Mon 24 Dec 07:39:55 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 2gb5-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-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/2gb5-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-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 07:39:59 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/2gb5-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.6-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 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-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: 2gb5-3.6-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 3.600 Wilson plot Bfac: 70.46 7206 reflections ( 99.41 % complete ) and 0 restraints for refining 4779 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3048 (Rfree = 0.000) for 4779 atoms. Found 17 (30 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 4821 seeds are put forward NCS extension: 0 residues added, 4821 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 8 peptides. Score 0.259 Round 2: 246 peptides, 44 chains. Longest chain 13 peptides. Score 0.381 Round 3: 239 peptides, 39 chains. Longest chain 11 peptides. Score 0.421 Round 4: 268 peptides, 44 chains. Longest chain 18 peptides. Score 0.440 Round 5: 273 peptides, 42 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 5 Chains 42, Residues 231, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9134 restraints for refining 3902 atoms. 8252 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 3902 atoms. Found 13 (25 requested) and removed 24 (12 requested) atoms. Cycle 2: After refmac, R = 0.2777 (Rfree = 0.000) for 3833 atoms. Found 21 (24 requested) and removed 24 (12 requested) atoms. Cycle 3: After refmac, R = 0.2580 (Rfree = 0.000) for 3803 atoms. Found 5 (24 requested) and removed 20 (12 requested) atoms. Cycle 4: After refmac, R = 0.2611 (Rfree = 0.000) for 3761 atoms. Found 14 (24 requested) and removed 19 (12 requested) atoms. Cycle 5: After refmac, R = 0.2661 (Rfree = 0.000) for 3740 atoms. Found 19 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 3847 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3868 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 8 peptides. Score 0.261 Round 2: 245 peptides, 43 chains. Longest chain 11 peptides. Score 0.390 Round 3: 260 peptides, 40 chains. Longest chain 16 peptides. Score 0.464 Round 4: 261 peptides, 41 chains. Longest chain 14 peptides. Score 0.455 Round 5: 278 peptides, 40 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 5 Chains 40, Residues 238, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8729 restraints for refining 3806 atoms. 7788 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2605 (Rfree = 0.000) for 3806 atoms. Found 11 (24 requested) and removed 29 (12 requested) atoms. Cycle 7: After refmac, R = 0.2589 (Rfree = 0.000) for 3757 atoms. Found 8 (24 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.2511 (Rfree = 0.000) for 3717 atoms. Found 8 (24 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2479 (Rfree = 0.000) for 3699 atoms. Found 13 (23 requested) and removed 24 (11 requested) atoms. Cycle 10: After refmac, R = 0.2439 (Rfree = 0.000) for 3679 atoms. Found 10 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3773 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 11 peptides. Score 0.313 Round 2: 257 peptides, 44 chains. Longest chain 15 peptides. Score 0.411 Round 3: 245 peptides, 40 chains. Longest chain 14 peptides. Score 0.425 Round 4: 266 peptides, 42 chains. Longest chain 16 peptides. Score 0.457 Round 5: 256 peptides, 40 chains. Longest chain 15 peptides. Score 0.454 Taking the results from Round 4 Chains 42, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9063 restraints for refining 3899 atoms. 8209 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2577 (Rfree = 0.000) for 3899 atoms. Found 18 (25 requested) and removed 25 (12 requested) atoms. Cycle 12: After refmac, R = 0.2512 (Rfree = 0.000) for 3872 atoms. Found 13 (24 requested) and removed 27 (12 requested) atoms. Cycle 13: After refmac, R = 0.2432 (Rfree = 0.000) for 3844 atoms. Found 16 (24 requested) and removed 25 (12 requested) atoms. Cycle 14: After refmac, R = 0.2385 (Rfree = 0.000) for 3828 atoms. Found 23 (24 requested) and removed 19 (12 requested) atoms. Cycle 15: After refmac, R = 0.2012 (Rfree = 0.000) for 3824 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 3931 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3945 seeds are put forward Round 1: 225 peptides, 46 chains. Longest chain 12 peptides. Score 0.296 Round 2: 251 peptides, 40 chains. Longest chain 18 peptides. Score 0.441 Round 3: 246 peptides, 40 chains. Longest chain 16 peptides. Score 0.428 Round 4: 247 peptides, 37 chains. Longest chain 16 peptides. Score 0.464 Round 5: 263 peptides, 40 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 5 Chains 40, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9030 restraints for refining 3901 atoms. 8178 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2468 (Rfree = 0.000) for 3901 atoms. Found 14 (25 requested) and removed 19 (12 requested) atoms. Cycle 17: After refmac, R = 0.2460 (Rfree = 0.000) for 3866 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. Cycle 18: After refmac, R = 0.2271 (Rfree = 0.000) for 3850 atoms. Found 21 (24 requested) and removed 18 (12 requested) atoms. Cycle 19: After refmac, R = 0.2291 (Rfree = 0.000) for 3838 atoms. Found 20 (24 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.1948 (Rfree = 0.000) for 3826 atoms. Found 9 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 3907 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3921 seeds are put forward Round 1: 196 peptides, 39 chains. Longest chain 14 peptides. Score 0.297 Round 2: 227 peptides, 38 chains. Longest chain 14 peptides. Score 0.400 Round 3: 247 peptides, 42 chains. Longest chain 19 peptides. Score 0.407 Round 4: 232 peptides, 39 chains. Longest chain 13 peptides. Score 0.402 Round 5: 239 peptides, 39 chains. Longest chain 15 peptides. Score 0.421 Taking the results from Round 5 Chains 39, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9240 restraints for refining 3901 atoms. 