null Mon 24 Dec 00:21:45 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-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 00:21:50 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-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 299 and 0 Target number of residues in the AU: 299 Target solvent content: 0.6678 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-3.8-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-3.8-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 3.801 Wilson plot Bfac: 90.41 4788 reflections ( 99.75 % complete ) and 0 restraints for refining 3761 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3452 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3406 (Rfree = 0.000) for 3761 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 0 residues added, 3873 seeds are put forward Round 1: 146 peptides, 29 chains. Longest chain 8 peptides. Score 0.289 Round 2: 188 peptides, 28 chains. Longest chain 12 peptides. Score 0.450 Round 3: 212 peptides, 31 chains. Longest chain 16 peptides. Score 0.483 Round 4: 206 peptides, 29 chains. Longest chain 18 peptides. Score 0.491 Round 5: 203 peptides, 30 chains. Longest chain 19 peptides. Score 0.469 Taking the results from Round 4 Chains 29, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7317 restraints for refining 3065 atoms. 6638 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2739 (Rfree = 0.000) for 3065 atoms. Found 14 (16 requested) and removed 28 (8 requested) atoms. Cycle 2: After refmac, R = 0.2519 (Rfree = 0.000) for 3014 atoms. Found 15 (16 requested) and removed 19 (8 requested) atoms. Cycle 3: After refmac, R = 0.2325 (Rfree = 0.000) for 2980 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 4: After refmac, R = 0.1864 (Rfree = 0.000) for 2953 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.1757 (Rfree = 0.000) for 2940 atoms. Found 2 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 3129 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3144 seeds are put forward Round 1: 187 peptides, 35 chains. Longest chain 10 peptides. Score 0.345 Round 2: 203 peptides, 31 chains. Longest chain 12 peptides. Score 0.455 Round 3: 200 peptides, 29 chains. Longest chain 13 peptides. Score 0.473 Round 4: 204 peptides, 29 chains. Longest chain 14 peptides. Score 0.485 Round 5: 206 peptides, 27 chains. Longest chain 13 peptides. Score 0.518 Taking the results from Round 5 Chains 27, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7072 restraints for refining 3018 atoms. 6383 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2487 (Rfree = 0.000) for 3018 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 7: After refmac, R = 0.2208 (Rfree = 0.000) for 2985 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2011 (Rfree = 0.000) for 2971 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2000 (Rfree = 0.000) for 2954 atoms. Found 13 (16 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.1940 (Rfree = 0.000) for 2939 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 3118 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3134 seeds are put forward Round 1: 177 peptides, 34 chains. Longest chain 10 peptides. Score 0.325 Round 2: 193 peptides, 30 chains. Longest chain 11 peptides. Score 0.437 Round 3: 212 peptides, 31 chains. Longest chain 13 peptides. Score 0.483 Round 4: 212 peptides, 31 chains. Longest chain 13 peptides. Score 0.483 Round 5: 214 peptides, 31 chains. Longest chain 13 peptides. Score 0.489 Taking the results from Round 5 Chains 31, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7107 restraints for refining 3051 atoms. 6406 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2219 (Rfree = 0.000) for 3051 atoms. Found 10 (16 requested) and removed 22 (8 requested) atoms. Cycle 12: After refmac, R = 0.2054 (Rfree = 0.000) for 3019 atoms. Found 10 (16 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.1958 (Rfree = 0.000) for 2997 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1897 (Rfree = 0.000) for 2987 atoms. Found 11 (16 requested) and removed 16 (8 requested) atoms. Cycle 15: After refmac, R = 0.1535 (Rfree = 0.000) for 2974 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 3155 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3166 seeds are put forward Round 1: 147 peptides, 28 chains. Longest chain 9 peptides. Score 0.309 Round 2: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.391 Round 3: 171 peptides, 25 chains. Longest chain 12 peptides. Score 0.438 Round 4: 180 peptides, 26 chains. Longest chain 14 peptides. Score 0.453 Round 5: 181 peptides, 26 chains. Longest chain 12 peptides. Score 0.456 Taking the results from Round 5 Chains 27, Residues 155, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6906 restraints for refining 3066 atoms. 6277 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2031 (Rfree = 0.000) for 3066 atoms. Found 11 (16 requested) and removed 24 (8 requested) atoms. Cycle 17: After refmac, R = 0.1993 (Rfree = 0.000) for 3033 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 18: After refmac, R = 0.1880 (Rfree = 0.000) for 3018 atoms. Found 15 (16 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.1790 (Rfree = 0.000) for 3007 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.1729 (Rfree = 0.000) for 2995 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 3162 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 3173 seeds are put forward Round 1: 168 peptides, 31 chains. Longest chain 9 peptides. Score 0.338 Round 2: 190 peptides, 29 chains. Longest chain 12 peptides. Score 0.442 Round 3: 196 peptides, 27 chains. Longest chain 13 peptides. Score 0.488 Round 4: 185 peptides, 28 chains. Longest chain 13 peptides. Score 0.440 Round 5: 194 peptides, 29 chains. Longest chain 12 peptides. Score 0.455 Taking the results from Round 3 Chains 28, Residues 169, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6850 restraints for refining 3066 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1901 (Rfree = 0.000) for 3066 