Sun 23 Dec 23:42:18 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 2okc-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-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/2okc-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-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 23:42:22 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/2okc-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-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 620 and 0 Target number of residues in the AU: 620 Target solvent content: 0.6596 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-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: 19 Cell parameters: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7120 target number of atoms Had to go as low as 0.75 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: 28.546 3.600 Wilson plot Bfac: 84.60 Failed to save intermediate PDB 10697 reflections ( 89.31 % complete ) and 0 restraints for refining 7833 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3071 (Rfree = 0.000) for 7833 atoms. Found 50 (50 requested) and removed 55 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 7996 seeds are put forward NCS extension: 0 residues added, 7996 seeds are put forward Round 1: 328 peptides, 66 chains. Longest chain 11 peptides. Score 0.292 Round 2: 425 peptides, 74 chains. Longest chain 13 peptides. Score 0.400 Round 3: 444 peptides, 75 chains. Longest chain 16 peptides. Score 0.423 Round 4: 449 peptides, 67 chains. Longest chain 16 peptides. Score 0.484 Round 5: 436 peptides, 66 chains. Longest chain 17 peptides. Score 0.471 Taking the results from Round 4 Chains 69, Residues 382, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14825 restraints for refining 6451 atoms. 13304 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2360 (Rfree = 0.000) for 6451 atoms. Found 35 (41 requested) and removed 50 (20 requested) atoms. Cycle 2: After refmac, R = 0.2232 (Rfree = 0.000) for 6363 atoms. Found 32 (41 requested) and removed 39 (20 requested) atoms. Cycle 3: After refmac, R = 0.2096 (Rfree = 0.000) for 6323 atoms. Found 21 (40 requested) and removed 36 (20 requested) atoms. Cycle 4: After refmac, R = 0.2044 (Rfree = 0.000) for 6282 atoms. Found 19 (40 requested) and removed 32 (20 requested) atoms. Cycle 5: After refmac, R = 0.1988 (Rfree = 0.000) for 6255 atoms. Found 23 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 6463 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6484 seeds are put forward Round 1: 404 peptides, 72 chains. Longest chain 12 peptides. Score 0.380 Round 2: 457 peptides, 65 chains. Longest chain 16 peptides. Score 0.509 Round 3: 468 peptides, 71 chains. Longest chain 16 peptides. Score 0.486 Round 4: 468 peptides, 68 chains. Longest chain 18 peptides. Score 0.505 Round 5: 453 peptides, 66 chains. Longest chain 20 peptides. Score 0.496 Taking the results from Round 2 Chains 65, Residues 392, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14895 restraints for refining 6368 atoms. 13372 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2193 (Rfree = 0.000) for 6368 atoms. Found 35 (40 requested) and removed 55 (20 requested) atoms. Cycle 7: After refmac, R = 0.2088 (Rfree = 0.000) for 6312 atoms. Found 31 (40 requested) and removed 36 (20 requested) atoms. Cycle 8: After refmac, R = 0.1960 (Rfree = 0.000) for 6291 atoms. Found 26 (40 requested) and removed 43 (20 requested) atoms. Cycle 9: After refmac, R = 0.1696 (Rfree = 0.000) for 6255 atoms. Found 5 (40 requested) and removed 27 (20 requested) atoms. Cycle 10: After refmac, R = 0.1645 (Rfree = 0.000) for 6222 atoms. Found 11 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 6429 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 6460 seeds are put forward Round 1: 385 peptides, 67 chains. Longest chain 11 peptides. Score 0.384 Round 2: 424 peptides, 69 chains. Longest chain 16 peptides. Score 0.433 Round 3: 434 peptides, 69 chains. Longest chain 14 peptides. Score 0.448 Round 4: 441 peptides, 73 chains. Longest chain 14 peptides. Score 0.432 Round 5: 435 peptides, 68 chains. Longest chain 18 peptides. Score 0.457 Taking the results from Round 5 Chains 68, Residues 367, Estimated correctness of the model 0.0 % 7 chains (49 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14991 restraints for refining 6453 atoms. 