Mon 24 Dec 07:28:13 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vp4-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vp4-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-parrot-noncs ############### 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 07:28:17 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/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.8-parrot-noncs/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 684 and 0 Target number of residues in the AU: 684 Target solvent content: 0.6562 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.8-parrot-noncs.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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 3.800 Wilson plot Bfac: 82.24 10675 reflections ( 99.70 % complete ) and 0 restraints for refining 7529 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3685 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3535 (Rfree = 0.000) for 7529 atoms. Found 41 (41 requested) and removed 636 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 6964 seeds are put forward NCS extension: 0 residues added, 6964 seeds are put forward Round 1: 210 peptides, 46 chains. Longest chain 7 peptides. Score 0.222 Round 2: 295 peptides, 57 chains. Longest chain 12 peptides. Score 0.293 Round 3: 332 peptides, 62 chains. Longest chain 12 peptides. Score 0.320 Round 4: 341 peptides, 64 chains. Longest chain 16 peptides. Score 0.320 Round 5: 329 peptides, 60 chains. Longest chain 11 peptides. Score 0.329 Taking the results from Round 5 Chains 60, Residues 269, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14121 restraints for refining 6150 atoms. 12986 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2959 (Rfree = 0.000) for 6150 atoms. Found 33 (33 requested) and removed 170 (16 requested) atoms. Cycle 2: After refmac, R = 0.2702 (Rfree = 0.000) for 5949 atoms. Found 31 (33 requested) and removed 53 (16 requested) atoms. Cycle 3: After refmac, R = 0.2588 (Rfree = 0.000) for 5895 atoms. Found 26 (32 requested) and removed 92 (16 requested) atoms. Cycle 4: After refmac, R = 0.2512 (Rfree = 0.000) for 5804 atoms. Found 18 (32 requested) and removed 36 (16 requested) atoms. Cycle 5: After refmac, R = 0.2545 (Rfree = 0.000) for 5767 atoms. Found 24 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 5960 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5973 seeds are put forward Round 1: 301 peptides, 60 chains. Longest chain 12 peptides. Score 0.281 Round 2: 388 peptides, 65 chains. Longest chain 19 peptides. Score 0.389 Round 3: 396 peptides, 64 chains. Longest chain 14 peptides. Score 0.407 Round 4: 395 peptides, 62 chains. Longest chain 18 peptides. Score 0.419 Round 5: 401 peptides, 63 chains. Longest chain 17 peptides. Score 0.421 Taking the results from Round 5 Chains 63, Residues 338, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13424 restraints for refining 5924 atoms. 12086 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2761 (Rfree = 0.000) for 5924 atoms. Found 32 (32 requested) and removed 107 (16 requested) atoms. Cycle 7: After refmac, R = 0.2378 (Rfree = 0.000) for 5778 atoms. Found 19 (32 requested) and removed 52 (16 requested) atoms. Cycle 8: After refmac, R = 0.2402 (Rfree = 0.000) for 5705 atoms. Found 15 (31 requested) and removed 25 (15 requested) atoms. Cycle 9: After refmac, R = 0.2138 (Rfree = 0.000) for 5670 atoms. Found 10 (31 requested) and removed 18 (15 requested) atoms. Cycle 10: After refmac, R = 0.2090 (Rfree = 0.000) for 5639 atoms. Found 10 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 5804 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5819 seeds are put forward Round 1: 369 peptides, 73 chains. Longest chain 11 peptides. Score 0.303 Round 2: 434 peptides, 70 chains. Longest chain 15 peptides. Score 0.425 Round 3: 460 peptides, 69 chains. Longest chain 17 peptides. Score 0.468 Round 4: 451 peptides, 64 chains. Longest chain 20 peptides. Score 0.486 Round 5: 462 peptides, 74 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 4 Chains 64, Residues 387, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13652 restraints for refining 6150 atoms. 