Mon 24 Dec 00:52:46 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 2gvh-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gvh-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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/2gvh-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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 00:52:51 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/2gvh-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gvh-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 710 and 0 Target number of residues in the AU: 710 Target solvent content: 0.6804 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6912 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: 121.211 3.800 Wilson plot Bfac: 101.15 Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 0 restraints for refining 7604 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3585 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3006 (Rfree = 0.000) for 7604 atoms. Found 41 (41 requested) and removed 93 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 3.34 Search for helices and strands: 0 residues in 0 chains, 7673 seeds are put forward NCS extension: 0 residues added, 7673 seeds are put forward Round 1: 382 peptides, 70 chains. Longest chain 17 peptides. Score 0.331 Round 2: 448 peptides, 66 chains. Longest chain 19 peptides. Score 0.447 Round 3: 454 peptides, 67 chains. Longest chain 23 peptides. Score 0.449 Round 4: 443 peptides, 57 chains. Longest chain 20 peptides. Score 0.492 Round 5: 469 peptides, 60 chains. Longest chain 27 peptides. Score 0.507 Taking the results from Round 5 Chains 66, Residues 409, Estimated correctness of the model 0.0 % 8 chains (99 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 13670 restraints for refining 6249 atoms. 11776 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2654 (Rfree = 0.000) for 6249 atoms. Found 21 (34 requested) and removed 47 (17 requested) atoms. Cycle 2: After refmac, R = 0.2645 (Rfree = 0.000) for 6121 atoms. Found 29 (34 requested) and removed 46 (17 requested) atoms. Cycle 3: After refmac, R = 0.2575 (Rfree = 0.000) for 6081 atoms. Found 17 (33 requested) and removed 41 (16 requested) atoms. Cycle 4: After refmac, R = 0.2605 (Rfree = 0.000) for 6032 atoms. Found 19 (33 requested) and removed 39 (16 requested) atoms. Cycle 5: After refmac, R = 0.2525 (Rfree = 0.000) for 6003 atoms. Found 9 (33 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 6154 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6166 seeds are put forward Round 1: 404 peptides, 68 chains. Longest chain 13 peptides. Score 0.376 Round 2: 428 peptides, 61 chains. Longest chain 15 peptides. Score 0.450 Round 3: 416 peptides, 63 chains. Longest chain 21 peptides. Score 0.423 Round 4: 429 peptides, 58 chains. Longest chain 18 peptides. Score 0.469 Round 5: 446 peptides, 61 chains. Longest chain 22 peptides. Score 0.473 Taking the results from Round 5 Chains 63, Residues 385, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14755 restraints for refining 6250 atoms. 13232 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2652 (Rfree = 0.000) for 6250 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 7: After refmac, R = 0.2445 (Rfree = 0.000) for 6214 atoms. Found 27 (34 requested) and removed 36 (17 requested) atoms. Cycle 8: After refmac, R = 0.2383 (Rfree = 0.000) for 6177 atoms. Found 19 (34 requested) and removed 40 (17 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 6135 atoms. Found 20 (33 requested) and removed 33 (16 requested) atoms. Cycle 10: After refmac, R = 0.2111 (Rfree = 0.000) for 6110 atoms. Found 4 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 6234 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 6264 seeds are put forward Round 1: 412 peptides, 72 chains. Longest chain 13 peptides. Score 0.362 Round 2: 422 peptides, 64 chains. Longest chain 22 peptides. Score 0.425 Round 3: 432 peptides, 63 chains. Longest chain 19 peptides. Score 0.444 Round 4: 447 peptides, 66 chains. Longest chain 16 peptides. Score 0.446 Round 5: 450 peptides, 66 chains. Longest chain 18 peptides. Score 0.450 Taking the results from Round 5 Chains 66, Residues 384, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14533 restraints for refining 6248 atoms. 