19 peptides. Score 0.533 Taking the results from Round 3 Chains 43, Residues 265, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8954 restraints for refining 3901 atoms. 7937 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2410 (Rfree = 0.000) for 3901 atoms. Found 16 (25 requested) and removed 21 (12 requested) atoms. Cycle 12: After refmac, R = 0.2368 (Rfree = 0.000) for 3875 atoms. Found 16 (24 requested) and removed 16 (12 requested) atoms. Cycle 13: After refmac, R = 0.2204 (Rfree = 0.000) for 3864 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.2302 (Rfree = 0.000) for 3843 atoms. Found 8 (24 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.2527 (Rfree = 0.000) for 3830 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3947 seeds are put forward Round 1: 243 peptides, 45 chains. Longest chain 15 peptides. Score 0.361 Round 2: 270 peptides, 45 chains. Longest chain 14 peptides. Score 0.434 Round 3: 283 peptides, 43 chains. Longest chain 19 peptides. Score 0.488 Round 4: 277 peptides, 43 chains. Longest chain 14 peptides. Score 0.474 Round 5: 288 peptides, 43 chains. Longest chain 19 peptides. Score 0.500 Taking the results from Round 5 Chains 43, Residues 245, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8905 restraints for refining 3902 atoms. 7882 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2618 (Rfree = 0.000) for 3902 atoms. Found 17 (25 requested) and removed 24 (12 requested) atoms. Cycle 17: After refmac, R = 0.2478 (Rfree = 0.000) for 3880 atoms. Found 11 (24 requested) and removed 18 (12 requested) atoms. Cycle 18: After refmac, R = 0.2465 (Rfree = 0.000) for 3867 atoms. Found 10 (24 requested) and removed 17 (12 requested) atoms. Cycle 19: After refmac, R = 0.2472 (Rfree = 0.000) for 3855 atoms. Found 14 (24 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.2082 (Rfree = 0.000) for 3836 atoms. Found 5 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 3917 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 3943 seeds are put forward Round 1: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.366 Round 2: 261 peptides, 43 chains. Longest chain 15 peptides. Score 0.433 Round 3: 264 peptides, 39 chains. Longest chain 23 peptides. Score 0.485 Round 4: 272 peptides, 43 chains. Longest chain 18 peptides. Score 0.461 Round 5: 268 peptides, 39 chains. Longest chain 19 peptides. Score 0.495 Taking the results from Round 5 Chains 39, Residues 229, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8896 restraints for refining 3901 atoms. 7957 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2463 (Rfree = 0.000) for 3901 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 3866 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 23: After refmac, R = 0.2361 (Rfree = 0.000) for 3854 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.2308 (Rfree = 0.000) for 3854 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 25: After refmac, R = 0.1954 (Rfree = 0.000) for 3854 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 3918 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3951 seeds are put forward Round 1: 225 peptides, 47 chains. Longest chain 9 peptides. Score 0.284 Round 2: 272 peptides, 47 chains. Longest chain 13 peptides. Score 0.416 Round 3: 265 peptides, 44 chains. Longest chain 14 peptides. Score 0.432 Round 4: 274 peptides, 48 chains. Longest chain 14 peptides. Score 0.410 Round 5: 268 peptides, 44 chains. Longest chain 15 peptides. Score 0.440 Taking the results from Round 5 Chains 44, Residues 224, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9012 restraints for refining 3902 atoms. 8133 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2365 (Rfree = 0.000) for 3902 atoms. Found 17 (25 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.2403 (Rfree = 0.000) for 3889 atoms. Found 20 (25 requested) and removed 18 (12 requested) atoms. Cycle 28: After refmac, R = 0.2481 (Rfree = 0.000) for 3874 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 29: After refmac, R = 0.2049 (Rfree = 0.000) for 3864 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2030 (Rfree = 0.000) for 3847 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 3910 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3928 seeds are put forward Round 1: 192 peptides, 37 chains. Longest chain 11 peptides. Score 0.311 Round 2: 213 peptides, 36 chains. Longest chain 11 peptides. Score 0.385 Round 3: 218 peptides, 33 chains. Longest chain 13 peptides. Score 0.435 Round 4: 218 peptides, 34 chains. Longest chain 16 peptides. Score 0.423 Round 5: 208 peptides, 36 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 3 Chains 33, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9171 restraints for refining 3902 atoms. 8464 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2255 (Rfree = 0.000) for 3902 atoms. Found 18 (25 requested) and removed 18 (12 requested) atoms. Cycle 32: After refmac, R = 0.2287 (Rfree = 0.000) for 3888 atoms. Found 25 (25 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.1923 (Rfree = 0.000) for 3887 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.1926 (Rfree = 0.000) for 3875 atoms. Found 14 (24 requested) and removed 14 (12 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 3872 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 3934 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3949 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 9 peptides. Score 0.282 Round 2: 209 peptides, 37 chains. Longest chain 16 peptides. Score 0.361 Round 3: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.355 Round 4: 195 peptides, 35 chains. Longest chain 9 peptides. Score 0.346 Round 5: 212 peptides, 39 chains. Longest chain 10 peptides. Score 0.345 Taking the results from Round 2 Chains 37, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9299 restraints for refining 3902 atoms. 8648 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2169 (Rfree = 0.000) for 3902 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. Cycle 37: After refmac, R = 0.2379 (Rfree = 0.000) for 3891 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. Cycle 38: After refmac, R = 0.2231 (Rfree = 0.000) for 3888 atoms. Found 15 (25 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 3881 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 40: After refmac, R = 0.1658 (Rfree = 0.000) for 3869 atoms. Found 2 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3959 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3978 seeds are put forward Round 1: 160 peptides, 36 chains. Longest chain 8 peptides. Score 0.222 Round 2: 197 peptides, 39 chains. Longest chain 11 peptides. Score 0.300 Round 3: 197 peptides, 36 chains. Longest chain 11 peptides. Score 0.339 Round 4: 199 peptides, 34 chains. Longest chain 11 peptides. Score 0.370 Round 5: 186 peptides, 32 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 4 Chains 34, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9316 restraints for refining 3902 atoms. 8690 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2161 (Rfree = 0.000) for 3902 atoms. Found 25 (25 requested) and removed 15 (12 requested) atoms. Cycle 42: After refmac, R = 0.2065 (Rfree = 0.000) for 3892 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. Cycle 43: After refmac, R = 0.1701 (Rfree = 0.000) for 3894 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 44: After refmac, R = 0.1754 (Rfree = 0.000) for 3882 atoms. Found 11 (24 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.1946 (Rfree = 0.000) for 3879 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 3966 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3978 seeds are put forward Round 1: 180 peptides, 39 chains. Longest chain 10 peptides. Score 0.247 Round 2: 190 peptides, 39 chains. Longest chain 9 peptides. Score 0.279 Round 3: 187 peptides, 33 chains. Longest chain 15 peptides. Score 0.348 Round 4: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.369 Round 5: 183 peptides, 30 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 153, 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 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7206 reflections ( 99.41 % complete ) and 9450 restraints for refining 3902 atoms. 8868 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2118 (Rfree = 0.000) for 3902 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2036 (Rfree = 0.000) for 3881 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1773 (Rfree = 0.000) for 3858 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1732 (Rfree = 0.000) for 3843 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:02:35 GMT 2018 Job finished. TimeTaking 49.97 Used memory is bytes: 10463680