13460 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2141 (Rfree = 0.000) for 6453 atoms. Found 17 (41 requested) and removed 48 (20 requested) atoms. Cycle 12: After refmac, R = 0.2034 (Rfree = 0.000) for 6375 atoms. Found 27 (41 requested) and removed 33 (20 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1935 (Rfree = 0.000) for 6338 atoms. Found 19 (40 requested) and removed 34 (20 requested) atoms. Cycle 14: After refmac, R = 0.1884 (Rfree = 0.000) for 6313 atoms. Found 21 (40 requested) and removed 24 (20 requested) atoms. Cycle 15: After refmac, R = 0.1864 (Rfree = 0.000) for 6297 atoms. Found 25 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 6474 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6489 seeds are put forward Round 1: 368 peptides, 70 chains. Longest chain 12 peptides. Score 0.333 Round 2: 409 peptides, 65 chains. Longest chain 18 peptides. Score 0.437 Round 3: 402 peptides, 61 chains. Longest chain 18 peptides. Score 0.453 Round 4: 417 peptides, 63 chains. Longest chain 18 peptides. Score 0.463 Round 5: 409 peptides, 64 chains. Longest chain 18 peptides. Score 0.444 Taking the results from Round 4 Chains 63, Residues 354, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15390 restraints for refining 6453 atoms. 14016 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2125 (Rfree = 0.000) for 6453 atoms. Found 34 (41 requested) and removed 30 (20 requested) atoms. Cycle 17: After refmac, R = 0.2004 (Rfree = 0.000) for 6444 atoms. Found 26 (41 requested) and removed 34 (20 requested) atoms. Cycle 18: After refmac, R = 0.1864 (Rfree = 0.000) for 6426 atoms. Found 22 (41 requested) and removed 27 (20 requested) atoms. Cycle 19: After refmac, R = 0.1806 (Rfree = 0.000) for 6414 atoms. Found 19 (41 requested) and removed 23 (20 requested) atoms. Cycle 20: After refmac, R = 0.1834 (Rfree = 0.000) for 6401 atoms. Found 16 (41 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 6594 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6612 seeds are put forward Round 1: 394 peptides, 73 chains. Longest chain 13 peptides. Score 0.356 Round 2: 429 peptides, 69 chains. Longest chain 23 peptides. Score 0.441 Round 3: 410 peptides, 61 chains. Longest chain 19 peptides. Score 0.465 Round 4: 413 peptides, 59 chains. Longest chain 22 peptides. Score 0.483 Round 5: 411 peptides, 62 chains. Longest chain 21 peptides. Score 0.460 Taking the results from Round 4 Chains 59, Residues 354, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15135 restraints for refining 6454 atoms. 13760 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2129 (Rfree = 0.000) for 6454 atoms. Found 31 (41 requested) and removed 37 (20 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2004 (Rfree = 0.000) for 6431 atoms. Found 29 (41 requested) and removed 22 (20 requested) atoms. Cycle 23: After refmac, R = 0.1917 (Rfree = 0.000) for 6423 atoms. Found 23 (41 requested) and removed 31 (20 requested) atoms. Cycle 24: After refmac, R = 0.1810 (Rfree = 0.000) for 6406 atoms. Found 16 (41 requested) and removed 29 (20 requested) atoms. Cycle 25: After refmac, R = 0.1846 (Rfree = 0.000) for 6381 atoms. Found 35 (41 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 6628 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6648 seeds are put forward Round 1: 340 peptides, 66 chains. Longest chain 11 peptides. Score 0.313 Round 2: 393 peptides, 61 chains. Longest chain 20 peptides. Score 0.439 Round 3: 400 peptides, 65 chains. Longest chain 24 peptides. Score 0.422 Round 4: 400 peptides, 63 chains. Longest chain 19 peptides. Score 0.436 Round 5: 391 peptides, 61 chains. Longest chain 24 peptides. Score 0.436 Taking the results from Round 2 Chains 62, Residues 332, Estimated correctness of the model 0.0 % 6 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15131 restraints for refining 6454 atoms. 13819 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1939 (Rfree = 0.000) for 6454 atoms. Found 28 (41 requested) and removed 32 (20 requested) atoms. Cycle 27: After refmac, R = 0.1860 (Rfree = 0.000) for 6430 atoms. Found 22 (41 requested) and removed 25 (20 requested) atoms. Cycle 28: After refmac, R = 0.1834 (Rfree = 0.000) for 6412 atoms. Found 31 (41 requested) and removed 28 (20 requested) atoms. Cycle 29: After refmac, R = 0.1751 (Rfree = 0.000) for 6409 atoms. Found 20 (41 requested) and removed 24 (20 requested) atoms. Cycle 30: After refmac, R = 0.1687 (Rfree = 0.000) for 6400 atoms. Found 17 (41 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 6579 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6600 seeds are put forward Round 1: 320 peptides, 62 chains. Longest chain 12 peptides. Score 0.308 Round 2: 342 peptides, 54 chains. Longest chain 21 peptides. Score 0.407 Round 3: 362 peptides, 61 chains. Longest chain 18 peptides. Score 0.389 Round 4: 367 peptides, 60 chains. Longest chain 14 peptides. Score 0.404 Round 5: 360 peptides, 54 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 5 Chains 54, Residues 306, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15275 restraints for refining 6454 atoms. 