null Mon 24 Dec 00:42:26 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 2gb5-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-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/2gb5-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-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 00:42:31 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/2gb5-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-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 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-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: 2gb5-3.2-parrot-mrncs.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 4744 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3157 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2749 (Rfree = 0.000) for 4744 atoms. Found 35 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 4827 seeds are put forward NCS extension: 0 residues added, 4827 seeds are put forward Round 1: 296 peptides, 51 chains. Longest chain 13 peptides. Score 0.434 Round 2: 334 peptides, 48 chains. Longest chain 17 peptides. Score 0.555 Round 3: 351 peptides, 43 chains. Longest chain 24 peptides. Score 0.634 Round 4: 360 peptides, 41 chains. Longest chain 26 peptides. Score 0.667 Round 5: 359 peptides, 42 chains. Longest chain 31 peptides. Score 0.657 Taking the results from Round 4 Chains 41, Residues 319, Estimated correctness of the model 57.9 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7933 restraints for refining 3928 atoms. 6410 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2710 (Rfree = 0.000) for 3928 atoms. Found 22 (35 requested) and removed 32 (17 requested) atoms. Cycle 2: After refmac, R = 0.2590 (Rfree = 0.000) for 3875 atoms. Found 10 (35 requested) and removed 23 (17 requested) atoms. Cycle 3: After refmac, R = 0.2497 (Rfree = 0.000) for 3837 atoms. Found 13 (34 requested) and removed 21 (17 requested) atoms. Cycle 4: After refmac, R = 0.2415 (Rfree = 0.000) for 3822 atoms. Found 4 (34 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2355 (Rfree = 0.000) for 3804 atoms. Found 4 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3898 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 3910 seeds are put forward Round 1: 331 peptides, 45 chains. Longest chain 29 peptides. Score 0.577 Round 2: 362 peptides, 40 chains. Longest chain 28 peptides. Score 0.678 Round 3: 375 peptides, 43 chains. Longest chain 26 peptides. Score 0.677 Round 4: 382 peptides, 43 chains. Longest chain 26 peptides. Score 0.688 Round 5: 378 peptides, 43 chains. Longest chain 26 peptides. Score 0.682 Taking the results from Round 4 Chains 46, Residues 339, Estimated correctness of the model 62.6 % 7 chains (70 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7755 restraints for refining 3929 atoms. 6170 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2573 (Rfree = 0.000) for 3929 atoms. Found 34 (35 requested) and removed 31 (17 requested) atoms. Cycle 7: After refmac, R = 0.2374 (Rfree = 0.000) for 3912 atoms. Found 16 (35 requested) and removed 23 (17 requested) atoms. Cycle 8: After refmac, R = 0.2308 (Rfree = 0.000) for 3894 atoms. Found 12 (35 requested) and removed 17 (17 requested) atoms. Cycle 9: After refmac, R = 0.2318 (Rfree = 0.000) for 3887 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.2293 (Rfree = 0.000) for 3872 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 3943 seeds are put forward NCS extension: 41 residues added (10 deleted due to clashes), 3984 seeds are put forward Round 1: 310 peptides, 43 chains. Longest chain 22 peptides. Score 0.551 Round 2: 336 peptides, 38 chains. Longest chain 25 peptides. Score 0.649 Round 3: 354 peptides, 37 chains. Longest chain 24 peptides. Score 0.688 Round 4: 356 peptides, 40 chains. Longest chain 26 peptides. Score 0.668 Round 5: 352 peptides, 38 chains. Longest chain 24 peptides. Score 0.677 Taking the results from Round 3 Chains 40, Residues 317, Estimated correctness of the model 62.6 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8120 restraints for refining 3929 atoms. 