Mon 24 Dec 08:08:10 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 1z82-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1z82-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1z82-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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/1z82-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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 08:08:15 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/1z82-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.6624 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-4.0-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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 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: 29.850 4.002 Wilson plot Bfac: 86.40 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 5179 reflections ( 99.50 % complete ) and 0 restraints for refining 5918 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3338 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2974 (Rfree = 0.000) for 5918 atoms. Found 28 (28 requested) and removed 124 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 4.22 Search for helices and strands: 0 residues in 0 chains, 5967 seeds are put forward NCS extension: 0 residues added, 5967 seeds are put forward Round 1: 118 peptides, 27 chains. Longest chain 6 peptides. Score 0.204 Round 2: 148 peptides, 33 chains. Longest chain 8 peptides. Score 0.222 Round 3: 187 peptides, 40 chains. Longest chain 7 peptides. Score 0.254 Round 4: 222 peptides, 46 chains. Longest chain 11 peptides. Score 0.284 Round 5: 237 peptides, 45 chains. Longest chain 11 peptides. Score 0.339 Taking the results from Round 5 Chains 46, Residues 192, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5179 reflections ( 99.50 % complete ) and 11681 restraints for refining 4840 atoms. 10899 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2669 (Rfree = 0.000) for 4840 atoms. Found 21 (22 requested) and removed 58 (11 requested) atoms. Cycle 2: After refmac, R = 0.2525 (Rfree = 0.000) for 4723 atoms. Found 22 (22 requested) and removed 47 (11 requested) atoms. Cycle 3: After refmac, R = 0.2458 (Rfree = 0.000) for 4650 atoms. Found 11 (22 requested) and removed 36 (11 requested) atoms. Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 4590 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. Cycle 5: After refmac, R = 0.2455 (Rfree = 0.000) for 4546 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 4.27 Search for helices and strands: 0 residues in 0 chains, 4688 seeds are put forward NCS extension: 0 residues added, 4688 seeds are put forward Round 1: 152 peptides, 34 chains. Longest chain 8 peptides. Score 0.222 Round 2: 211 peptides, 42 chains. Longest chain 11 peptides. Score 0.301 Round 3: 219 peptides, 42 chains. Longest chain 8 peptides. Score 0.324 Round 4: 238 peptides, 41 chains. Longest chain 13 peptides. Score 0.389 Round 5: 217 peptides, 40 chains. Longest chain 11 peptides. Score 0.343 Taking the results from Round 4 Chains 41, Residues 197, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9440 restraints for refining 4163 atoms. 8649 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2316 (Rfree = 0.000) for 4163 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 4106 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 4059 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 9: After refmac, R = 0.2153 (Rfree = 0.000) for 4020 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 10: After refmac, R = 0.2089 (Rfree = 0.000) for 3995 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 4189 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4206 seeds are put forward Round 1: 179 peptides, 40 chains. Longest chain 9 peptides. Score 0.229 Round 2: 236 peptides, 45 chains. Longest chain 12 peptides. Score 0.336 Round 3: 232 peptides, 40 chains. Longest chain 14 peptides. Score 0.384 Round 4: 231 peptides, 38 chains. Longest chain 17 peptides. Score 0.405 Round 5: 243 peptides, 45 chains. Longest chain 17 peptides. Score 0.356 Taking the results from Round 4 Chains 38, Residues 193, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8689 restraints for refining 3942 atoms. 7930 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2143 (Rfree = 0.000) for 3942 atoms. Found 15 (18 requested) and removed 20 (9 requested) atoms. Cycle 12: After refmac, R = 0.2048 (Rfree = 0.000) for 3911 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.1989 (Rfree = 0.000) for 3896 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1925 (Rfree = 0.000) for 3878 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 15: After refmac, R = 0.2065 (Rfree = 0.000) for 3866 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 4.35 Search for helices and strands: 0 residues in 0 chains, 4020 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4036 seeds are put forward Round 1: 215 peptides, 44 chains. Longest chain 9 peptides. Score 0.288 Round 2: 239 peptides, 44 chains. Longest chain 10 peptides. Score 0.357 Round 3: 256 peptides, 44 chains. Longest chain 10 peptides. Score 0.402 Round 4: 255 peptides, 44 chains. Longest chain 11 peptides. Score 0.400 Round 5: 246 peptides, 41 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 5 Chains 41, Residues 205, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8852 restraints for refining 3958 atoms. 8046 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2022 (Rfree = 0.000) for 3958 atoms. Found 17 (18 requested) and removed 190 (9 requested) atoms. Cycle 17: After refmac, R = 0.2034 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. Cycle 18: After refmac, R = 0.2109 (Rfree = 0.000) for 3715 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 19: After refmac, R = 0.2046 (Rfree = 0.000) for 3696 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 20: After refmac, R = 0.1587 (Rfree = 0.000) for 3682 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 4.29 Search for helices and strands: 0 residues in 0 chains, 3855 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3868 seeds are put forward Round 1: 191 peptides, 43 chains. Longest chain 7 peptides. Score 0.228 Round 2: 248 peptides, 49 chains. Longest chain 10 peptides. Score 0.323 Round 3: 245 peptides, 45 chains. Longest chain 10 peptides. Score 0.361 Round 4: 237 peptides, 44 chains. Longest chain 11 peptides. Score 0.351 Round 5: 252 peptides, 44 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 5 Chains 44, Residues 208, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8490 restraints for refining 3917 atoms. 