Mon 24 Dec 07:43:31 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 2gb5-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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/2gb5-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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 07:43:36 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/2gb5-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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 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-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: 2gb5-3.4-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 3.400 Wilson plot Bfac: 65.77 Failed to save intermediate PDB 8528 reflections ( 99.50 % complete ) and 0 restraints for refining 4767 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3324 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3114 (Rfree = 0.000) for 4767 atoms. Found 21 (35 requested) and removed 45 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 4813 seeds are put forward NCS extension: 0 residues added, 4813 seeds are put forward Round 1: 216 peptides, 46 chains. Longest chain 10 peptides. Score 0.269 Round 2: 260 peptides, 45 chains. Longest chain 15 peptides. Score 0.407 Round 3: 279 peptides, 44 chains. Longest chain 14 peptides. Score 0.468 Round 4: 292 peptides, 43 chains. Longest chain 17 peptides. Score 0.510 Round 5: 292 peptides, 44 chains. Longest chain 18 peptides. Score 0.499 Taking the results from Round 4 Chains 43, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 9062 restraints for refining 3912 atoms. 8109 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2777 (Rfree = 0.000) for 3912 atoms. Found 26 (29 requested) and removed 23 (14 requested) atoms. Cycle 2: After refmac, R = 0.2541 (Rfree = 0.000) for 3869 atoms. Found 16 (29 requested) and removed 20 (14 requested) atoms. Cycle 3: After refmac, R = 0.2397 (Rfree = 0.000) for 3839 atoms. Found 19 (29 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.2263 (Rfree = 0.000) for 3824 atoms. Found 9 (28 requested) and removed 24 (14 requested) atoms. Cycle 5: After refmac, R = 0.1980 (Rfree = 0.000) for 3802 atoms. Found 8 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3937 seeds are put forward Round 1: 246 peptides, 47 chains. Longest chain 10 peptides. Score 0.345 Round 2: 291 peptides, 49 chains. Longest chain 13 peptides. Score 0.443 Round 3: 302 peptides, 43 chains. Longest chain 18 peptides. Score 0.533 Round 4: 307 peptides, 42 chains. Longest chain 16 peptides. Score 0.554 Round 5: 312 peptides, 43 chains. Longest chain 21 peptides. Score 0.555 Taking the results from Round 5 Chains 46, Residues 269, Estimated correctness of the model 13.3 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8480 restraints for refining 3914 atoms. 7362 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2540 (Rfree = 0.000) for 3914 atoms. Found 14 (29 requested) and removed 28 (14 requested) atoms. Cycle 7: After refmac, R = 0.2304 (Rfree = 0.000) for 3876 atoms. Found 12 (29 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.2279 (Rfree = 0.000) for 3855 atoms. Found 11 (29 requested) and removed 21 (14 requested) atoms. Cycle 9: After refmac, R = 0.2198 (Rfree = 0.000) for 3844 atoms. Found 12 (29 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.2210 (Rfree = 0.000) for 3832 atoms. Found 12 (28 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 3924 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3946 seeds are put forward Round 1: 283 peptides, 51 chains. Longest chain 12 peptides. Score 0.400 Round 2: 301 peptides, 44 chains. Longest chain 18 peptides. Score 0.521 Round 3: 312 peptides, 46 chains. Longest chain 16 peptides. Score 0.526 Round 4: 299 peptides, 43 chains. Longest chain 18 peptides. Score 0.526 Round 5: 305 peptides, 43 chains. Longest chain 20 peptides. Score 0.540 Taking the results from Round 5 Chains 48, Residues 262, Estimated correctness of the model 7.9 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8359 restraints for refining 3914 atoms. 