null Sun 23 Dec 22:23:13 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 1vkh-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-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/1vkh-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-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 22:23:22 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/1vkh-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6036 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.6-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: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4368 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: 19.289 3.600 Wilson plot Bfac: 53.96 5789 reflections ( 99.30 % complete ) and 0 restraints for refining 4837 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3216 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3190 (Rfree = 0.000) for 4837 atoms. Found 31 (31 requested) and removed 54 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 0 residues added, 4919 seeds are put forward Round 1: 202 peptides, 42 chains. Longest chain 12 peptides. Score 0.291 Round 2: 253 peptides, 42 chains. Longest chain 12 peptides. Score 0.454 Round 3: 270 peptides, 41 chains. Longest chain 20 peptides. Score 0.514 Round 4: 272 peptides, 37 chains. Longest chain 23 peptides. Score 0.566 Round 5: 275 peptides, 43 chains. Longest chain 13 peptides. Score 0.504 Taking the results from Round 4 Chains 37, Residues 235, Estimated correctness of the model 0.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9031 restraints for refining 3959 atoms. 8128 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2436 (Rfree = 0.000) for 3959 atoms. Found 17 (25 requested) and removed 31 (12 requested) atoms. Cycle 2: After refmac, R = 0.2426 (Rfree = 0.000) for 3901 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2467 (Rfree = 0.000) for 3894 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 4: After refmac, R = 0.1857 (Rfree = 0.000) for 3880 atoms. Found 15 (24 requested) and removed 19 (12 requested) atoms. Cycle 5: After refmac, R = 0.1738 (Rfree = 0.000) for 3872 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 4020 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4046 seeds are put forward Round 1: 218 peptides, 44 chains. Longest chain 12 peptides. Score 0.317 Round 2: 266 peptides, 47 chains. Longest chain 14 peptides. Score 0.429 Round 3: 289 peptides, 48 chains. Longest chain 16 peptides. Score 0.484 Round 4: 265 peptides, 41 chains. Longest chain 17 peptides. Score 0.501 Round 5: 271 peptides, 42 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 5 Chains 42, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9315 restraints for refining 3952 atoms. 8441 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2205 (Rfree = 0.000) for 3952 atoms. Found 22 (25 requested) and removed 34 (12 requested) atoms. Cycle 7: After refmac, R = 0.2151 (Rfree = 0.000) for 3922 atoms. Found 24 (25 requested) and removed 29 (12 requested) atoms. Cycle 8: After refmac, R = 0.2090 (Rfree = 0.000) for 3906 atoms. Found 23 (25 requested) and removed 21 (12 requested) atoms. Cycle 9: After refmac, R = 0.2009 (Rfree = 0.000) for 3900 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 10: After refmac, R = 0.1658 (Rfree = 0.000) for 3899 atoms. Found 4 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 4036 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 4056 seeds are put forward Round 1: 220 peptides, 41 chains. Longest chain 13 peptides. Score 0.365 Round 2: 247 peptides, 41 chains. Longest chain 15 peptides. Score 0.449 Round 3: 248 peptides, 39 chains. Longest chain 15 peptides. Score 0.477 Round 4: 242 peptides, 36 chains. Longest chain 17 peptides. Score 0.498 Round 5: 268 peptides, 40 chains. Longest chain 16 peptides. Score 0.521 Taking the results from Round 5 Chains 40, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9311 restraints for refining 3960 atoms. 8439 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2364 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 12: After refmac, R = 0.2402 (Rfree = 0.000) for 3939 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 13: After refmac, R = 0.2481 (Rfree = 0.000) for 3910 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 14: After refmac, R = 0.1884 (Rfree = 0.000) for 3894 atoms. Found 18 (25 requested) and removed 19 (12 requested) atoms. Cycle 15: After refmac, R = 0.1755 (Rfree = 0.000) for 3890 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 4038 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4050 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 16 peptides. Score 0.357 Round 2: 256 peptides, 45 chains. Longest chain 13 peptides. Score 0.425 Round 3: 271 peptides, 44 chains. Longest chain 16 peptides. Score 0.481 Round 4: 274 peptides, 41 chains. Longest chain 18 peptides. Score 0.525 Round 5: 264 peptides, 43 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 4 Chains 41, Residues 233, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9322 restraints for refining 3960 atoms. 8431 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2268 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 17: After refmac, R = 0.2337 (Rfree = 0.000) for 3940 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 18: After refmac, R = 0.2175 (Rfree = 0.000) for 3927 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 19: After refmac, R = 0.1657 (Rfree = 0.000) for 3921 atoms. Found 6 (25 requested) and removed 16 (12 requested) atoms. Cycle 20: After refmac, R = 0.1579 (Rfree = 0.000) for 3906 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 4039 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 4058 seeds are put forward Round 1: 210 peptides, 42 chains. Longest chain 10 peptides. Score 0.318 Round 2: 230 peptides, 40 chains. Longest chain 12 peptides. Score 0.411 Round 3: 246 peptides, 40 chains. Longest chain 13 peptides. Score 0.459 Round 4: 241 peptides, 41 chains. Longest chain 14 peptides. Score 0.431 Round 5: 256 peptides, 43 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 3 Chains 40, Residues 206, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9251 restraints for refining 3960 atoms. 