7636 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1964 (Rfree = 0.000) for 3917 atoms. Found 15 (18 requested) and removed 47 (9 requested) atoms. Cycle 22: After refmac, R = 0.1954 (Rfree = 0.000) for 3858 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 23: After refmac, R = 0.1907 (Rfree = 0.000) for 3839 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.1452 (Rfree = 0.000) for 3824 atoms. Found 4 (18 requested) and removed 16 (9 requested) atoms. Cycle 25: After refmac, R = 0.1343 (Rfree = 0.000) for 3802 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 4.33 Search for helices and strands: 0 residues in 0 chains, 3963 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3980 seeds are put forward Round 1: 196 peptides, 43 chains. Longest chain 9 peptides. Score 0.243 Round 2: 234 peptides, 44 chains. Longest chain 10 peptides. Score 0.343 Round 3: 230 peptides, 40 chains. Longest chain 18 peptides. Score 0.379 Round 4: 233 peptides, 38 chains. Longest chain 22 peptides. Score 0.410 Round 5: 220 peptides, 39 chains. Longest chain 16 peptides. Score 0.363 Taking the results from Round 4 Chains 38, Residues 195, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8759 restraints for refining 3934 atoms. 7999 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1829 (Rfree = 0.000) for 3934 atoms. Found 13 (18 requested) and removed 30 (9 requested) atoms. Cycle 27: After refmac, R = 0.1981 (Rfree = 0.000) for 3893 atoms. Found 14 (18 requested) and removed 26 (9 requested) atoms. Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 3869 atoms. Found 14 (18 requested) and removed 21 (9 requested) atoms. Cycle 29: After refmac, R = 0.1985 (Rfree = 0.000) for 3852 atoms. Found 17 (18 requested) and removed 21 (9 requested) atoms. Cycle 30: After refmac, R = 0.1799 (Rfree = 0.000) for 3836 atoms. Found 10 (18 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 4.25 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3982 seeds are put forward Round 1: 205 peptides, 44 chains. Longest chain 13 peptides. Score 0.258 Round 2: 212 peptides, 40 chains. Longest chain 20 peptides. Score 0.329 Round 3: 217 peptides, 42 chains. Longest chain 15 peptides. Score 0.319 Round 4: 203 peptides, 39 chains. Longest chain 10 peptides. Score 0.315 Round 5: 207 peptides, 37 chains. Longest chain 15 peptides. Score 0.351 Taking the results from Round 5 Chains 37, Residues 170, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8801 restraints for refining 3928 atoms. 8124 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1883 (Rfree = 0.000) for 3928 atoms. Found 15 (18 requested) and removed 24 (9 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 3899 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.1923 (Rfree = 0.000) for 3889 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 34: After refmac, R = 0.2021 (Rfree = 0.000) for 3870 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 35: After refmac, R = 0.2058 (Rfree = 0.000) for 3859 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 4.27 Search for helices and strands: 0 residues in 0 chains, 3984 seeds are put forward NCS extension: 0 residues added, 3984 seeds are put forward Round 1: 150 peptides, 34 chains. Longest chain 6 peptides. Score 0.215 Round 2: 210 peptides, 38 chains. Longest chain 15 peptides. Score 0.347 Round 3: 206 peptides, 34 chains. Longest chain 19 peptides. Score 0.385 Round 4: 226 peptides, 38 chains. Longest chain 19 peptides. Score 0.392 Round 5: 212 peptides, 36 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 4 Chains 38, Residues 188, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8359 restraints for refining 3871 atoms. 7601 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2080 (Rfree = 0.000) for 3871 atoms. Found 18 (18 requested) and removed 68 (9 requested) atoms. Cycle 37: After refmac, R = 0.2020 (Rfree = 0.000) for 3799 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 38: After refmac, R = 0.1909 (Rfree = 0.000) for 3771 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 39: After refmac, R = 0.1848 (Rfree = 0.000) for 3763 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 4.33 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3906 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 8 peptides. Score 0.233 Round 2: 175 peptides, 34 chains. Longest chain 14 peptides. Score 0.295 Round 3: 171 peptides, 33 chains. Longest chain 12 peptides. Score 0.296 Round 4: 179 peptides, 33 chains. Longest chain 10 peptides. Score 0.320 Round 5: 190 peptides, 35 chains. Longest chain 12 peptides. Score 0.327 Taking the results from Round 5 Chains 35, Residues 155, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 8663 restraints for refining 3861 atoms. 8048 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2147 (Rfree = 0.000) for 3861 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 42: After refmac, R = 0.1940 (Rfree = 0.000) for 3844 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 43: After refmac, R = 0.1940 (Rfree = 0.000) for 3827 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 44: After refmac, R = 0.1938 (Rfree = 0.000) for 3814 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.1985 (Rfree = 0.000) for 3810 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 4.31 Search for helices and strands: 0 residues in 0 chains, 3955 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3971 seeds are put forward Round 1: 119 peptides, 28 chains. Longest chain 6 peptides. Score 0.193 Round 2: 126 peptides, 25 chains. Longest chain 10 peptides. Score 0.262 Round 3: 133 peptides, 27 chains. Longest chain 8 peptides. Score 0.257 Round 4: 140 peptides, 27 chains. Longest chain 10 peptides. Score 0.280 Round 5: 137 peptides, 27 chains. Longest chain 10 peptides. Score 0.270 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 113, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1z82-4_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (113 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5179 reflections ( 99.50 % complete ) and 8550 restraints for refining 3734 atoms. 8096 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2080 (Rfree = 0.000) for 3734 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2162 (Rfree = 0.000) for 3711 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1914 (Rfree = 0.000) for 3696 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2000 (Rfree = 0.000) for 3680 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 46.15