8479 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2379 (Rfree = 0.000) for 3901 atoms. Found 15 (25 requested) and removed 15 (12 requested) atoms. Cycle 22: After refmac, R = 0.2415 (Rfree = 0.000) for 3886 atoms. Found 19 (25 requested) and removed 19 (12 requested) atoms. Cycle 23: After refmac, R = 0.2283 (Rfree = 0.000) for 3872 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. Cycle 24: After refmac, R = 0.2259 (Rfree = 0.000) for 3864 atoms. Found 10 (24 requested) and removed 19 (12 requested) atoms. Cycle 25: After refmac, R = 0.2236 (Rfree = 0.000) for 3848 atoms. Found 11 (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, 3947 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3968 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 12 peptides. Score 0.328 Round 2: 223 peptides, 39 chains. Longest chain 13 peptides. Score 0.377 Round 3: 216 peptides, 39 chains. Longest chain 18 peptides. Score 0.357 Round 4: 227 peptides, 41 chains. Longest chain 10 peptides. Score 0.364 Round 5: 213 peptides, 33 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Chains 33, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9236 restraints for refining 3901 atoms. 8549 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2419 (Rfree = 0.000) for 3901 atoms. Found 21 (25 requested) and removed 15 (12 requested) atoms. Cycle 27: After refmac, R = 0.2441 (Rfree = 0.000) for 3893 atoms. Found 25 (25 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.2075 (Rfree = 0.000) for 3892 atoms. Found 19 (25 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.1765 (Rfree = 0.000) for 3893 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. Cycle 30: After refmac, R = 0.1790 (Rfree = 0.000) for 3886 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3967 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3987 seeds are put forward Round 1: 177 peptides, 36 chains. Longest chain 9 peptides. Score 0.278 Round 2: 204 peptides, 36 chains. Longest chain 13 peptides. Score 0.359 Round 3: 205 peptides, 33 chains. Longest chain 11 peptides. Score 0.400 Round 4: 201 peptides, 31 chains. Longest chain 12 peptides. Score 0.413 Round 5: 229 peptides, 35 chains. Longest chain 14 peptides. Score 0.441 Taking the results from Round 5 Chains 37, Residues 194, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9038 restraints for refining 3901 atoms. 8260 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2258 (Rfree = 0.000) for 3901 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 32: After refmac, R = 0.2199 (Rfree = 0.000) for 3886 atoms. Found 15 (25 requested) and removed 17 (12 requested) atoms. Cycle 33: After refmac, R = 0.2192 (Rfree = 0.000) for 3876 atoms. Found 21 (24 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2087 (Rfree = 0.000) for 3879 atoms. Found 14 (24 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1811 (Rfree = 0.000) for 3875 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 3923 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3937 seeds are put forward Round 1: 208 peptides, 43 chains. Longest chain 10 peptides. Score 0.283 Round 2: 217 peptides, 40 chains. Longest chain 11 peptides. Score 0.347 Round 3: 213 peptides, 38 chains. Longest chain 12 peptides. Score 0.360 Round 4: 230 peptides, 41 chains. Longest chain 12 peptides. Score 0.372 Round 5: 218 peptides, 37 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 5 Chains 37, Residues 181, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 9151 restraints for refining 3902 atoms. 8448 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2179 (Rfree = 0.000) for 3902 atoms. Found 9 (25 requested) and removed 20 (12 requested) atoms. Cycle 37: After refmac, R = 0.2084 (Rfree = 0.000) for 3883 atoms. Found 11 (24 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2056 (Rfree = 0.000) for 3881 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2135 (Rfree = 0.000) for 3876 atoms. Found 17 (24 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2071 (Rfree = 0.000) for 3879 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 3936 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3958 seeds are put forward Round 1: 205 peptides, 40 chains. Longest chain 8 peptides. Score 0.312 Round 2: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.390 Round 3: 211 peptides, 34 chains. Longest chain 19 peptides. Score 0.404 Round 4: 224 peptides, 36 chains. Longest chain 11 peptides. Score 0.415 Round 5: 221 peptides, 34 chains. Longest chain 18 peptides. Score 0.431 Taking the results from Round 5 Chains 34, Residues 187, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7206 reflections ( 99.41 % complete ) and 8960 restraints for refining 3902 atoms. 8205 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2080 (Rfree = 0.000) for 3902 atoms. Found 14 (25 requested) and removed 13 (12 requested) atoms. Cycle 42: After refmac, R = 0.2009 (Rfree = 0.000) for 3887 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2020 (Rfree = 0.000) for 3874 atoms. Found 19 (24 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.1850 (Rfree = 0.000) for 3871 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.1667 (Rfree = 0.000) for 3861 atoms. Found 1 (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, 3932 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3959 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 7 peptides. Score 0.260 Round 2: 174 peptides, 30 chains. Longest chain 13 peptides. Score 0.348 Round 3: 191 peptides, 35 chains. Longest chain 9 peptides. Score 0.334 Round 4: 194 peptides, 33 chains. Longest chain 13 peptides. Score 0.368 Round 5: 191 peptides, 33 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 161, 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 9425 restraints for refining 3901 atoms. 8814 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1936 (Rfree = 0.000) for 3901 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1891 (Rfree = 0.000) for 3882 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 3865 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1786 (Rfree = 0.000) for 3850 atoms. TimeTaking 41.93