null Sun 23 Dec 22:22:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zkg-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:03 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/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.8-parrot-hancs/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-hancs.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-hancs.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 3772 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3439 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3258 (Rfree = 0.000) for 3772 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 3905 seeds are put forward NCS extension: 0 residues added, 3905 seeds are put forward Round 1: 179 peptides, 37 chains. Longest chain 10 peptides. Score 0.286 Round 2: 211 peptides, 34 chains. Longest chain 12 peptides. Score 0.439 Round 3: 217 peptides, 32 chains. Longest chain 16 peptides. Score 0.484 Round 4: 216 peptides, 33 chains. Longest chain 13 peptides. Score 0.468 Round 5: 232 peptides, 28 chains. Longest chain 33 peptides. Score 0.576 Taking the results from Round 5 Chains 31, Residues 204, Estimated correctness of the model 0.0 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6649 restraints for refining 3068 atoms. 5693 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2560 (Rfree = 0.000) for 3068 atoms. Found 12 (16 requested) and removed 35 (8 requested) atoms. Cycle 2: After refmac, R = 0.2250 (Rfree = 0.000) for 2991 atoms. Found 14 (16 requested) and removed 18 (8 requested) atoms. Cycle 3: After refmac, R = 0.2283 (Rfree = 0.000) for 2966 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 2948 atoms. Found 12 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2051 (Rfree = 0.000) for 2931 atoms. Found 13 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.58 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 3124 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 12 peptides. Score 0.371 Round 2: 196 peptides, 25 chains. Longest chain 19 peptides. Score 0.515 Round 3: 193 peptides, 27 chains. Longest chain 13 peptides. Score 0.479 Round 4: 206 peptides, 28 chains. Longest chain 17 peptides. Score 0.505 Round 5: 207 peptides, 30 chains. Longest chain 13 peptides. Score 0.481 Taking the results from Round 2 Chains 25, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6991 restraints for refining 2980 atoms. 6332 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2044 (Rfree = 0.000) for 2980 atoms. Found 10 (16 requested) and removed 22 (8 requested) atoms. Cycle 7: After refmac, R = 0.2027 (Rfree = 0.000) for 2938 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.1969 (Rfree = 0.000) for 2924 atoms. Found 11 (16 requested) and removed 18 (8 requested) atoms. Cycle 9: After refmac, R = 0.1964 (Rfree = 0.000) for 2910 atoms. Found 14 (16 requested) and removed 27 (8 requested) atoms. Cycle 10: After refmac, R = 0.1814 (Rfree = 0.000) for 2889 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 3079 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3098 seeds are put forward Round 1: 185 peptides, 34 chains. Longest chain 13 peptides. Score 0.353 Round 2: 202 peptides, 33 chains. Longest chain 14 peptides. Score 0.424 Round 3: 211 peptides, 32 chains. Longest chain 17 peptides. Score 0.466 Round 4: 230 peptides, 32 chains. Longest chain 25 peptides. Score 0.522 Round 5: 211 peptides, 30 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 4 Chains 32, Residues 198, Estimated correctness of the model 0.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6416 restraints for refining 3045 atoms. 5506 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2160 (Rfree = 0.000) for 3045 atoms. Found 11 (16 requested) and removed 34 (8 requested) atoms. Cycle 12: After refmac, R = 0.1972 (Rfree = 0.000) for 3010 atoms. Found 8 (16 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.1930 (Rfree = 0.000) for 2991 atoms. Found 7 (16 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.1900 (Rfree = 0.000) for 2969 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.1803 (Rfree = 0.000) for 2956 atoms. Found 9 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 3092 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 3126 seeds are put forward Round 1: 179 peptides, 31 chains. Longest chain 14 peptides. Score 0.377 Round 2: 193 peptides, 30 chains. Longest chain 11 peptides. Score 0.437 Round 3: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.427 Round 4: 196 peptides, 29 chains. Longest chain 10 peptides. Score 0.461 Round 5: 193 peptides, 29 chains. Longest chain 11 peptides. Score 0.451 Taking the results from Round 4 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7099 restraints for refining 3068 atoms. 6460 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2019 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 17: After refmac, R = 0.2007 (Rfree = 0.000) for 3038 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 18: After refmac, R = 0.1838 (Rfree = 0.000) for 3022 atoms. Found 8 (16 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.1859 (Rfree = 0.000) for 3008 atoms. Found 15 (16 requested) and removed 19 (8 requested) atoms. Cycle 20: After refmac, R = 0.1780 (Rfree = 0.000) for 3000 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 3178 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3189 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 7 peptides. Score 0.280 Round 2: 187 peptides, 30 chains. Longest chain 13 peptides. Score 0.418 Round 3: 197 peptides, 31 chains. Longest chain 14 peptides. Score 0.436 Round 4: 199 peptides, 30 chains. Longest chain 15 peptides. Score 0.456 Round 5: 203 peptides, 29 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 5 Chains 29, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7055 restraints for refining 3068 atoms. 