7182 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2559 (Rfree = 0.000) for 3914 atoms. Found 18 (29 requested) and removed 33 (14 requested) atoms. Cycle 12: After refmac, R = 0.2395 (Rfree = 0.000) for 3881 atoms. Found 17 (29 requested) and removed 25 (14 requested) atoms. Cycle 13: After refmac, R = 0.2292 (Rfree = 0.000) for 3860 atoms. Found 10 (29 requested) and removed 16 (14 requested) atoms. Cycle 14: After refmac, R = 0.2279 (Rfree = 0.000) for 3843 atoms. Found 10 (29 requested) and removed 20 (14 requested) atoms. Cycle 15: After refmac, R = 0.2219 (Rfree = 0.000) for 3828 atoms. Found 10 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3944 seeds are put forward Round 1: 237 peptides, 39 chains. Longest chain 17 peptides. Score 0.415 Round 2: 276 peptides, 43 chains. Longest chain 13 peptides. Score 0.471 Round 3: 279 peptides, 46 chains. Longest chain 13 peptides. Score 0.446 Round 4: 284 peptides, 41 chains. Longest chain 16 peptides. Score 0.512 Round 5: 276 peptides, 41 chains. Longest chain 18 peptides. Score 0.493 Taking the results from Round 4 Chains 41, Residues 243, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8935 restraints for refining 3914 atoms. 7990 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2390 (Rfree = 0.000) for 3914 atoms. Found 11 (29 requested) and removed 24 (14 requested) atoms. Cycle 17: After refmac, R = 0.2415 (Rfree = 0.000) for 3890 atoms. Found 9 (29 requested) and removed 16 (14 requested) atoms. Cycle 18: After refmac, R = 0.2282 (Rfree = 0.000) for 3875 atoms. Found 14 (29 requested) and removed 16 (14 requested) atoms. Cycle 19: After refmac, R = 0.2245 (Rfree = 0.000) for 3864 atoms. Found 21 (29 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2211 (Rfree = 0.000) for 3857 atoms. Found 25 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 3954 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3971 seeds are put forward Round 1: 247 peptides, 47 chains. Longest chain 12 peptides. Score 0.348 Round 2: 270 peptides, 42 chains. Longest chain 14 peptides. Score 0.467 Round 3: 282 peptides, 44 chains. Longest chain 16 peptides. Score 0.475 Round 4: 270 peptides, 45 chains. Longest chain 14 peptides. Score 0.434 Round 5: 274 peptides, 45 chains. Longest chain 14 peptides. Score 0.444 Taking the results from Round 3 Chains 45, Residues 238, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8937 restraints for refining 3914 atoms. 8000 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2385 (Rfree = 0.000) for 3914 atoms. Found 13 (29 requested) and removed 19 (14 requested) atoms. Cycle 22: After refmac, R = 0.2372 (Rfree = 0.000) for 3892 atoms. Found 18 (29 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.2215 (Rfree = 0.000) for 3883 atoms. Found 13 (29 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.2175 (Rfree = 0.000) for 3880 atoms. Found 17 (29 requested) and removed 15 (14 requested) atoms. Cycle 25: After refmac, R = 0.2175 (Rfree = 0.000) for 3877 atoms. Found 18 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 3971 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3990 seeds are put forward Round 1: 250 peptides, 50 chains. Longest chain 14 peptides. Score 0.320 Round 2: 272 peptides, 44 chains. Longest chain 15 peptides. Score 0.450 Round 3: 277 peptides, 48 chains. Longest chain 16 peptides. Score 0.418 Round 4: 293 peptides, 47 chains. Longest chain 17 peptides. Score 0.470 Round 5: 276 peptides, 43 chains. Longest chain 17 peptides. Score 0.471 Taking the results from Round 5 Chains 43, Residues 233, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8952 restraints for refining 3912 atoms. 8009 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2433 (Rfree = 0.000) for 3912 atoms. Found 16 (29 requested) and removed 20 (14 requested) atoms. Cycle 27: After refmac, R = 0.2383 (Rfree = 0.000) for 3890 atoms. Found 19 (29 requested) and removed 15 (14 requested) atoms. Cycle 28: After refmac, R = 0.2289 (Rfree = 0.000) for 3884 atoms. Found 15 (29 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.2252 (Rfree = 0.000) for 3874 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. Cycle 30: After refmac, R = 0.2173 (Rfree = 0.000) for 3856 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 3934 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3958 seeds are put forward Round 1: 247 peptides, 49 chains. Longest chain 16 peptides. Score 0.324 Round 2: 261 peptides, 42 chains. Longest chain 17 peptides. Score 0.444 Round 3: 270 peptides, 46 chains. Longest chain 13 peptides. Score 0.422 Round 4: 262 peptides, 41 chains. Longest chain 14 peptides. Score 0.458 Round 5: 289 peptides, 45 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 5 Chains 45, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8951 restraints for refining 3914 atoms. 