null Mon 24 Dec 07:36:55 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 2gb5-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-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/2gb5-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-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 07:37:00 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/2gb5-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-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 413 and 0 Target number of residues in the AU: 413 Target solvent content: 0.6204 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: 2gb5-3.2-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: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.75 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 3.200 Wilson plot Bfac: 61.35 10184 reflections ( 99.58 % complete ) and 0 restraints for refining 4794 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3283 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2850 (Rfree = 0.000) for 4794 atoms. Found 21 (43 requested) and removed 39 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 3.09 Search for helices and strands: 0 residues in 0 chains, 4842 seeds are put forward NCS extension: 0 residues added, 4842 seeds are put forward Round 1: 234 peptides, 49 chains. Longest chain 9 peptides. Score 0.286 Round 2: 301 peptides, 51 chains. Longest chain 14 peptides. Score 0.447 Round 3: 318 peptides, 49 chains. Longest chain 17 peptides. Score 0.509 Round 4: 319 peptides, 49 chains. Longest chain 19 peptides. Score 0.512 Round 5: 318 peptides, 42 chains. Longest chain 24 peptides. Score 0.578 Taking the results from Round 5 Chains 43, Residues 276, Estimated correctness of the model 35.0 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8257 restraints for refining 3928 atoms. 7001 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2617 (Rfree = 0.000) for 3928 atoms. Found 19 (35 requested) and removed 32 (17 requested) atoms. Cycle 2: After refmac, R = 0.2532 (Rfree = 0.000) for 3854 atoms. Found 10 (35 requested) and removed 21 (17 requested) atoms. Cycle 3: After refmac, R = 0.2430 (Rfree = 0.000) for 3829 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 4: After refmac, R = 0.2279 (Rfree = 0.000) for 3804 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2229 (Rfree = 0.000) for 3784 atoms. Found 4 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 3895 seeds are put forward Round 1: 291 peptides, 45 chains. Longest chain 17 peptides. Score 0.486 Round 2: 333 peptides, 47 chains. Longest chain 18 peptides. Score 0.562 Round 3: 331 peptides, 40 chains. Longest chain 36 peptides. Score 0.622 Round 4: 352 peptides, 50 chains. Longest chain 19 peptides. Score 0.575 Round 5: 362 peptides, 44 chains. Longest chain 24 peptides. Score 0.646 Taking the results from Round 5 Chains 46, Residues 318, Estimated correctness of the model 52.9 % 5 chains (65 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7844 restraints for refining 3927 atoms. 6345 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2719 (Rfree = 0.000) for 3927 atoms. Found 32 (35 requested) and removed 27 (17 requested) atoms. Cycle 7: After refmac, R = 0.2646 (Rfree = 0.000) for 3914 atoms. Found 19 (35 requested) and removed 19 (17 requested) atoms. Cycle 8: After refmac, R = 0.2585 (Rfree = 0.000) for 3893 atoms. Found 12 (35 requested) and removed 23 (17 requested) atoms. Cycle 9: After refmac, R = 0.2448 (Rfree = 0.000) for 3873 atoms. Found 7 (34 requested) and removed 20 (17 requested) atoms. Cycle 10: After refmac, R = 0.2393 (Rfree = 0.000) for 3853 atoms. Found 5 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 3.09 Search for helices and strands: 0 residues in 0 chains, 3924 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 3960 seeds are put forward Round 1: 304 peptides, 51 chains. Longest chain 13 peptides. Score 0.455 Round 2: 345 peptides, 46 chains. Longest chain 27 peptides. Score 0.597 Round 3: 350 peptides, 46 chains. Longest chain 23 peptides. Score 0.607 Round 4: 336 peptides, 45 chains. Longest chain 24 peptides. Score 0.587 Round 5: 337 peptides, 46 chains. Longest chain 19 peptides. Score 0.580 Taking the results from Round 3 Chains 47, Residues 304, Estimated correctness of the model 42.9 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8010 restraints for refining 3928 atoms. 