12972 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2403 (Rfree = 0.000) for 6248 atoms. Found 24 (34 requested) and removed 43 (17 requested) atoms. Cycle 12: After refmac, R = 0.2298 (Rfree = 0.000) for 6170 atoms. Found 16 (34 requested) and removed 30 (17 requested) atoms. Cycle 13: After refmac, R = 0.2259 (Rfree = 0.000) for 6127 atoms. Found 18 (33 requested) and removed 27 (16 requested) atoms. Cycle 14: After refmac, R = 0.2263 (Rfree = 0.000) for 6094 atoms. Found 17 (33 requested) and removed 35 (16 requested) atoms. Cycle 15: After refmac, R = 0.2169 (Rfree = 0.000) for 6069 atoms. Found 13 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 3.31 Search for helices and strands: 0 residues in 0 chains, 6215 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6234 seeds are put forward Round 1: 399 peptides, 67 chains. Longest chain 14 peptides. Score 0.375 Round 2: 411 peptides, 65 chains. Longest chain 13 peptides. Score 0.404 Round 3: 398 peptides, 58 chains. Longest chain 16 peptides. Score 0.428 Round 4: 408 peptides, 56 chains. Longest chain 17 peptides. Score 0.454 Round 5: 415 peptides, 56 chains. Longest chain 20 peptides. Score 0.463 Taking the results from Round 5 Chains 58, Residues 359, Estimated correctness of the model 0.0 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14296 restraints for refining 6252 atoms. 12752 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2327 (Rfree = 0.000) for 6252 atoms. Found 26 (34 requested) and removed 46 (17 requested) atoms. Cycle 17: After refmac, R = 0.2265 (Rfree = 0.000) for 6188 atoms. Found 17 (34 requested) and removed 38 (17 requested) atoms. Cycle 18: After refmac, R = 0.2197 (Rfree = 0.000) for 6154 atoms. Found 31 (33 requested) and removed 40 (16 requested) atoms. Cycle 19: After refmac, R = 0.2177 (Rfree = 0.000) for 6137 atoms. Found 22 (33 requested) and removed 36 (16 requested) atoms. Cycle 20: After refmac, R = 0.2139 (Rfree = 0.000) for 6112 atoms. Found 21 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.32 Search for helices and strands: 0 residues in 0 chains, 6350 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 6378 seeds are put forward Round 1: 368 peptides, 64 chains. Longest chain 14 peptides. Score 0.349 Round 2: 397 peptides, 60 chains. Longest chain 16 peptides. Score 0.415 Round 3: 436 peptides, 62 chains. Longest chain 22 peptides. Score 0.455 Round 4: 430 peptides, 61 chains. Longest chain 17 peptides. Score 0.453 Round 5: 434 peptides, 59 chains. Longest chain 23 peptides. Score 0.469 Taking the results from Round 5 Chains 62, Residues 375, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14231 restraints for refining 6252 atoms. 12605 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2291 (Rfree = 0.000) for 6252 atoms. Found 14 (34 requested) and removed 28 (17 requested) atoms. Cycle 22: After refmac, R = 0.2257 (Rfree = 0.000) for 6203 atoms. Found 24 (34 requested) and removed 31 (17 requested) atoms. Cycle 23: After refmac, R = 0.2230 (Rfree = 0.000) for 6176 atoms. Found 8 (34 requested) and removed 34 (17 requested) atoms. Cycle 24: After refmac, R = 0.2141 (Rfree = 0.000) for 6135 atoms. Found 18 (33 requested) and removed 26 (16 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2172 (Rfree = 0.000) for 6122 atoms. Found 16 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.86 3.33 Search for helices and strands: 0 residues in 0 chains, 6250 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6272 seeds are put forward Round 1: 367 peptides, 64 chains. Longest chain 15 peptides. Score 0.348 Round 2: 415 peptides, 63 chains. Longest chain 13 peptides. Score 0.421 Round 3: 415 peptides, 59 chains. Longest chain 19 peptides. Score 0.445 Round 4: 427 peptides, 64 chains. Longest chain 19 peptides. Score 0.431 Round 5: 408 peptides, 60 chains. Longest chain 23 peptides. Score 0.430 Taking the results from Round 3 Chains 59, Residues 356, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14399 restraints for refining 6251 atoms. 12965 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2231 (Rfree = 0.000) for 6251 atoms. Found 28 (34 requested) and removed 30 (17 requested) atoms. Cycle 27: After refmac, R = 0.2229 (Rfree = 0.000) for 6231 atoms. Found 21 (34 requested) and removed 23 (17 requested) atoms. Cycle 28: After refmac, R = 0.2169 (Rfree = 0.000) for 6210 atoms. Found 16 (34 requested) and removed 24 (17 requested) atoms. Cycle 29: After refmac, R = 0.2182 (Rfree = 0.000) for 6186 atoms. Found 17 (34 requested) and removed 25 (17 requested) atoms. Cycle 30: After refmac, R = 0.2133 (Rfree = 0.000) for 6167 atoms. Found 18 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 3.31 Search for helices and strands: 0 residues in 0 chains, 6306 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 6333 seeds are put forward Round 1: 346 peptides, 67 chains. Longest chain 12 peptides. Score 0.297 Round 2: 372 peptides, 59 chains. Longest chain 19 peptides. Score 0.387 Round 3: 400 peptides, 61 chains. Longest chain 20 peptides. Score 0.413 Round 4: 406 peptides, 56 chains. Longest chain 18 peptides. Score 0.451 Round 5: 414 peptides, 66 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 4 Chains 57, Residues 350, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14837 restraints for refining 6252 atoms. 