8020 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2413 (Rfree = 0.000) for 3914 atoms. Found 19 (29 requested) and removed 21 (14 requested) atoms. Cycle 32: After refmac, R = 0.2310 (Rfree = 0.000) for 3895 atoms. Found 15 (29 requested) and removed 19 (14 requested) atoms. Cycle 33: After refmac, R = 0.2174 (Rfree = 0.000) for 3882 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. Cycle 34: After refmac, R = 0.1943 (Rfree = 0.000) for 3872 atoms. Found 5 (29 requested) and removed 16 (14 requested) atoms. Cycle 35: After refmac, R = 0.1882 (Rfree = 0.000) for 3858 atoms. Found 5 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 3943 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3958 seeds are put forward Round 1: 219 peptides, 43 chains. Longest chain 13 peptides. Score 0.316 Round 2: 251 peptides, 40 chains. Longest chain 16 peptides. Score 0.441 Round 3: 243 peptides, 38 chains. Longest chain 15 peptides. Score 0.443 Round 4: 252 peptides, 41 chains. Longest chain 14 peptides. Score 0.432 Round 5: 264 peptides, 39 chains. Longest chain 23 peptides. Score 0.485 Taking the results from Round 5 Chains 40, Residues 225, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8626 restraints for refining 3914 atoms. 7693 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2325 (Rfree = 0.000) for 3914 atoms. Found 18 (29 requested) and removed 22 (14 requested) atoms. Cycle 37: After refmac, R = 0.2217 (Rfree = 0.000) for 3898 atoms. Found 9 (29 requested) and removed 20 (14 requested) atoms. Cycle 38: After refmac, R = 0.2181 (Rfree = 0.000) for 3879 atoms. Found 12 (29 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.2202 (Rfree = 0.000) for 3871 atoms. Found 10 (29 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2190 (Rfree = 0.000) for 3866 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 3941 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3964 seeds are put forward Round 1: 228 peptides, 44 chains. Longest chain 9 peptides. Score 0.330 Round 2: 241 peptides, 40 chains. Longest chain 17 peptides. Score 0.414 Round 3: 243 peptides, 40 chains. Longest chain 14 peptides. Score 0.420 Round 4: 244 peptides, 40 chains. Longest chain 19 peptides. Score 0.422 Round 5: 250 peptides, 41 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 5 Chains 41, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 9011 restraints for refining 3913 atoms. 8216 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2343 (Rfree = 0.000) for 3913 atoms. Found 13 (29 requested) and removed 15 (14 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2230 (Rfree = 0.000) for 3898 atoms. Found 19 (29 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.2273 (Rfree = 0.000) for 3898 atoms. Found 11 (29 requested) and removed 20 (14 requested) atoms. Cycle 44: After refmac, R = 0.2112 (Rfree = 0.000) for 3882 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. Cycle 45: After refmac, R = 0.2208 (Rfree = 0.000) for 3873 atoms. Found 19 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 3954 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3974 seeds are put forward Round 1: 202 peptides, 42 chains. Longest chain 11 peptides. Score 0.277 Round 2: 215 peptides, 39 chains. Longest chain 12 peptides. Score 0.354 Round 3: 205 peptides, 35 chains. Longest chain 15 peptides. Score 0.375 Round 4: 227 peptides, 38 chains. Longest chain 15 peptides. Score 0.400 Round 5: 222 peptides, 38 chains. Longest chain 15 peptides. Score 0.386 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 189, Estimated correctness of the model 0.0 % 3 chains (20 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 40 chains (189 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8528 reflections ( 99.50 % complete ) and 8911 restraints for refining 3913 atoms. 8116 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2404 (Rfree = 0.000) for 3913 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2301 (Rfree = 0.000) for 3881 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2224 (Rfree = 0.000) for 3858 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2107 (Rfree = 0.000) for 3838 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 46.38