null Mon 24 Dec 00:39:45 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 1zkg-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-4.0-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/1zkg-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-4.0-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 00:39:49 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/1zkg-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-4.0-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 290 and 0 Target number of residues in the AU: 290 Target solvent content: 0.6778 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-4.0-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: 4 Cell parameters: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3392 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: 29.148 4.000 Wilson plot Bfac: 98.52 4114 reflections ( 99.71 % complete ) and 0 restraints for refining 3769 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3535 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3780 (Rfree = 0.000) for 3769 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.67 Search for helices and strands: 0 residues in 0 chains, 3868 seeds are put forward NCS extension: 0 residues added, 3868 seeds are put forward Round 1: 127 peptides, 24 chains. Longest chain 10 peptides. Score 0.298 Round 2: 147 peptides, 25 chains. Longest chain 13 peptides. Score 0.356 Round 3: 168 peptides, 27 chains. Longest chain 12 peptides. Score 0.399 Round 4: 182 peptides, 26 chains. Longest chain 14 peptides. Score 0.459 Round 5: 180 peptides, 24 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 5 Chains 25, Residues 156, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 7471 restraints for refining 3063 atoms. 6832 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 3063 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 2: After refmac, R = 0.2398 (Rfree = 0.000) for 2972 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 3: After refmac, R = 0.2335 (Rfree = 0.000) for 2939 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 4: After refmac, R = 0.2193 (Rfree = 0.000) for 2912 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.2016 (Rfree = 0.000) for 2892 atoms. Found 11 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3076 seeds are put forward Round 1: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.304 Round 2: 179 peptides, 31 chains. Longest chain 13 peptides. Score 0.377 Round 3: 185 peptides, 30 chains. Longest chain 11 peptides. Score 0.411 Round 4: 181 peptides, 27 chains. Longest chain 14 peptides. Score 0.442 Round 5: 167 peptides, 26 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 4 Chains 27, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6652 restraints for refining 2850 atoms. 6063 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2460 (Rfree = 0.000) for 2850 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 7: After refmac, R = 0.1997 (Rfree = 0.000) for 2804 atoms. Found 6 (13 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.1909 (Rfree = 0.000) for 2785 atoms. Found 10 (13 requested) and removed 17 (6 requested) atoms. Cycle 9: After refmac, R = 0.1883 (Rfree = 0.000) for 2764 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.1444 (Rfree = 0.000) for 2758 atoms. Found 2 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 2931 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2951 seeds are put forward Round 1: 152 peptides, 28 chains. Longest chain 8 peptides. Score 0.327 Round 2: 186 peptides, 31 chains. Longest chain 10 peptides. Score 0.400 Round 3: 179 peptides, 29 chains. Longest chain 11 peptides. Score 0.406 Round 4: 191 peptides, 28 chains. Longest chain 11 peptides. Score 0.459 Round 5: 179 peptides, 28 chains. Longest chain 11 peptides. Score 0.421 Taking the results from Round 4 Chains 28, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6844 restraints for refining 2944 atoms. 6220 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2344 (Rfree = 0.000) for 2944 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 12: After refmac, R = 0.2188 (Rfree = 0.000) for 2901 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 13: After refmac, R = 0.2307 (Rfree = 0.000) for 2873 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 14: After refmac, R = 0.2017 (Rfree = 0.000) for 2845 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 15: After refmac, R = 0.1946 (Rfree = 0.000) for 2839 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.89 3.74 Search for helices and strands: 0 residues in 0 chains, 3024 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3030 seeds are put forward Round 1: 169 peptides, 34 chains. Longest chain 11 peptides. Score 0.296 Round 2: 193 peptides, 30 chains. Longest chain 11 peptides. Score 0.437 Round 3: 183 peptides, 30 chains. Longest chain 10 peptides. Score 0.405 Round 4: 180 peptides, 30 chains. Longest chain 12 peptides. Score 0.395 Round 5: 182 peptides, 29 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 2 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6511 restraints for refining 2890 atoms. 5889 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2332 (Rfree = 0.000) for 2890 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 17: After refmac, R = 0.1989 (Rfree = 0.000) for 2866 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 18: After refmac, R = 0.1954 (Rfree = 0.000) for 2851 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1979 (Rfree = 0.000) for 2847 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 20: After refmac, R = 0.1976 (Rfree = 0.000) for 2834 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 3028 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3041 seeds are put forward Round 1: 167 peptides, 34 chains. Longest chain 9 peptides. Score 0.288 Round 2: 188 peptides, 31 chains. Longest chain 11 peptides. Score 0.407 Round 3: 181 peptides, 26 chains. Longest chain 20 peptides. Score 0.456 Round 4: 175 peptides, 28 chains. Longest chain 18 peptides. Score 0.407 Round 5: 179 peptides, 27 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 3 Chains 26, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6847 restraints for refining 2994 atoms. 