6388 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1984 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.1837 (Rfree = 0.000) for 3058 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.1788 (Rfree = 0.000) for 3056 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 24: After refmac, R = 0.1702 (Rfree = 0.000) for 3052 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.1676 (Rfree = 0.000) for 3040 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3228 seeds are put forward Round 1: 154 peptides, 31 chains. Longest chain 9 peptides. Score 0.287 Round 2: 169 peptides, 27 chains. Longest chain 12 peptides. Score 0.402 Round 3: 182 peptides, 29 chains. Longest chain 12 peptides. Score 0.416 Round 4: 188 peptides, 27 chains. Longest chain 17 peptides. Score 0.464 Round 5: 183 peptides, 29 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 4 Chains 27, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6986 restraints for refining 3067 atoms. 6369 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1912 (Rfree = 0.000) for 3067 atoms. Found 14 (16 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.1801 (Rfree = 0.000) for 3058 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.1728 (Rfree = 0.000) for 3045 atoms. Found 10 (16 requested) and removed 18 (8 requested) atoms. Cycle 29: After refmac, R = 0.1682 (Rfree = 0.000) for 3036 atoms. Found 4 (16 requested) and removed 15 (8 requested) atoms. Cycle 30: After refmac, R = 0.1711 (Rfree = 0.000) for 3020 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.54 Search for helices and strands: 0 residues in 0 chains, 3165 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3192 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 12 peptides. Score 0.288 Round 2: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.391 Round 3: 181 peptides, 29 chains. Longest chain 11 peptides. Score 0.413 Round 4: 179 peptides, 29 chains. Longest chain 11 peptides. Score 0.406 Round 5: 172 peptides, 28 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 3 Chains 29, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7194 restraints for refining 3067 atoms. 6615 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1870 (Rfree = 0.000) for 3067 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.1842 (Rfree = 0.000) for 3059 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 33: After refmac, R = 0.1858 (Rfree = 0.000) for 3058 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.1784 (Rfree = 0.000) for 3057 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.1359 (Rfree = 0.000) for 3055 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3213 seeds are put forward Round 1: 149 peptides, 32 chains. Longest chain 9 peptides. Score 0.252 Round 2: 186 peptides, 33 chains. Longest chain 12 peptides. Score 0.371 Round 3: 182 peptides, 31 chains. Longest chain 10 peptides. Score 0.387 Round 4: 184 peptides, 29 chains. Longest chain 13 peptides. Score 0.423 Round 5: 184 peptides, 31 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 4 Chains 30, Residues 155, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 6983 restraints for refining 3068 atoms. 6332 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1926 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.1751 (Rfree = 0.000) for 3055 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 38: After refmac, R = 0.1750 (Rfree = 0.000) for 3043 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 39: After refmac, R = 0.1655 (Rfree = 0.000) for 3040 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.1333 (Rfree = 0.000) for 3031 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.56 Search for helices and strands: 0 residues in 0 chains, 3196 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3204 seeds are put forward Round 1: 138 peptides, 27 chains. Longest chain 11 peptides. Score 0.291 Round 2: 154 peptides, 30 chains. Longest chain 11 peptides. Score 0.303 Round 3: 158 peptides, 28 chains. Longest chain 11 peptides. Score 0.349 Round 4: 149 peptides, 26 chains. Longest chain 11 peptides. Score 0.348 Round 5: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 5 Chains 24, Residues 126, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4788 reflections ( 99.75 % complete ) and 7338 restraints for refining 3068 atoms. 6837 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2142 (Rfree = 0.000) for 3068 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 42: After refmac, R = 0.1886 (Rfree = 0.000) for 3064 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.1816 (Rfree = 0.000) for 3059 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.1750 (Rfree = 0.000) for 3058 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.1721 (Rfree = 0.000) for 3059 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.60 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3253 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 8 peptides. Score 0.232 Round 2: 155 peptides, 32 chains. Longest chain 9 peptides. Score 0.275 Round 3: 163 peptides, 31 chains. Longest chain 9 peptides. Score 0.320 Round 4: 151 peptides, 28 chains. Longest chain 9 peptides. Score 0.323 Round 5: 154 peptides, 28 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 126, 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 7290 restraints for refining 3068 atoms. 6814 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2279 (Rfree = 0.000) for 3068 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1945 (Rfree = 0.000) for 3041 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1863 (Rfree = 0.000) for 3024 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1822 (Rfree = 0.000) for 3011 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:14 GMT 2018 Job finished. TimeTaking 51.35 Used memory is bytes: 18374736