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 22: After refmac, R = 0.1779 (Rfree = 0.000) for 3034 atoms. Found 14 (16 requested) and removed 16 (8 requested) atoms. Cycle 23: After refmac, R = 0.1790 (Rfree = 0.000) for 3023 atoms. Found 8 (16 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.1725 (Rfree = 0.000) for 3008 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. Cycle 25: After refmac, R = 0.1705 (Rfree = 0.000) for 2999 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 3176 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3188 seeds are put forward Round 1: 163 peptides, 31 chains. Longest chain 9 peptides. Score 0.320 Round 2: 197 peptides, 33 chains. Longest chain 14 peptides. Score 0.408 Round 3: 212 peptides, 33 chains. Longest chain 13 peptides. Score 0.456 Round 4: 210 peptides, 33 chains. Longest chain 12 peptides. Score 0.450 Round 5: 191 peptides, 33 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 3 Chains 33, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6822 restraints for refining 3061 atoms. 6139 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1820 (Rfree = 0.000) for 3061 atoms. Found 6 (16 requested) and removed 30 (8 requested) atoms. Cycle 27: After refmac, R = 0.1766 (Rfree = 0.000) for 3021 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.1743 (Rfree = 0.000) for 3006 atoms. Found 3 (16 requested) and removed 15 (8 requested) atoms. Cycle 29: After refmac, R = 0.1704 (Rfree = 0.000) for 2989 atoms. Found 7 (16 requested) and removed 14 (8 requested) atoms. Cycle 30: After refmac, R = 0.1651 (Rfree = 0.000) for 2981 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 3170 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3188 seeds are put forward Round 1: 166 peptides, 32 chains. Longest chain 9 peptides. Score 0.316 Round 2: 189 peptides, 33 chains. Longest chain 11 peptides. Score 0.381 Round 3: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.428 Round 4: 180 peptides, 29 chains. Longest chain 17 peptides. Score 0.409 Round 5: 189 peptides, 29 chains. Longest chain 14 peptides. Score 0.439 Taking the results from Round 5 Chains 29, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6891 restraints for refining 3067 atoms. 6280 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2189 (Rfree = 0.000) for 3067 atoms. Found 12 (16 requested) and removed 17 (8 requested) atoms. Cycle 32: After refmac, R = 0.1900 (Rfree = 0.000) for 3051 atoms. Found 10 (16 requested) and removed 17 (8 requested) atoms. Cycle 33: After refmac, R = 0.1852 (Rfree = 0.000) for 3038 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1784 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.1705 (Rfree = 0.000) for 3023 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.52 Search for helices and strands: 0 residues in 0 chains, 3193 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3206 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 14 peptides. Score 0.291 Round 2: 166 peptides, 28 chains. Longest chain 11 peptides. Score 0.377 Round 3: 159 peptides, 25 chains. Longest chain 14 peptides. Score 0.398 Round 4: 163 peptides, 28 chains. Longest chain 14 peptides. Score 0.366 Round 5: 152 peptides, 24 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 3 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7296 restraints for refining 3066 atoms. 6785 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2183 (Rfree = 0.000) for 3066 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.1881 (Rfree = 0.000) for 3058 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 38: After refmac, R = 0.1814 (Rfree = 0.000) for 3046 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.1815 (Rfree = 0.000) for 3035 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.1791 (Rfree = 0.000) for 3031 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 3167 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3186 seeds are put forward Round 1: 149 peptides, 30 chains. Longest chain 9 peptides. Score 0.284 Round 2: 164 peptides, 28 chains. Longest chain 13 peptides. Score 0.370 Round 3: 170 peptides, 25 chains. Longest chain 16 peptides. Score 0.435 Round 4: 168 peptides, 27 chains. Longest chain 13 peptides. Score 0.399 Round 5: 166 peptides, 27 chains. Longest chain 12 peptides. Score 0.392 Taking the results from Round 3 Chains 25, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6923 restraints for refining 3062 atoms. 6368 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2027 (Rfree = 0.000) for 3062 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.1816 (Rfree = 0.000) for 3050 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.1841 (Rfree = 0.000) for 3042 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 44: After refmac, R = 0.1822 (Rfree = 0.000) for 3029 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.1846 (Rfree = 0.000) for 3031 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.59 Search for helices and strands: 0 residues in 0 chains, 3180 seeds are put forward NCS extension: 0 residues added, 3180 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 12 peptides. Score 0.292 Round 2: 152 peptides, 29 chains. Longest chain 9 peptides. Score 0.311 Round 3: 169 peptides, 28 chains. Longest chain 12 peptides. Score 0.387 Round 4: 166 peptides, 28 chains. Longest chain 12 peptides. Score 0.377 Round 5: 160 peptides, 26 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 134, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4788 reflections ( 99.75 % complete ) and 7053 restraints for refining 3067 atoms. 6543 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2103 (Rfree = 0.000) for 3067 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1948 (Rfree = 0.000) for 3054 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1882 (Rfree = 0.000) for 3042 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1844 (Rfree = 0.000) for 3029 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:01:10 GMT 2018 Job finished. TimeTaking 39.43 Used memory is bytes: 10909752