6627 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2523 (Rfree = 0.000) for 3928 atoms. Found 18 (35 requested) and removed 21 (17 requested) atoms. Cycle 12: After refmac, R = 0.2409 (Rfree = 0.000) for 3900 atoms. Found 6 (35 requested) and removed 19 (17 requested) atoms. Cycle 13: After refmac, R = 0.2350 (Rfree = 0.000) for 3880 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2329 (Rfree = 0.000) for 3862 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.2286 (Rfree = 0.000) for 3849 atoms. Found 2 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3918 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 3938 seeds are put forward Round 1: 295 peptides, 48 chains. Longest chain 14 peptides. Score 0.464 Round 2: 313 peptides, 48 chains. Longest chain 18 peptides. Score 0.508 Round 3: 329 peptides, 45 chains. Longest chain 22 peptides. Score 0.573 Round 4: 320 peptides, 45 chains. Longest chain 18 peptides. Score 0.553 Round 5: 331 peptides, 45 chains. Longest chain 18 peptides. Score 0.577 Taking the results from Round 5 Chains 47, Residues 286, Estimated correctness of the model 34.7 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8119 restraints for refining 3929 atoms. 6815 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2559 (Rfree = 0.000) for 3929 atoms. Found 26 (35 requested) and removed 25 (17 requested) atoms. Cycle 17: After refmac, R = 0.2485 (Rfree = 0.000) for 3912 atoms. Found 18 (35 requested) and removed 18 (17 requested) atoms. Cycle 18: After refmac, R = 0.2379 (Rfree = 0.000) for 3897 atoms. Found 12 (35 requested) and removed 19 (17 requested) atoms. Cycle 19: After refmac, R = 0.2326 (Rfree = 0.000) for 3878 atoms. Found 13 (34 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.2252 (Rfree = 0.000) for 3864 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 3953 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3968 seeds are put forward Round 1: 292 peptides, 51 chains. Longest chain 20 peptides. Score 0.424 Round 2: 318 peptides, 48 chains. Longest chain 22 peptides. Score 0.519 Round 3: 295 peptides, 45 chains. Longest chain 16 peptides. Score 0.496 Round 4: 296 peptides, 44 chains. Longest chain 27 peptides. Score 0.509 Round 5: 301 peptides, 44 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 5 Chains 47, Residues 257, Estimated correctness of the model 18.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8372 restraints for refining 3929 atoms. 7200 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2457 (Rfree = 0.000) for 3929 atoms. Found 13 (35 requested) and removed 22 (17 requested) atoms. Cycle 22: After refmac, R = 0.2402 (Rfree = 0.000) for 3904 atoms. Found 13 (35 requested) and removed 19 (17 requested) atoms. Cycle 23: After refmac, R = 0.2380 (Rfree = 0.000) for 3883 atoms. Found 20 (34 requested) and removed 22 (17 requested) atoms. Cycle 24: After refmac, R = 0.2174 (Rfree = 0.000) for 3873 atoms. Found 5 (34 requested) and removed 19 (17 requested) atoms. Cycle 25: After refmac, R = 0.2260 (Rfree = 0.000) for 3855 atoms. Found 12 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3951 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3971 seeds are put forward Round 1: 242 peptides, 44 chains. Longest chain 16 peptides. Score 0.370 Round 2: 293 peptides, 43 chains. Longest chain 20 peptides. Score 0.512 Round 3: 293 peptides, 43 chains. Longest chain 20 peptides. Score 0.512 Round 4: 297 peptides, 43 chains. Longest chain 21 peptides. Score 0.521 Round 5: 276 peptides, 43 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 4 Chains 46, Residues 254, Estimated correctness of the model 18.0 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8210 restraints for refining 3929 atoms. 7052 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2462 (Rfree = 0.000) for 3929 atoms. Found 33 (35 requested) and removed 22 (17 requested) atoms. Cycle 27: After refmac, R = 0.2332 (Rfree = 0.000) for 3923 atoms. Found 13 (35 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.2266 (Rfree = 0.000) for 3911 atoms. Found 13 (35 requested) and removed 18 (17 requested) atoms. Cycle 29: After refmac, R = 0.2211 (Rfree = 0.000) for 3892 atoms. Found 10 (35 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.2192 (Rfree = 0.000) for 3880 atoms. Found 7 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3969 seeds are put forward Round 1: 272 peptides, 48 chains. Longest chain 15 peptides. Score 0.405 Round 2: 302 peptides, 46 chains. Longest chain 16 peptides. Score 0.502 Round 3: 313 peptides, 45 chains. Longest chain 28 peptides. Score 0.538 Round 4: 317 peptides, 44 chains. Longest chain 27 peptides. Score 0.556 Round 5: 333 peptides, 50 chains. Longest chain 25 peptides. Score 0.534 Taking the results from Round 4 Chains 46, Residues 273, Estimated correctness of the model 28.7 % 8 chains (82 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7752 restraints for refining 3928 atoms. 