6734 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2479 (Rfree = 0.000) for 3929 atoms. Found 20 (35 requested) and removed 23 (17 requested) atoms. Cycle 12: After refmac, R = 0.2388 (Rfree = 0.000) for 3912 atoms. Found 8 (35 requested) and removed 20 (17 requested) atoms. Cycle 13: After refmac, R = 0.2371 (Rfree = 0.000) for 3895 atoms. Found 9 (35 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2307 (Rfree = 0.000) for 3881 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.2239 (Rfree = 0.000) for 3867 atoms. Found 10 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 3948 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 3987 seeds are put forward Round 1: 308 peptides, 42 chains. Longest chain 20 peptides. Score 0.556 Round 2: 337 peptides, 41 chains. Longest chain 19 peptides. Score 0.625 Round 3: 340 peptides, 38 chains. Longest chain 23 peptides. Score 0.656 Round 4: 329 peptides, 40 chains. Longest chain 20 peptides. Score 0.618 Round 5: 333 peptides, 38 chains. Longest chain 21 peptides. Score 0.643 Taking the results from Round 3 Chains 43, Residues 302, Estimated correctness of the model 55.3 % 7 chains (96 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7629 restraints for refining 3929 atoms. 6048 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2540 (Rfree = 0.000) for 3929 atoms. Found 16 (35 requested) and removed 30 (17 requested) atoms. Cycle 17: After refmac, R = 0.2472 (Rfree = 0.000) for 3900 atoms. Found 5 (35 requested) and removed 21 (17 requested) atoms. Cycle 18: After refmac, R = 0.2465 (Rfree = 0.000) for 3873 atoms. Found 14 (34 requested) and removed 20 (17 requested) atoms. Cycle 19: After refmac, R = 0.2353 (Rfree = 0.000) for 3859 atoms. Found 4 (34 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.2310 (Rfree = 0.000) for 3839 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3913 seeds are put forward NCS extension: 23 residues added (7 deleted due to clashes), 3936 seeds are put forward Round 1: 330 peptides, 45 chains. Longest chain 20 peptides. Score 0.575 Round 2: 345 peptides, 42 chains. Longest chain 21 peptides. Score 0.631 Round 3: 337 peptides, 42 chains. Longest chain 21 peptides. Score 0.616 Round 4: 344 peptides, 41 chains. Longest chain 22 peptides. Score 0.638 Round 5: 359 peptides, 42 chains. Longest chain 25 peptides. Score 0.657 Taking the results from Round 5 Chains 46, Residues 317, Estimated correctness of the model 55.5 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7937 restraints for refining 3928 atoms. 6492 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2520 (Rfree = 0.000) for 3928 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Cycle 22: After refmac, R = 0.2377 (Rfree = 0.000) for 3923 atoms. Found 10 (35 requested) and removed 21 (17 requested) atoms. Cycle 23: After refmac, R = 0.2331 (Rfree = 0.000) for 3903 atoms. Found 11 (35 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.2277 (Rfree = 0.000) for 3893 atoms. Found 9 (34 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.2247 (Rfree = 0.000) for 3878 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3974 seeds are put forward Round 1: 319 peptides, 46 chains. Longest chain 18 peptides. Score 0.541 Round 2: 335 peptides, 43 chains. Longest chain 20 peptides. Score 0.603 Round 3: 330 peptides, 44 chains. Longest chain 21 peptides. Score 0.584 Round 4: 337 peptides, 47 chains. Longest chain 19 peptides. Score 0.571 Round 5: 327 peptides, 44 chains. Longest chain 19 peptides. Score 0.578 Taking the results from Round 2 Chains 44, Residues 292, Estimated correctness of the model 41.9 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8501 restraints for refining 3929 atoms. 7324 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2393 (Rfree = 0.000) for 3929 atoms. Found 19 (35 requested) and removed 19 (17 requested) atoms. Cycle 27: After refmac, R = 0.2284 (Rfree = 0.000) for 3921 atoms. Found 4 (35 requested) and removed 17 (17 requested) atoms. Cycle 28: After refmac, R = 0.2287 (Rfree = 0.000) for 3903 atoms. Found 8 (35 requested) and removed 17 (17 requested) atoms. Cycle 29: After refmac, R = 0.2283 (Rfree = 0.000) for 3893 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 30: After refmac, R = 0.2274 (Rfree = 0.000) for 3878 atoms. Found 10 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3966 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3983 seeds are put forward Round 1: 297 peptides, 44 chains. Longest chain 20 peptides. Score 0.511 Round 2: 333 peptides, 42 chains. Longest chain 20 peptides. Score 0.608 Round 3: 329 peptides, 36 chains. Longest chain 47 peptides. Score 0.653 Round 4: 333 peptides, 38 chains. Longest chain 21 peptides. Score 0.643 Round 5: 327 peptides, 39 chains. Longest chain 21 peptides. Score 0.623 Taking the results from Round 3 Chains 39, Residues 293, Estimated correctness of the model 54.6 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8250 restraints for refining 3929 atoms. 