8410 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2196 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 22: After refmac, R = 0.2203 (Rfree = 0.000) for 3942 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 23: After refmac, R = 0.2129 (Rfree = 0.000) for 3930 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 24: After refmac, R = 0.2286 (Rfree = 0.000) for 3922 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 25: After refmac, R = 0.1718 (Rfree = 0.000) for 3914 atoms. Found 10 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 4048 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4060 seeds are put forward Round 1: 186 peptides, 39 chains. Longest chain 9 peptides. Score 0.278 Round 2: 206 peptides, 36 chains. Longest chain 11 peptides. Score 0.389 Round 3: 214 peptides, 40 chains. Longest chain 11 peptides. Score 0.360 Round 4: 223 peptides, 38 chains. Longest chain 13 peptides. Score 0.416 Round 5: 214 peptides, 37 chains. Longest chain 10 peptides. Score 0.401 Taking the results from Round 4 Chains 38, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9434 restraints for refining 3960 atoms. 8732 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2183 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 27: After refmac, R = 0.2156 (Rfree = 0.000) for 3940 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 28: After refmac, R = 0.1776 (Rfree = 0.000) for 3930 atoms. Found 18 (25 requested) and removed 25 (12 requested) atoms. Cycle 29: After refmac, R = 0.1662 (Rfree = 0.000) for 3922 atoms. Found 5 (25 requested) and removed 20 (12 requested) atoms. Cycle 30: After refmac, R = 0.1593 (Rfree = 0.000) for 3907 atoms. Found 2 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 4027 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4043 seeds are put forward Round 1: 177 peptides, 36 chains. Longest chain 11 peptides. Score 0.291 Round 2: 186 peptides, 35 chains. Longest chain 11 peptides. Score 0.337 Round 3: 193 peptides, 33 chains. Longest chain 13 peptides. Score 0.389 Round 4: 194 peptides, 34 chains. Longest chain 13 peptides. Score 0.378 Round 5: 205 peptides, 35 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 5 Chains 35, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9569 restraints for refining 3960 atoms. 8924 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2181 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 32: After refmac, R = 0.2367 (Rfree = 0.000) for 3949 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 33: After refmac, R = 0.2316 (Rfree = 0.000) for 3944 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 34: After refmac, R = 0.2180 (Rfree = 0.000) for 3930 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 35: After refmac, R = 0.2343 (Rfree = 0.000) for 3932 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 4060 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4072 seeds are put forward Round 1: 138 peptides, 30 chains. Longest chain 10 peptides. Score 0.239 Round 2: 170 peptides, 33 chains. Longest chain 12 peptides. Score 0.311 Round 3: 169 peptides, 31 chains. Longest chain 13 peptides. Score 0.337 Round 4: 167 peptides, 28 chains. Longest chain 13 peptides. Score 0.375 Round 5: 167 peptides, 29 chains. Longest chain 13 peptides. Score 0.360 Taking the results from Round 4 Chains 28, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9572 restraints for refining 3959 atoms. 9044 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2168 (Rfree = 0.000) for 3959 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 37: After refmac, R = 0.2144 (Rfree = 0.000) for 3952 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.2227 (Rfree = 0.000) for 3953 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 39: After refmac, R = 0.1532 (Rfree = 0.000) for 3948 atoms. Found 16 (25 requested) and removed 22 (12 requested) atoms. Cycle 40: After refmac, R = 0.1364 (Rfree = 0.000) for 3936 atoms. Found 16 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 4050 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4074 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 10 peptides. Score 0.268 Round 2: 181 peptides, 34 chains. Longest chain 9 peptides. Score 0.334 Round 3: 182 peptides, 32 chains. Longest chain 11 peptides. Score 0.367 Round 4: 176 peptides, 33 chains. Longest chain 13 peptides. Score 0.332 Round 5: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 5 Chains 32, Residues 152, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9395 restraints for refining 3958 atoms. 8795 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2102 (Rfree = 0.000) for 3958 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 42: After refmac, R = 0.2330 (Rfree = 0.000) for 3939 atoms. Found 25 (25 requested) and removed 35 (12 requested) atoms. Cycle 43: After refmac, R = 0.2192 (Rfree = 0.000) for 3922 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 44: After refmac, R = 0.2138 (Rfree = 0.000) for 3911 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 45: After refmac, R = 0.2051 (Rfree = 0.000) for 3906 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.56 Search for helices and strands: 0 residues in 0 chains, 4036 seeds are put forward NCS extension: 0 residues added, 4036 seeds are put forward Round 1: 132 peptides, 29 chains. Longest chain 10 peptides. Score 0.232 Round 2: 136 peptides, 25 chains. Longest chain 10 peptides. Score 0.312 Round 3: 136 peptides, 25 chains. Longest chain 16 peptides. Score 0.312 Round 4: 129 peptides, 24 chains. Longest chain 9 peptides. Score 0.302 Round 5: 157 peptides, 26 chains. Longest chain 16 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 131, 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 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5789 reflections ( 99.30 % complete ) and 9441 restraints for refining 3928 atoms. 8943 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2196 (Rfree = 0.000) for 3928 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 3903 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2237 (Rfree = 0.000) for 3886 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2302 (Rfree = 0.000) for 3867 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:29 GMT 2018 Job finished. TimeTaking 59.27 Used memory is bytes: 3090440