6253 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2208 (Rfree = 0.000) for 2994 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.2099 (Rfree = 0.000) for 2971 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 23: After refmac, R = 0.1988 (Rfree = 0.000) for 2944 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 24: After refmac, R = 0.1873 (Rfree = 0.000) for 2923 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 25: After refmac, R = 0.1806 (Rfree = 0.000) for 2907 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 3054 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3078 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 9 peptides. Score 0.311 Round 2: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.372 Round 3: 188 peptides, 28 chains. Longest chain 19 peptides. Score 0.450 Round 4: 178 peptides, 29 chains. Longest chain 10 peptides. Score 0.403 Round 5: 181 peptides, 28 chains. Longest chain 19 peptides. Score 0.427 Taking the results from Round 3 Chains 28, Residues 160, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6646 restraints for refining 2961 atoms. 6014 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2206 (Rfree = 0.000) for 2961 atoms. Found 14 (14 requested) and removed 33 (7 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 2903 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.1958 (Rfree = 0.000) for 2880 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2036 (Rfree = 0.000) for 2866 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.1885 (Rfree = 0.000) for 2860 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.74 Search for helices and strands: 0 residues in 0 chains, 3035 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 3048 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 8 peptides. Score 0.244 Round 2: 169 peptides, 30 chains. Longest chain 13 peptides. Score 0.357 Round 3: 178 peptides, 30 chains. Longest chain 13 peptides. Score 0.388 Round 4: 185 peptides, 30 chains. Longest chain 14 peptides. Score 0.411 Round 5: 174 peptides, 31 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 4 Chains 30, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6981 restraints for refining 3024 atoms. 6391 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2400 (Rfree = 0.000) for 3024 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 32: After refmac, R = 0.2052 (Rfree = 0.000) for 2980 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 33: After refmac, R = 0.2191 (Rfree = 0.000) for 2961 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.1903 (Rfree = 0.000) for 2955 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.2032 (Rfree = 0.000) for 2941 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 3105 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3127 seeds are put forward Round 1: 128 peptides, 30 chains. Longest chain 7 peptides. Score 0.201 Round 2: 155 peptides, 29 chains. Longest chain 11 peptides. Score 0.322 Round 3: 156 peptides, 28 chains. Longest chain 12 peptides. Score 0.342 Round 4: 162 peptides, 29 chains. Longest chain 15 peptides. Score 0.348 Round 5: 166 peptides, 27 chains. Longest chain 17 peptides. Score 0.392 Taking the results from Round 5 Chains 27, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 7182 restraints for refining 3032 atoms. 6653 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2089 (Rfree = 0.000) for 3032 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 37: After refmac, R = 0.2130 (Rfree = 0.000) for 3004 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 38: After refmac, R = 0.2091 (Rfree = 0.000) for 2983 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 39: After refmac, R = 0.1966 (Rfree = 0.000) for 2969 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1518 (Rfree = 0.000) for 2954 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.71 Search for helices and strands: 0 residues in 0 chains, 3079 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3105 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 7 peptides. Score 0.264 Round 2: 142 peptides, 26 chains. Longest chain 9 peptides. Score 0.322 Round 3: 155 peptides, 26 chains. Longest chain 10 peptides. Score 0.369 Round 4: 158 peptides, 29 chains. Longest chain 10 peptides. Score 0.333 Round 5: 164 peptides, 27 chains. Longest chain 9 peptides. Score 0.385 Taking the results from Round 5 Chains 27, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4114 reflections ( 99.71 % complete ) and 6847 restraints for refining 2970 atoms. 6326 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2314 (Rfree = 0.000) for 2970 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 42: After refmac, R = 0.2064 (Rfree = 0.000) for 2943 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.2019 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 44: After refmac, R = 0.2000 (Rfree = 0.000) for 2913 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 45: After refmac, R = 0.1933 (Rfree = 0.000) for 2893 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.87 3.72 Search for helices and strands: 0 residues in 0 chains, 3039 seeds are put forward NCS extension: 0 residues added, 3039 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 8 peptides. Score 0.232 Round 2: 144 peptides, 29 chains. Longest chain 8 peptides. Score 0.281 Round 3: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.378 Round 4: 151 peptides, 26 chains. Longest chain 14 peptides. Score 0.355 Round 5: 151 peptides, 25 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 128, 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 1zkg-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4114 reflections ( 99.71 % complete ) and 6670 restraints for refining 2876 atoms. 6183 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2316 (Rfree = 0.000) for 2876 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 2853 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2311 (Rfree = 0.000) for 2842 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2125 (Rfree = 0.000) for 2824 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:17:07 GMT 2018 Job finished. TimeTaking 37.37 Used memory is bytes: 21399896