13460 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2387 (Rfree = 0.000) for 6252 atoms. Found 32 (34 requested) and removed 29 (17 requested) atoms. Cycle 32: After refmac, R = 0.2346 (Rfree = 0.000) for 6218 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 33: After refmac, R = 0.2245 (Rfree = 0.000) for 6206 atoms. Found 31 (34 requested) and removed 26 (17 requested) atoms. Cycle 34: After refmac, R = 0.2178 (Rfree = 0.000) for 6189 atoms. Found 26 (34 requested) and removed 27 (17 requested) atoms. Cycle 35: After refmac, R = 0.1888 (Rfree = 0.000) for 6175 atoms. Found 2 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.88 3.34 Search for helices and strands: 0 residues in 0 chains, 6282 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 6313 seeds are put forward Round 1: 335 peptides, 65 chains. Longest chain 11 peptides. Score 0.293 Round 2: 392 peptides, 68 chains. Longest chain 11 peptides. Score 0.359 Round 3: 386 peptides, 63 chains. Longest chain 14 peptides. Score 0.381 Round 4: 393 peptides, 60 chains. Longest chain 18 peptides. Score 0.410 Round 5: 403 peptides, 58 chains. Longest chain 15 peptides. Score 0.435 Taking the results from Round 5 Chains 60, Residues 345, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11825 reflections ( 99.61 % complete ) and 14740 restraints for refining 6252 atoms. 13349 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2357 (Rfree = 0.000) for 6252 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 37: After refmac, R = 0.2328 (Rfree = 0.000) for 6214 atoms. Found 34 (34 requested) and removed 89 (17 requested) atoms. Cycle 38: After refmac, R = 0.2243 (Rfree = 0.000) for 6140 atoms. Found 32 (33 requested) and removed 35 (16 requested) atoms. Cycle 39: After refmac, R = 0.1966 (Rfree = 0.000) for 6125 atoms. Found 8 (33 requested) and removed 27 (16 requested) atoms. Cycle 40: After refmac, R = 0.1927 (Rfree = 0.000) for 6095 atoms. Found 5 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 3.32 Search for helices and strands: 0 residues in 0 chains, 6226 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6246 seeds are put forward Round 1: 345 peptides, 70 chains. Longest chain 8 peptides. Score 0.275 Round 2: 348 peptides, 59 chains. Longest chain 18 peptides. Score 0.352 Round 3: 372 peptides, 57 chains. Longest chain 27 peptides. Score 0.399 Round 4: 370 peptides, 55 chains. Longest chain 16 peptides. Score 0.409 Round 5: 367 peptides, 58 chains. Longest chain 14 peptides. Score 0.386 Taking the results from Round 4 Chains 56, Residues 315, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11825 reflections ( 99.61 % complete ) and 14955 restraints for refining 6252 atoms. 13671 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2329 (Rfree = 0.000) for 6252 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 42: After refmac, R = 0.2318 (Rfree = 0.000) for 6240 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 43: After refmac, R = 0.2289 (Rfree = 0.000) for 6235 atoms. Found 34 (34 requested) and removed 49 (17 requested) atoms. Cycle 44: After refmac, R = 0.2195 (Rfree = 0.000) for 6214 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 45: After refmac, R = 0.1898 (Rfree = 0.000) for 6211 atoms. Found 8 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.31 Search for helices and strands: 0 residues in 0 chains, 6350 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6366 seeds are put forward Round 1: 303 peptides, 61 chains. Longest chain 10 peptides. Score 0.269 Round 2: 347 peptides, 63 chains. Longest chain 15 peptides. Score 0.325 Round 3: 349 peptides, 55 chains. Longest chain 15 peptides. Score 0.379 Round 4: 343 peptides, 55 chains. Longest chain 16 peptides. Score 0.371 Round 5: 341 peptides, 51 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 290, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2gvh-3_warpNtrace.pdb as input Building loops using Loopy2018 52 chains (290 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11825 reflections ( 99.61 % complete ) and 15199 restraints for refining 6248 atoms. 14016 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2295 (Rfree = 0.000) for 6248 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2328 (Rfree = 0.000) for 6204 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2252 (Rfree = 0.000) for 6174 atoms. Found 0 (34 requested) and removed 13 (17 requested) atoms. Cycle 49: After refmac, R = 0.2199 (Rfree = 0.000) for 6153 atoms. TimeTaking 66.53