null Tue 25 Dec 19:27:55 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 2gb5-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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/2gb5-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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 ============================================================ Tue 25 Dec 19:28:05 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/2gb5-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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 404 and 0 Target number of residues in the AU: 404 Target solvent content: 0.6287 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: 2gb5-3.4-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 65.77 8528 reflections ( 99.50 % complete ) and 0 restraints for refining 4777 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2954 (Rfree = 0.000) for 4777 atoms. Found 30 (36 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 4845 seeds are put forward NCS extension: 0 residues added, 4845 seeds are put forward Round 1: 238 peptides, 46 chains. Longest chain 11 peptides. Score 0.334 Round 2: 292 peptides, 48 chains. Longest chain 18 peptides. Score 0.457 Round 3: 312 peptides, 46 chains. Longest chain 19 peptides. Score 0.526 Round 4: 340 peptides, 46 chains. Longest chain 21 peptides. Score 0.586 Round 5: 325 peptides, 47 chains. Longest chain 17 peptides. Score 0.545 Taking the results from Round 4 Chains 46, Residues 294, Estimated correctness of the model 24.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8521 restraints for refining 3913 atoms. 7350 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2555 (Rfree = 0.000) for 3913 atoms. Found 16 (29 requested) and removed 26 (14 requested) atoms. Cycle 2: After refmac, R = 0.2534 (Rfree = 0.000) for 3842 atoms. Found 18 (29 requested) and removed 23 (14 requested) atoms. Cycle 3: After refmac, R = 0.2431 (Rfree = 0.000) for 3813 atoms. Found 8 (28 requested) and removed 16 (14 requested) atoms. Cycle 4: After refmac, R = 0.2190 (Rfree = 0.000) for 3783 atoms. Found 5 (28 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.2136 (Rfree = 0.000) for 3757 atoms. Found 3 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 3851 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3873 seeds are put forward Round 1: 270 peptides, 49 chains. Longest chain 13 peptides. Score 0.388 Round 2: 298 peptides, 45 chains. Longest chain 21 peptides. Score 0.503 Round 3: 313 peptides, 44 chains. Longest chain 18 peptides. Score 0.548 Round 4: 320 peptides, 46 chains. Longest chain 24 peptides. Score 0.544 Round 5: 297 peptides, 41 chains. Longest chain 19 peptides. Score 0.542 Taking the results from Round 3 Chains 44, Residues 269, Estimated correctness of the model 10.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8919 restraints for refining 3914 atoms. 7887 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2629 (Rfree = 0.000) for 3914 atoms. Found 22 (29 requested) and removed 23 (14 requested) atoms. Cycle 7: After refmac, R = 0.2463 (Rfree = 0.000) for 3890 atoms. Found 19 (29 requested) and removed 18 (14 requested) atoms. Cycle 8: After refmac, R = 0.2329 (Rfree = 0.000) for 3872 atoms. Found 13 (29 requested) and removed 15 (14 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 3861 atoms. Found 17 (29 requested) and removed 16 (14 requested) atoms. Cycle 10: After refmac, R = 0.2244 (Rfree = 0.000) for 3855 atoms. Found 10 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 3949 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3963 seeds are put forward Round 1: 268 peptides, 44 chains. Longest chain 15 peptides. Score 0.440 Round 2: 312 peptides, 45 chains. Longest chain 20 peptides. Score 0.536 Round 3: 320 peptides, 43 chains. Longest chain 22 peptides. Score 0.572 Round 4: 312 peptides, 42 chains. Longest chain 16 peptides. Score 0.565 Round 5: 317 peptides, 45 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 3 Chains 43, Residues 277, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8830 restraints for refining 3914 atoms. 