12141 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2520 (Rfree = 0.000) for 6150 atoms. Found 33 (33 requested) and removed 40 (16 requested) atoms. Cycle 12: After refmac, R = 0.2332 (Rfree = 0.000) for 6107 atoms. Found 31 (33 requested) and removed 26 (16 requested) atoms. Cycle 13: After refmac, R = 0.2095 (Rfree = 0.000) for 6080 atoms. Found 16 (33 requested) and removed 21 (16 requested) atoms. Cycle 14: After refmac, R = 0.2011 (Rfree = 0.000) for 6052 atoms. Found 7 (33 requested) and removed 19 (16 requested) atoms. Cycle 15: After refmac, R = 0.2035 (Rfree = 0.000) for 6025 atoms. Found 11 (33 requested) and removed 29 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 6222 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6241 seeds are put forward Round 1: 339 peptides, 66 chains. Longest chain 9 peptides. Score 0.303 Round 2: 410 peptides, 63 chains. Longest chain 15 peptides. Score 0.435 Round 3: 427 peptides, 60 chains. Longest chain 16 peptides. Score 0.478 Round 4: 445 peptides, 62 chains. Longest chain 21 peptides. Score 0.490 Round 5: 434 peptides, 56 chains. Longest chain 17 peptides. Score 0.512 Taking the results from Round 5 Chains 56, Residues 378, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13807 restraints for refining 6151 atoms. 12341 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2453 (Rfree = 0.000) for 6151 atoms. Found 29 (33 requested) and removed 27 (16 requested) atoms. Cycle 17: After refmac, R = 0.2250 (Rfree = 0.000) for 6138 atoms. Found 9 (33 requested) and removed 26 (16 requested) atoms. Cycle 18: After refmac, R = 0.2191 (Rfree = 0.000) for 6110 atoms. Found 6 (33 requested) and removed 19 (16 requested) atoms. Cycle 19: After refmac, R = 0.2153 (Rfree = 0.000) for 6090 atoms. Found 4 (33 requested) and removed 23 (16 requested) atoms. Cycle 20: After refmac, R = 0.2211 (Rfree = 0.000) for 6064 atoms. Found 12 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 6283 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 6303 seeds are put forward Round 1: 399 peptides, 74 chains. Longest chain 16 peptides. Score 0.345 Round 2: 417 peptides, 68 chains. Longest chain 20 peptides. Score 0.413 Round 3: 424 peptides, 68 chains. Longest chain 19 peptides. Score 0.423 Round 4: 437 peptides, 62 chains. Longest chain 23 peptides. Score 0.479 Round 5: 422 peptides, 60 chains. Longest chain 23 peptides. Score 0.471 Taking the results from Round 4 Chains 62, Residues 375, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13954 restraints for refining 6151 atoms. 12474 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2444 (Rfree = 0.000) for 6151 atoms. Found 26 (33 requested) and removed 57 (16 requested) atoms. Cycle 22: After refmac, R = 0.2425 (Rfree = 0.000) for 6073 atoms. Found 33 (33 requested) and removed 23 (16 requested) atoms. Cycle 23: After refmac, R = 0.2113 (Rfree = 0.000) for 6051 atoms. Found 11 (33 requested) and removed 20 (16 requested) atoms. Cycle 24: After refmac, R = 0.2054 (Rfree = 0.000) for 6035 atoms. Found 8 (33 requested) and removed 16 (16 requested) atoms. Cycle 25: After refmac, R = 0.2017 (Rfree = 0.000) for 6007 atoms. Found 10 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 6226 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6252 seeds are put forward Round 1: 376 peptides, 72 chains. Longest chain 15 peptides. Score 0.322 Round 2: 429 peptides, 75 chains. Longest chain 12 peptides. Score 0.385 Round 3: 415 peptides, 65 chains. Longest chain 17 peptides. Score 0.429 Round 4: 417 peptides, 64 chains. Longest chain 16 peptides. Score 0.438 Round 5: 443 peptides, 63 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 5 Chains 65, Residues 380, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 13903 restraints for refining 6150 atoms. 12397 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2358 (Rfree = 0.000) for 6150 atoms. Found 22 (33 requested) and removed 24 (16 requested) atoms. Cycle 27: After refmac, R = 0.2189 (Rfree = 0.000) for 6094 atoms. Found 12 (33 requested) and removed 24 (16 requested) atoms. Cycle 28: After refmac, R = 0.2066 (Rfree = 0.000) for 6050 atoms. Found 10 (33 requested) and removed 24 (16 requested) atoms. Cycle 29: After refmac, R = 0.2111 (Rfree = 0.000) for 6011 atoms. Found 24 (33 requested) and removed 24 (16 requested) atoms. Cycle 30: After refmac, R = 0.1956 (Rfree = 0.000) for 5994 atoms. Found 10 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 6197 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6213 seeds are put forward Round 1: 349 peptides, 67 chains. Longest chain 10 peptides. Score 0.312 Round 2: 409 peptides, 62 chains. Longest chain 16 peptides. Score 0.440 Round 3: 413 peptides, 67 chains. Longest chain 16 peptides. Score 0.413 Round 4: 402 peptides, 60 chains. Longest chain 18 peptides. Score 0.442 Round 5: 409 peptides, 63 chains. Longest chain 18 peptides. Score 0.433 Taking the results from Round 4 Chains 60, Residues 342, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14179 restraints for refining 6150 atoms. 