Sun 23 Dec 23:56:35 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 1vqs-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.6-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/1vqs-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.6-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 ============================================================ Sun 23 Dec 23:56:40 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/1vqs-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.6-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 474 and 0 Target number of residues in the AU: 474 Target solvent content: 0.6231 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-3.6-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 3.600 Wilson plot Bfac: 62.92 8432 reflections ( 99.56 % complete ) and 0 restraints for refining 5114 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3256 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3146 (Rfree = 0.000) for 5114 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 5216 seeds are put forward NCS extension: 0 residues added, 5216 seeds are put forward Round 1: 266 peptides, 47 chains. Longest chain 16 peptides. Score 0.377 Round 2: 310 peptides, 44 chains. Longest chain 17 peptides. Score 0.505 Round 3: 356 peptides, 43 chains. Longest chain 20 peptides. Score 0.602 Round 4: 355 peptides, 44 chains. Longest chain 19 peptides. Score 0.592 Round 5: 365 peptides, 38 chains. Longest chain 19 peptides. Score 0.655 Taking the results from Round 5 Chains 40, Residues 327, Estimated correctness of the model 34.9 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 8665 restraints for refining 4206 atoms. 7232 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2963 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 2: After refmac, R = 0.2705 (Rfree = 0.000) for 4128 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 3: After refmac, R = 0.2502 (Rfree = 0.000) for 4097 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 4: After refmac, R = 0.2475 (Rfree = 0.000) for 4084 atoms. Found 16 (26 requested) and removed 19 (13 requested) atoms. Cycle 5: After refmac, R = 0.2399 (Rfree = 0.000) for 4067 atoms. Found 14 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 4182 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 4204 seeds are put forward Round 1: 314 peptides, 45 chains. Longest chain 20 peptides. Score 0.504 Round 2: 354 peptides, 42 chains. Longest chain 22 peptides. Score 0.606 Round 3: 346 peptides, 38 chains. Longest chain 25 peptides. Score 0.624 Round 4: 351 peptides, 37 chains. Longest chain 25 peptides. Score 0.640 Round 5: 358 peptides, 40 chains. Longest chain 25 peptides. Score 0.629 Taking the results from Round 4 Chains 37, Residues 314, Estimated correctness of the model 29.6 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 8573 restraints for refining 4205 atoms. 7083 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2967 (Rfree = 0.000) for 4205 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 7: After refmac, R = 0.2857 (Rfree = 0.000) for 4149 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 8: After refmac, R = 0.2767 (Rfree = 0.000) for 4112 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 9: After refmac, R = 0.2623 (Rfree = 0.000) for 4092 atoms. Found 26 (26 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2239 (Rfree = 0.000) for 4090 atoms. Found 10 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4220 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4237 seeds are put forward Round 1: 277 peptides, 42 chains. Longest chain 23 peptides. Score 0.453 Round 2: 317 peptides, 41 chains. Longest chain 22 peptides. Score 0.546 Round 3: 343 peptides, 46 chains. Longest chain 24 peptides. Score 0.553 Round 4: 318 peptides, 42 chains. Longest chain 14 peptides. Score 0.540 Round 5: 344 peptides, 43 chains. Longest chain 19 peptides. Score 0.580 Taking the results from Round 5 Chains 43, Residues 301, Estimated correctness of the model 6.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8432 reflections ( 99.56 % complete ) and 9306 restraints for refining 4206 atoms. 8145 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2724 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 12: After refmac, R = 0.2449 (Rfree = 0.000) for 4171 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 13: After refmac, R = 0.2350 (Rfree = 0.000) for 4152 atoms. Found 17 (26 requested) and removed 22 (13 requested) atoms. Cycle 14: After refmac, R = 0.2363 (Rfree = 0.000) for 4139 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 15: After refmac, R = 0.2234 (Rfree = 0.000) for 4138 atoms. Found 23 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4293 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 4312 seeds are put forward Round 1: 290 peptides, 55 chains. Longest chain 14 peptides. Score 0.352 Round 2: 330 peptides, 54 chains. Longest chain 17 peptides. Score 0.454 Round 3: 315 peptides, 49 chains. Longest chain 15 peptides. Score 0.469 Round 4: 332 peptides, 53 chains. Longest chain 13 peptides. Score 0.468 Round 5: 318 peptides, 47 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 5 Chains 47, Residues 271, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9564 restraints for refining 4206 atoms. 8527 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3020 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 17: After refmac, R = 0.2435 (Rfree = 0.000) for 4160 atoms. Found 20 (26 requested) and removed 18 (13 requested) atoms. Cycle 18: After refmac, R = 0.2398 (Rfree = 0.000) for 4147 atoms. Found 24 (26 requested) and removed 21 (13 requested) atoms. Cycle 19: After refmac, R = 0.2255 (Rfree = 0.000) for 4142 atoms. Found 15 (26 requested) and removed 17 (13 requested) atoms. Cycle 20: After refmac, R = 0.2241 (Rfree = 0.000) for 4133 atoms. Found 15 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4261 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 4282 seeds are put forward Round 1: 286 peptides, 57 chains. Longest chain 12 peptides. Score 0.321 Round 2: 299 peptides, 47 chains. Longest chain 15 peptides. Score 0.453 Round 3: 312 peptides, 50 chains. Longest chain 16 peptides. Score 0.453 Round 4: 300 peptides, 47 chains. Longest chain 14 peptides. Score 0.455 Round 5: 297 peptides, 45 chains. Longest chain 19 peptides. Score 0.468 Taking the results from Round 5 Chains 45, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9601 restraints for refining 4206 atoms. 