6391 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2405 (Rfree = 0.000) for 3928 atoms. Found 25 (35 requested) and removed 26 (17 requested) atoms. Cycle 32: After refmac, R = 0.2268 (Rfree = 0.000) for 3920 atoms. Found 5 (35 requested) and removed 22 (17 requested) atoms. Cycle 33: After refmac, R = 0.2291 (Rfree = 0.000) for 3898 atoms. Found 8 (35 requested) and removed 18 (17 requested) atoms. Cycle 34: After refmac, R = 0.2275 (Rfree = 0.000) for 3884 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.2203 (Rfree = 0.000) for 3864 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3936 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3965 seeds are put forward Round 1: 267 peptides, 47 chains. Longest chain 15 peptides. Score 0.403 Round 2: 315 peptides, 46 chains. Longest chain 19 peptides. Score 0.532 Round 3: 306 peptides, 43 chains. Longest chain 17 peptides. Score 0.542 Round 4: 308 peptides, 43 chains. Longest chain 25 peptides. Score 0.546 Round 5: 294 peptides, 41 chains. Longest chain 20 peptides. Score 0.535 Taking the results from Round 4 Chains 44, Residues 265, Estimated correctness of the model 25.7 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8479 restraints for refining 3929 atoms. 7364 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2408 (Rfree = 0.000) for 3929 atoms. Found 25 (35 requested) and removed 19 (17 requested) atoms. Cycle 37: After refmac, R = 0.2318 (Rfree = 0.000) for 3930 atoms. Found 11 (35 requested) and removed 17 (17 requested) atoms. Cycle 38: After refmac, R = 0.2297 (Rfree = 0.000) for 3918 atoms. Found 13 (35 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.2208 (Rfree = 0.000) for 3910 atoms. Found 5 (35 requested) and removed 18 (17 requested) atoms. Cycle 40: After refmac, R = 0.2206 (Rfree = 0.000) for 3894 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3943 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3955 seeds are put forward Round 1: 254 peptides, 43 chains. Longest chain 21 peptides. Score 0.414 Round 2: 266 peptides, 41 chains. Longest chain 16 peptides. Score 0.468 Round 3: 263 peptides, 40 chains. Longest chain 17 peptides. Score 0.471 Round 4: 260 peptides, 39 chains. Longest chain 17 peptides. Score 0.475 Round 5: 271 peptides, 39 chains. Longest chain 17 peptides. Score 0.502 Taking the results from Round 5 Chains 40, Residues 232, Estimated correctness of the model 12.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8609 restraints for refining 3929 atoms. 7589 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2311 (Rfree = 0.000) for 3929 atoms. Found 20 (35 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.2257 (Rfree = 0.000) for 3922 atoms. Found 16 (35 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.2172 (Rfree = 0.000) for 3919 atoms. Found 11 (35 requested) and removed 18 (17 requested) atoms. Cycle 44: After refmac, R = 0.2080 (Rfree = 0.000) for 3905 atoms. Found 11 (35 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.2061 (Rfree = 0.000) for 3897 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 3961 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3985 seeds are put forward Round 1: 225 peptides, 42 chains. Longest chain 13 peptides. Score 0.346 Round 2: 240 peptides, 38 chains. Longest chain 14 peptides. Score 0.435 Round 3: 253 peptides, 37 chains. Longest chain 18 peptides. Score 0.479 Round 4: 239 peptides, 33 chains. Longest chain 17 peptides. Score 0.489 Round 5: 234 peptides, 32 chains. Longest chain 19 peptides. Score 0.488 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 206, Estimated correctness of the model 7.7 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2gb5-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (206 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10184 reflections ( 99.58 % complete ) and 8895 restraints for refining 3929 atoms. 8068 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2188 (Rfree = 0.000) for 3929 atoms. Found 0 (35 requested) and removed 11 (17 requested) atoms. Cycle 47: After refmac, R = 0.2081 (Rfree = 0.000) for 3916 atoms. Found 0 (35 requested) and removed 5 (17 requested) atoms. Cycle 48: After refmac, R = 0.2045 (Rfree = 0.000) for 3909 atoms. Found 0 (35 requested) and removed 0 (17 requested) atoms. Cycle 49: After refmac, R = 0.2016 (Rfree = 0.000) for 3909 atoms. Found 0 (35 requested) and removed 1 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:24:53 GMT 2018 Job finished. TimeTaking 47.96 Used memory is bytes: 15790328