7765 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2483 (Rfree = 0.000) for 3914 atoms. Found 20 (29 requested) and removed 20 (14 requested) atoms. Cycle 12: After refmac, R = 0.2317 (Rfree = 0.000) for 3895 atoms. Found 18 (29 requested) and removed 19 (14 requested) atoms. Cycle 13: After refmac, R = 0.2063 (Rfree = 0.000) for 3884 atoms. Found 11 (29 requested) and removed 14 (14 requested) atoms. Cycle 14: After refmac, R = 0.2007 (Rfree = 0.000) for 3876 atoms. Found 2 (29 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.1985 (Rfree = 0.000) for 3862 atoms. Found 3 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 3978 seeds are put forward Round 1: 262 peptides, 47 chains. Longest chain 11 peptides. Score 0.390 Round 2: 290 peptides, 44 chains. Longest chain 15 peptides. Score 0.495 Round 3: 325 peptides, 48 chains. Longest chain 26 peptides. Score 0.535 Round 4: 318 peptides, 43 chains. Longest chain 22 peptides. Score 0.568 Round 5: 313 peptides, 46 chains. Longest chain 20 peptides. Score 0.528 Taking the results from Round 4 Chains 44, Residues 275, Estimated correctness of the model 17.9 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8484 restraints for refining 3914 atoms. 7389 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2495 (Rfree = 0.000) for 3914 atoms. Found 22 (29 requested) and removed 21 (14 requested) atoms. Cycle 17: After refmac, R = 0.2377 (Rfree = 0.000) for 3899 atoms. Found 16 (29 requested) and removed 17 (14 requested) atoms. Cycle 18: After refmac, R = 0.2281 (Rfree = 0.000) for 3883 atoms. Found 15 (29 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.2275 (Rfree = 0.000) for 3877 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.1966 (Rfree = 0.000) for 3873 atoms. Found 2 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3977 seeds are put forward Round 1: 262 peptides, 46 chains. Longest chain 14 peptides. Score 0.401 Round 2: 282 peptides, 44 chains. Longest chain 15 peptides. Score 0.475 Round 3: 295 peptides, 43 chains. Longest chain 16 peptides. Score 0.517 Round 4: 292 peptides, 43 chains. Longest chain 14 peptides. Score 0.510 Round 5: 295 peptides, 41 chains. Longest chain 14 peptides. Score 0.537 Taking the results from Round 5 Chains 41, Residues 254, Estimated correctness of the model 6.8 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8893 restraints for refining 3912 atoms. 7903 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2539 (Rfree = 0.000) for 3912 atoms. Found 22 (29 requested) and removed 18 (14 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 3906 atoms. Found 14 (29 requested) and removed 15 (14 requested) atoms. Cycle 23: After refmac, R = 0.2426 (Rfree = 0.000) for 3897 atoms. Found 8 (29 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.2396 (Rfree = 0.000) for 3885 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 25: After refmac, R = 0.2389 (Rfree = 0.000) for 3880 atoms. Found 11 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 3947 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3967 seeds are put forward Round 1: 281 peptides, 48 chains. Longest chain 15 peptides. Score 0.429 Round 2: 296 peptides, 40 chains. Longest chain 15 peptides. Score 0.549 Round 3: 297 peptides, 47 chains. Longest chain 14 peptides. Score 0.480 Round 4: 308 peptides, 46 chains. Longest chain 17 peptides. Score 0.516 Round 5: 296 peptides, 42 chains. Longest chain 20 peptides. Score 0.529 Taking the results from Round 2 Chains 40, Residues 256, Estimated correctness of the model 11.2 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8812 restraints for refining 3914 atoms. 7803 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2347 (Rfree = 0.000) for 3914 atoms. Found 16 (29 requested) and removed 17 (14 requested) atoms. Cycle 27: After refmac, R = 0.2348 (Rfree = 0.000) for 3899 atoms. Found 9 (29 requested) and removed 15 (14 requested) atoms. Cycle 28: After refmac, R = 0.2340 (Rfree = 0.000) for 3884 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. Cycle 29: After refmac, R = 0.2230 (Rfree = 0.000) for 3868 atoms. Found 7 (29 requested) and removed 15 (14 requested) atoms. Cycle 30: After refmac, R = 0.2252 (Rfree = 0.000) for 3857 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 3929 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3948 seeds are put forward Round 1: 263 peptides, 47 chains. Longest chain 16 peptides. Score 0.392 Round 2: 289 peptides, 42 chains. Longest chain 19 peptides. Score 0.513 Round 3: 291 peptides, 40 chains. Longest chain 16 peptides. Score 0.538 Round 4: 277 peptides, 37 chains. Longest chain 18 peptides. Score 0.537 Round 5: 278 peptides, 40 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 3 Chains 41, Residues 251, Estimated correctness of the model 7.2 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8718 restraints for refining 3914 atoms. 