Mon 24 Dec 01:13:18 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 1z82-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z82-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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/1z82-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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 01:13:22 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/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z82-4.0-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 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-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: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-4.0-parrot-mrncs.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 5920 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3241 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3023 (Rfree = 0.000) for 5920 atoms. Found 28 (28 requested) and removed 101 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 4.06 Search for helices and strands: 0 residues in 0 chains, 5913 seeds are put forward NCS extension: 0 residues added, 5913 seeds are put forward Round 1: 148 peptides, 33 chains. Longest chain 7 peptides. Score 0.222 Round 2: 185 peptides, 39 chains. Longest chain 7 peptides. Score 0.261 Round 3: 201 peptides, 41 chains. Longest chain 8 peptides. Score 0.284 Round 4: 196 peptides, 38 chains. Longest chain 9 peptides. Score 0.307 Round 5: 196 peptides, 38 chains. Longest chain 9 peptides. Score 0.307 Taking the results from Round 5 Chains 38, Residues 158, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 12222 restraints for refining 4839 atoms. 11599 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2689 (Rfree = 0.000) for 4839 atoms. Found 22 (22 requested) and removed 64 (11 requested) atoms. Cycle 2: After refmac, R = 0.2466 (Rfree = 0.000) for 4745 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 3: After refmac, R = 0.2408 (Rfree = 0.000) for 4698 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 4: After refmac, R = 0.1789 (Rfree = 0.000) for 4670 atoms. Found 9 (22 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.1706 (Rfree = 0.000) for 4644 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 4.30 Search for helices and strands: 0 residues in 0 chains, 4821 seeds are put forward NCS extension: 0 residues added, 4821 seeds are put forward Round 1: 189 peptides, 40 chains. Longest chain 8 peptides. Score 0.260 Round 2: 239 peptides, 46 chains. Longest chain 10 peptides. Score 0.333 Round 3: 265 peptides, 47 chains. Longest chain 11 peptides. Score 0.392 Round 4: 266 peptides, 48 chains. Longest chain 10 peptides. Score 0.384 Round 5: 292 peptides, 47 chains. Longest chain 12 peptides. Score 0.461 Taking the results from Round 5 Chains 47, Residues 245, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9822 restraints for refining 4295 atoms. 8872 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2192 (Rfree = 0.000) for 4295 atoms. Found 20 (20 requested) and removed 44 (10 requested) atoms. Cycle 7: After refmac, R = 0.2031 (Rfree = 0.000) for 4226 atoms. Found 16 (20 requested) and removed 36 (10 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2034 (Rfree = 0.000) for 4179 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 9: After refmac, R = 0.1869 (Rfree = 0.000) for 4157 atoms. Found 17 (19 requested) and removed 27 (9 requested) atoms. Cycle 10: After refmac, R = 0.1446 (Rfree = 0.000) for 4133 atoms. Found 7 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 4.28 Search for helices and strands: 0 residues in 0 chains, 4327 seeds are put forward NCS extension: 10 residues added (1 deleted due to clashes), 4337 seeds are put forward Round 1: 210 peptides, 41 chains. Longest chain 11 peptides. Score 0.311 Round 2: 253 peptides, 42 chains. Longest chain 13 peptides. Score 0.417 Round 3: 246 peptides, 43 chains. Longest chain 12 peptides. Score 0.387 Round 4: 263 peptides, 42 chains. Longest chain 13 peptides. Score 0.443 Round 5: 277 peptides, 42 chains. Longest chain 13 peptides. Score 0.477 Taking the results from Round 5 Chains 43, Residues 235, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9275 restraints for refining 4217 atoms. 8298 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1838 (Rfree = 0.000) for 4217 atoms. Found 18 (20 requested) and removed 40 (10 requested) atoms. Cycle 12: After refmac, R = 0.1816 (Rfree = 0.000) for 4162 atoms. Found 15 (19 requested) and removed 20 (9 requested) atoms. Cycle 13: After refmac, R = 0.1401 (Rfree = 0.000) for 4137 atoms. Found 5 (19 requested) and removed 15 (9 requested) atoms. Cycle 14: After refmac, R = 0.1295 (Rfree = 0.000) for 4116 atoms. Found 5 (19 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.1268 (Rfree = 0.000) for 4099 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 4.31 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4297 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 8 peptides. Score 0.283 Round 2: 255 peptides, 46 chains. Longest chain 10 peptides. Score 0.377 Round 3: 257 peptides, 47 chains. Longest chain 10 peptides. Score 0.371 Round 4: 265 peptides, 44 chains. Longest chain 12 peptides. Score 0.426 Round 5: 279 peptides, 48 chains. Longest chain 14 peptides. Score 0.417 Taking the results from Round 4 Chains 44, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 10030 restraints for refining 4303 atoms. 9190 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1791 (Rfree = 0.000) for 4303 atoms. Found 16 (20 requested) and removed 35 (10 requested) atoms. Cycle 17: After refmac, R = 0.1896 (Rfree = 0.000) for 4265 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 18: After refmac, R = 0.2015 (Rfree = 0.000) for 4247 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1850 (Rfree = 0.000) for 4228 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 20: After refmac, R = 0.1372 (Rfree = 0.000) for 4216 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 4.33 Search for helices and strands: 0 residues in 0 chains, 4382 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4397 seeds are put forward Round 1: 224 peptides, 50 chains. Longest chain 7 peptides. Score 0.241 Round 2: 252 peptides, 47 chains. Longest chain 12 peptides. Score 0.357 Round 3: 250 peptides, 45 chains. Longest chain 11 peptides. Score 0.375 Round 4: 256 peptides, 44 chains. Longest chain 13 peptides. Score 0.402 Round 5: 258 peptides, 45 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 4 Chains 46, Residues 212, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9774 restraints for refining 4281 atoms. 