6981 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2393 (Rfree = 0.000) for 3929 atoms. Found 24 (35 requested) and removed 19 (17 requested) atoms. Cycle 32: After refmac, R = 0.2255 (Rfree = 0.000) for 3923 atoms. Found 15 (35 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.2245 (Rfree = 0.000) for 3916 atoms. Found 12 (35 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 3907 atoms. Found 6 (35 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.2211 (Rfree = 0.000) for 3893 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3968 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 3988 seeds are put forward Round 1: 261 peptides, 41 chains. Longest chain 20 peptides. Score 0.455 Round 2: 307 peptides, 40 chains. Longest chain 21 peptides. Score 0.573 Round 3: 311 peptides, 39 chains. Longest chain 21 peptides. Score 0.591 Round 4: 308 peptides, 42 chains. Longest chain 21 peptides. Score 0.556 Round 5: 310 peptides, 44 chains. Longest chain 19 peptides. Score 0.541 Taking the results from Round 3 Chains 41, Residues 272, Estimated correctness of the model 38.6 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8185 restraints for refining 3929 atoms. 6956 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2373 (Rfree = 0.000) for 3929 atoms. Found 24 (35 requested) and removed 25 (17 requested) atoms. Cycle 37: After refmac, R = 0.2265 (Rfree = 0.000) for 3915 atoms. Found 8 (35 requested) and removed 19 (17 requested) atoms. Cycle 38: After refmac, R = 0.2272 (Rfree = 0.000) for 3900 atoms. Found 13 (35 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.2194 (Rfree = 0.000) for 3891 atoms. Found 4 (34 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.2165 (Rfree = 0.000) for 3876 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 3990 seeds are put forward Round 1: 240 peptides, 40 chains. Longest chain 19 peptides. Score 0.411 Round 2: 288 peptides, 39 chains. Longest chain 19 peptides. Score 0.541 Round 3: 291 peptides, 40 chains. Longest chain 21 peptides. Score 0.538 Round 4: 300 peptides, 35 chains. Longest chain 28 peptides. Score 0.606 Round 5: 288 peptides, 41 chains. Longest chain 20 peptides. Score 0.521 Taking the results from Round 4 Chains 37, Residues 265, Estimated correctness of the model 42.7 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7933 restraints for refining 3929 atoms. 6611 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2365 (Rfree = 0.000) for 3929 atoms. Found 23 (35 requested) and removed 22 (17 requested) atoms. Cycle 42: After refmac, R = 0.2220 (Rfree = 0.000) for 3918 atoms. Found 8 (35 requested) and removed 19 (17 requested) atoms. Cycle 43: After refmac, R = 0.2184 (Rfree = 0.000) for 3895 atoms. Found 11 (35 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.2134 (Rfree = 0.000) for 3886 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.2108 (Rfree = 0.000) for 3866 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3953 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3967 seeds are put forward Round 1: 252 peptides, 44 chains. Longest chain 18 peptides. Score 0.397 Round 2: 282 peptides, 44 chains. Longest chain 19 peptides. Score 0.475 Round 3: 279 peptides, 40 chains. Longest chain 26 peptides. Score 0.510 Round 4: 273 peptides, 39 chains. Longest chain 27 peptides. Score 0.507 Round 5: 291 peptides, 42 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 249, Estimated correctness of the model 17.1 % 3 chains (25 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2gb5-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (249 residues) following loop building 3 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10184 reflections ( 99.58 % complete ) and 8541 restraints for refining 3929 atoms. 7484 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2307 (Rfree = 0.000) for 3929 atoms. Found 0 (35 requested) and removed 15 (17 requested) atoms. Cycle 47: After refmac, R = 0.2251 (Rfree = 0.000) for 3904 atoms. Found 0 (35 requested) and removed 2 (17 requested) atoms. Cycle 48: After refmac, R = 0.2241 (Rfree = 0.000) for 3897 atoms. Found 0 (35 requested) and removed 3 (17 requested) atoms. Cycle 49: After refmac, R = 0.2200 (Rfree = 0.000) for 3891 atoms. Found 0 (34 requested) and removed 7 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:28:09 GMT 2018 Job finished. TimeTaking 45.71 Used memory is bytes: 20473648