12871 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2292 (Rfree = 0.000) for 6150 atoms. Found 33 (33 requested) and removed 46 (16 requested) atoms. Cycle 32: After refmac, R = 0.1998 (Rfree = 0.000) for 6079 atoms. Found 12 (33 requested) and removed 23 (16 requested) atoms. Cycle 33: After refmac, R = 0.2105 (Rfree = 0.000) for 6037 atoms. Found 19 (33 requested) and removed 22 (16 requested) atoms. Cycle 34: After refmac, R = 0.1904 (Rfree = 0.000) for 6021 atoms. Found 5 (33 requested) and removed 17 (16 requested) atoms. Cycle 35: After refmac, R = 0.2045 (Rfree = 0.000) for 5987 atoms. Found 16 (33 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 6161 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6184 seeds are put forward Round 1: 310 peptides, 65 chains. Longest chain 9 peptides. Score 0.260 Round 2: 367 peptides, 64 chains. Longest chain 12 peptides. Score 0.363 Round 3: 378 peptides, 66 chains. Longest chain 14 peptides. Score 0.366 Round 4: 356 peptides, 62 chains. Longest chain 17 peptides. Score 0.359 Round 5: 353 peptides, 60 chains. Longest chain 12 peptides. Score 0.368 Taking the results from Round 5 Chains 60, Residues 293, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14682 restraints for refining 6150 atoms. 13570 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2179 (Rfree = 0.000) for 6150 atoms. Found 33 (33 requested) and removed 24 (16 requested) atoms. Cycle 37: After refmac, R = 0.2122 (Rfree = 0.000) for 6134 atoms. Found 27 (33 requested) and removed 27 (16 requested) atoms. Cycle 38: After refmac, R = 0.2199 (Rfree = 0.000) for 6107 atoms. Found 33 (33 requested) and removed 19 (16 requested) atoms. Cycle 39: After refmac, R = 0.1891 (Rfree = 0.000) for 6100 atoms. Found 15 (33 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.1729 (Rfree = 0.000) for 6088 atoms. Found 5 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 6318 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6334 seeds are put forward Round 1: 279 peptides, 58 chains. Longest chain 9 peptides. Score 0.257 Round 2: 360 peptides, 69 chains. Longest chain 10 peptides. Score 0.316 Round 3: 352 peptides, 63 chains. Longest chain 13 peptides. Score 0.345 Round 4: 349 peptides, 60 chains. Longest chain 13 peptides. Score 0.362 Round 5: 346 peptides, 60 chains. Longest chain 16 peptides. Score 0.357 Taking the results from Round 4 Chains 60, Residues 289, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10675 reflections ( 99.70 % complete ) and 14507 restraints for refining 6151 atoms. 13382 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2012 (Rfree = 0.000) for 6151 atoms. Found 31 (33 requested) and removed 22 (16 requested) atoms. Cycle 42: After refmac, R = 0.2008 (Rfree = 0.000) for 6139 atoms. Found 23 (33 requested) and removed 23 (16 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1827 (Rfree = 0.000) for 6122 atoms. Found 12 (33 requested) and removed 19 (16 requested) atoms. Cycle 44: After refmac, R = 0.1878 (Rfree = 0.000) for 6092 atoms. Found 26 (33 requested) and removed 20 (16 requested) atoms. Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 6081 atoms. Found 11 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 6244 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6262 seeds are put forward Round 1: 288 peptides, 58 chains. Longest chain 9 peptides. Score 0.273 Round 2: 338 peptides, 67 chains. Longest chain 10 peptides. Score 0.294 Round 3: 342 peptides, 64 chains. Longest chain 11 peptides. Score 0.322 Round 4: 355 peptides, 65 chains. Longest chain 10 peptides. Score 0.336 Round 5: 362 peptides, 67 chains. Longest chain 14 peptides. Score 0.334 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 290, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 65 chains (290 residues) following loop building 3 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10675 reflections ( 99.70 % complete ) and 14207 restraints for refining 6151 atoms. 13079 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2118 (Rfree = 0.000) for 6151 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1887 (Rfree = 0.000) for 6103 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1994 (Rfree = 0.000) for 6069 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1787 (Rfree = 0.000) for 6038 atoms. TimeTaking 62.98