8934 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2011 (Rfree = 0.000) for 4281 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 22: After refmac, R = 0.1856 (Rfree = 0.000) for 4235 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 23: After refmac, R = 0.1374 (Rfree = 0.000) for 4210 atoms. Found 5 (20 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.1206 (Rfree = 0.000) for 4183 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1182 (Rfree = 0.000) for 4171 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 4.36 Search for helices and strands: 0 residues in 0 chains, 4355 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4369 seeds are put forward Round 1: 200 peptides, 42 chains. Longest chain 9 peptides. Score 0.268 Round 2: 232 peptides, 43 chains. Longest chain 12 peptides. Score 0.349 Round 3: 246 peptides, 45 chains. Longest chain 10 peptides. Score 0.364 Round 4: 246 peptides, 42 chains. Longest chain 16 peptides. Score 0.399 Round 5: 233 peptides, 41 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 4 Chains 42, Residues 204, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9804 restraints for refining 4265 atoms. 9008 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1779 (Rfree = 0.000) for 4265 atoms. Found 18 (20 requested) and removed 30 (10 requested) atoms. Cycle 27: After refmac, R = 0.2013 (Rfree = 0.000) for 4227 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 28: After refmac, R = 0.1852 (Rfree = 0.000) for 4208 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 29: After refmac, R = 0.1902 (Rfree = 0.000) for 4196 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 30: After refmac, R = 0.1817 (Rfree = 0.000) for 4182 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 4.36 Search for helices and strands: 0 residues in 0 chains, 4382 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4406 seeds are put forward Round 1: 179 peptides, 41 chains. Longest chain 7 peptides. Score 0.216 Round 2: 201 peptides, 41 chains. Longest chain 10 peptides. Score 0.284 Round 3: 224 peptides, 42 chains. Longest chain 11 peptides. Score 0.339 Round 4: 207 peptides, 38 chains. Longest chain 12 peptides. Score 0.339 Round 5: 219 peptides, 37 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 5 Chains 37, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9733 restraints for refining 4185 atoms. 9042 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1966 (Rfree = 0.000) for 4185 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 32: After refmac, R = 0.2071 (Rfree = 0.000) for 4157 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 33: After refmac, R = 0.1894 (Rfree = 0.000) for 4139 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 34: After refmac, R = 0.1953 (Rfree = 0.000) for 4127 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.1923 (Rfree = 0.000) for 4119 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 4.31 Search for helices and strands: 0 residues in 0 chains, 4297 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4309 seeds are put forward Round 1: 155 peptides, 34 chains. Longest chain 8 peptides. Score 0.232 Round 2: 214 peptides, 41 chains. Longest chain 11 peptides. Score 0.322 Round 3: 202 peptides, 37 chains. Longest chain 12 peptides. Score 0.337 Round 4: 207 peptides, 36 chains. Longest chain 13 peptides. Score 0.363 Round 5: 204 peptides, 36 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 4 Chains 36, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9235 restraints for refining 4043 atoms. 8587 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1914 (Rfree = 0.000) for 4043 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 37: After refmac, R = 0.1993 (Rfree = 0.000) for 4022 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 38: After refmac, R = 0.1407 (Rfree = 0.000) for 4011 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.1295 (Rfree = 0.000) for 4001 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.1247 (Rfree = 0.000) for 3992 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 4.36 Search for helices and strands: 0 residues in 0 chains, 4149 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4171 seeds are put forward Round 1: 169 peptides, 37 chains. Longest chain 9 peptides. Score 0.237 Round 2: 179 peptides, 33 chains. Longest chain 9 peptides. Score 0.320 Round 3: 191 peptides, 33 chains. Longest chain 13 peptides. Score 0.355 Round 4: 205 peptides, 37 chains. Longest chain 9 peptides. Score 0.345 Round 5: 194 peptides, 37 chains. Longest chain 9 peptides. Score 0.314 Taking the results from Round 3 Chains 33, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5179 reflections ( 99.50 % complete ) and 9166 restraints for refining 4051 atoms. 8567 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1924 (Rfree = 0.000) for 4051 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 42: After refmac, R = 0.1832 (Rfree = 0.000) for 4028 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 43: After refmac, R = 0.1831 (Rfree = 0.000) for 4021 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1328 (Rfree = 0.000) for 4014 atoms. Found 7 (19 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.1239 (Rfree = 0.000) for 4000 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 4.34 Search for helices and strands: 0 residues in 0 chains, 4165 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4184 seeds are put forward Round 1: 147 peptides, 33 chains. Longest chain 8 peptides. Score 0.219 Round 2: 168 peptides, 34 chains. Longest chain 8 peptides. Score 0.273 Round 3: 184 peptides, 36 chains. Longest chain 9 peptides. Score 0.296 Round 4: 170 peptides, 34 chains. Longest chain 8 peptides. Score 0.280 Round 5: 195 peptides, 35 chains. Longest chain 10 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 160, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1z82-4_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (160 residues) following loop building 3 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5179 reflections ( 99.50 % complete ) and 9039 restraints for refining 4071 atoms. 8366 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1850 (Rfree = 0.000) for 4071 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1814 (Rfree = 0.000) for 4050 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1779 (Rfree = 0.000) for 4034 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1334 (Rfree = 0.000) for 4017 atoms. TimeTaking 40.45