7690 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2260 (Rfree = 0.000) for 3914 atoms. Found 17 (29 requested) and removed 16 (14 requested) atoms. Cycle 32: After refmac, R = 0.2240 (Rfree = 0.000) for 3909 atoms. Found 11 (29 requested) and removed 16 (14 requested) atoms. Cycle 33: After refmac, R = 0.2223 (Rfree = 0.000) for 3901 atoms. Found 10 (29 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2153 (Rfree = 0.000) for 3891 atoms. Found 14 (29 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2132 (Rfree = 0.000) for 3886 atoms. Found 8 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 3952 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3969 seeds are put forward Round 1: 250 peptides, 47 chains. Longest chain 12 peptides. Score 0.356 Round 2: 268 peptides, 36 chains. Longest chain 16 peptides. Score 0.526 Round 3: 277 peptides, 43 chains. Longest chain 13 peptides. Score 0.474 Round 4: 266 peptides, 41 chains. Longest chain 21 peptides. Score 0.468 Round 5: 268 peptides, 38 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 2 Chains 37, Residues 232, Estimated correctness of the model 2.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8741 restraints for refining 3914 atoms. 7812 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2282 (Rfree = 0.000) for 3914 atoms. Found 10 (29 requested) and removed 15 (14 requested) atoms. Cycle 37: After refmac, R = 0.2073 (Rfree = 0.000) for 3905 atoms. Found 10 (29 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.2011 (Rfree = 0.000) for 3896 atoms. Found 7 (29 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.2006 (Rfree = 0.000) for 3886 atoms. Found 2 (29 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2001 (Rfree = 0.000) for 3873 atoms. Found 6 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 3948 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3967 seeds are put forward Round 1: 234 peptides, 46 chains. Longest chain 11 peptides. Score 0.323 Round 2: 275 peptides, 44 chains. Longest chain 16 peptides. Score 0.458 Round 3: 271 peptides, 44 chains. Longest chain 12 peptides. Score 0.447 Round 4: 269 peptides, 39 chains. Longest chain 17 peptides. Score 0.497 Round 5: 261 peptides, 33 chains. Longest chain 39 peptides. Score 0.542 Taking the results from Round 5 Chains 35, Residues 228, Estimated correctness of the model 8.6 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8408 restraints for refining 3914 atoms. 7342 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2351 (Rfree = 0.000) for 3914 atoms. Found 16 (29 requested) and removed 22 (14 requested) atoms. Cycle 42: After refmac, R = 0.2278 (Rfree = 0.000) for 3890 atoms. Found 16 (29 requested) and removed 15 (14 requested) atoms. Cycle 43: After refmac, R = 0.2297 (Rfree = 0.000) for 3882 atoms. Found 12 (29 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.2061 (Rfree = 0.000) for 3876 atoms. Found 7 (29 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.2040 (Rfree = 0.000) for 3864 atoms. Found 4 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 3916 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3940 seeds are put forward Round 1: 205 peptides, 37 chains. Longest chain 16 peptides. Score 0.350 Round 2: 245 peptides, 37 chains. Longest chain 19 peptides. Score 0.459 Round 3: 243 peptides, 36 chains. Longest chain 22 peptides. Score 0.466 Round 4: 247 peptides, 34 chains. Longest chain 36 peptides. Score 0.498 Round 5: 249 peptides, 37 chains. Longest chain 31 peptides. Score 0.469 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 213, 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. 8528 reflections ( 99.50 % complete ) and 9123 restraints for refining 3914 atoms. 8305 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2207 (Rfree = 0.000) for 3914 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2326 (Rfree = 0.000) for 3893 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2308 (Rfree = 0.000) for 3876 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2036 (Rfree = 0.000) for 3858 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:34:15 GMT 2018 Job finished. TimeTaking 66.33 Used memory is bytes: 16304128