14056 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1893 (Rfree = 0.000) for 6454 atoms. Found 20 (41 requested) and removed 27 (20 requested) atoms. Cycle 32: After refmac, R = 0.1892 (Rfree = 0.000) for 6434 atoms. Found 25 (41 requested) and removed 24 (20 requested) atoms. Cycle 33: After refmac, R = 0.1738 (Rfree = 0.000) for 6430 atoms. Found 21 (41 requested) and removed 23 (20 requested) atoms. Cycle 34: After refmac, R = 0.1747 (Rfree = 0.000) for 6425 atoms. Found 16 (41 requested) and removed 22 (20 requested) atoms. Cycle 35: After refmac, R = 0.1597 (Rfree = 0.000) for 6413 atoms. Found 18 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 6577 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6594 seeds are put forward Round 1: 315 peptides, 64 chains. Longest chain 14 peptides. Score 0.283 Round 2: 341 peptides, 59 chains. Longest chain 13 peptides. Score 0.368 Round 3: 361 peptides, 60 chains. Longest chain 24 peptides. Score 0.394 Round 4: 357 peptides, 59 chains. Longest chain 21 peptides. Score 0.395 Round 5: 346 peptides, 58 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 4 Chains 61, Residues 298, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15240 restraints for refining 6453 atoms. 14037 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1901 (Rfree = 0.000) for 6453 atoms. Found 31 (41 requested) and removed 30 (20 requested) atoms. Cycle 37: After refmac, R = 0.1777 (Rfree = 0.000) for 6433 atoms. Found 32 (41 requested) and removed 27 (20 requested) atoms. Cycle 38: After refmac, R = 0.1721 (Rfree = 0.000) for 6428 atoms. Found 28 (41 requested) and removed 25 (20 requested) atoms. Cycle 39: After refmac, R = 0.1672 (Rfree = 0.000) for 6426 atoms. Found 22 (41 requested) and removed 27 (20 requested) atoms. Cycle 40: After refmac, R = 0.1614 (Rfree = 0.000) for 6411 atoms. Found 28 (41 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 6584 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 6595 seeds are put forward Round 1: 295 peptides, 62 chains. Longest chain 10 peptides. Score 0.261 Round 2: 327 peptides, 61 chains. Longest chain 12 peptides. Score 0.328 Round 3: 334 peptides, 56 chains. Longest chain 23 peptides. Score 0.379 Round 4: 337 peptides, 57 chains. Longest chain 17 peptides. Score 0.376 Round 5: 341 peptides, 53 chains. Longest chain 29 peptides. Score 0.413 Taking the results from Round 5 Chains 55, Residues 288, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15087 restraints for refining 6454 atoms. 13895 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1905 (Rfree = 0.000) for 6454 atoms. Found 37 (41 requested) and removed 30 (20 requested) atoms. Cycle 42: After refmac, R = 0.1829 (Rfree = 0.000) for 6446 atoms. Found 33 (41 requested) and removed 26 (20 requested) atoms. Cycle 43: After refmac, R = 0.1711 (Rfree = 0.000) for 6440 atoms. Found 32 (41 requested) and removed 29 (20 requested) atoms. Cycle 44: After refmac, R = 0.1697 (Rfree = 0.000) for 6434 atoms. Found 25 (41 requested) and removed 29 (20 requested) atoms. Cycle 45: After refmac, R = 0.1692 (Rfree = 0.000) for 6419 atoms. Found 41 (41 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 6610 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6634 seeds are put forward Round 1: 254 peptides, 56 chains. Longest chain 11 peptides. Score 0.230 Round 2: 312 peptides, 58 chains. Longest chain 17 peptides. Score 0.325 Round 3: 338 peptides, 61 chains. Longest chain 15 peptides. Score 0.348 Round 4: 332 peptides, 57 chains. Longest chain 16 peptides. Score 0.368 Round 5: 323 peptides, 56 chains. Longest chain 16 peptides. Score 0.359 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 275, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (275 residues) following loop building 3 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10697 reflections ( 89.31 % complete ) and 15379 restraints for refining 6454 atoms. 14284 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1926 (Rfree = 0.000) for 6454 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1759 (Rfree = 0.000) for 6423 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1665 (Rfree = 0.000) for 6394 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1682 (Rfree = 0.000) for 6365 atoms. TimeTaking 58.5