8638 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2670 (Rfree = 0.000) for 4206 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 22: After refmac, R = 0.2348 (Rfree = 0.000) for 4173 atoms. Found 17 (26 requested) and removed 22 (13 requested) atoms. Cycle 23: After refmac, R = 0.2221 (Rfree = 0.000) for 4157 atoms. Found 12 (26 requested) and removed 17 (13 requested) atoms. Cycle 24: After refmac, R = 0.2194 (Rfree = 0.000) for 4144 atoms. Found 13 (26 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.2150 (Rfree = 0.000) for 4135 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 4244 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 4266 seeds are put forward Round 1: 268 peptides, 52 chains. Longest chain 11 peptides. Score 0.329 Round 2: 300 peptides, 50 chains. Longest chain 14 peptides. Score 0.426 Round 3: 305 peptides, 52 chains. Longest chain 17 peptides. Score 0.418 Round 4: 301 peptides, 47 chains. Longest chain 15 peptides. Score 0.458 Round 5: 307 peptides, 51 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 4 Chains 47, Residues 254, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9551 restraints for refining 4205 atoms. 8551 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2595 (Rfree = 0.000) for 4205 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 27: After refmac, R = 0.2495 (Rfree = 0.000) for 4165 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 28: After refmac, R = 0.2320 (Rfree = 0.000) for 4153 atoms. Found 15 (26 requested) and removed 18 (13 requested) atoms. Cycle 29: After refmac, R = 0.2198 (Rfree = 0.000) for 4133 atoms. Found 14 (26 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2088 (Rfree = 0.000) for 4126 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4253 seeds are put forward Round 1: 228 peptides, 47 chains. Longest chain 12 peptides. Score 0.280 Round 2: 273 peptides, 48 chains. Longest chain 14 peptides. Score 0.383 Round 3: 277 peptides, 49 chains. Longest chain 16 peptides. Score 0.382 Round 4: 290 peptides, 47 chains. Longest chain 15 peptides. Score 0.433 Round 5: 280 peptides, 48 chains. Longest chain 14 peptides. Score 0.400 Taking the results from Round 4 Chains 47, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9751 restraints for refining 4206 atoms. 8826 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2318 (Rfree = 0.000) for 4206 atoms. Found 19 (26 requested) and removed 21 (13 requested) atoms. Cycle 32: After refmac, R = 0.2175 (Rfree = 0.000) for 4188 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2145 (Rfree = 0.000) for 4173 atoms. Found 12 (26 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.2154 (Rfree = 0.000) for 4168 atoms. Found 5 (26 requested) and removed 17 (13 requested) atoms. Cycle 35: After refmac, R = 0.2255 (Rfree = 0.000) for 4153 atoms. Found 20 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 4301 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4323 seeds are put forward Round 1: 253 peptides, 53 chains. Longest chain 9 peptides. Score 0.280 Round 2: 275 peptides, 49 chains. Longest chain 15 peptides. Score 0.378 Round 3: 274 peptides, 46 chains. Longest chain 15 peptides. Score 0.406 Round 4: 293 peptides, 47 chains. Longest chain 13 peptides. Score 0.440 Round 5: 282 peptides, 45 chains. Longest chain 11 peptides. Score 0.435 Taking the results from Round 4 Chains 47, Residues 246, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9727 restraints for refining 4206 atoms. 8790 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2319 (Rfree = 0.000) for 4206 atoms. Found 23 (26 requested) and removed 15 (13 requested) atoms. Cycle 37: After refmac, R = 0.2115 (Rfree = 0.000) for 4192 atoms. Found 9 (27 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.2038 (Rfree = 0.000) for 4170 atoms. Found 6 (26 requested) and removed 17 (13 requested) atoms. Cycle 39: After refmac, R = 0.2032 (Rfree = 0.000) for 4152 atoms. Found 6 (26 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.1974 (Rfree = 0.000) for 4140 atoms. Found 3 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 4230 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4243 seeds are put forward Round 1: 237 peptides, 48 chains. Longest chain 9 peptides. Score 0.292 Round 2: 263 peptides, 47 chains. Longest chain 15 peptides. Score 0.369 Round 3: 268 peptides, 45 chains. Longest chain 15 peptides. Score 0.402 Round 4: 268 peptides, 42 chains. Longest chain 15 peptides. Score 0.433 Round 5: 259 peptides, 40 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 4 Chains 42, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8432 reflections ( 99.56 % complete ) and 9592 restraints for refining 4205 atoms. 8730 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2393 (Rfree = 0.000) for 4205 atoms. Found 24 (26 requested) and removed 24 (13 requested) atoms. Cycle 42: After refmac, R = 0.2212 (Rfree = 0.000) for 4195 atoms. Found 7 (26 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.2170 (Rfree = 0.000) for 4180 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.2145 (Rfree = 0.000) for 4168 atoms. Found 11 (26 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2101 (Rfree = 0.000) for 4164 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 4267 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4285 seeds are put forward Round 1: 236 peptides, 47 chains. Longest chain 10 peptides. Score 0.301 Round 2: 259 peptides, 45 chains. Longest chain 10 peptides. Score 0.381 Round 3: 265 peptides, 40 chains. Longest chain 14 peptides. Score 0.446 Round 4: 247 peptides, 42 chains. Longest chain 12 peptides. Score 0.383 Round 5: 254 peptides, 42 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 225, 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 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8432 reflections ( 99.56 % complete ) and 9709 restraints for refining 4205 atoms. 8849 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2349 (Rfree = 0.000) for 4205 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2180 (Rfree = 0.000) for 4182 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2183 (Rfree = 0.000) for 4166 atoms. Found 0 (26 requested) and removed 8 (13 requested) atoms. Cycle 49: After refmac, R = 0.2123 (Rfree = 0.000) for 4157 atoms. TimeTaking 60.4