Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2okc-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.6-parrot-hancs/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-hancs.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-hancs.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 10697 reflections ( 89.31 % complete ) and 0 restraints for refining 7843 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3345 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3049 (Rfree = 0.000) for 7843 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, 7989 seeds are put forward NCS extension: 0 residues added, 7989 seeds are put forward Round 1: 335 peptides, 66 chains. Longest chain 11 peptides. Score 0.304 Round 2: 402 peptides, 61 chains. Longest chain 19 peptides. Score 0.453 Round 3: 397 peptides, 55 chains. Longest chain 18 peptides. Score 0.486 Round 4: 421 peptides, 63 chains. Longest chain 20 peptides. Score 0.469 Round 5: 447 peptides, 67 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 3 Chains 55, Residues 342, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10697 reflections ( 89.31 % complete ) and 15365 restraints for refining 6453 atoms. 14020 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2444 (Rfree = 0.000) for 6453 atoms. Found 40 (41 requested) and removed 36 (20 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2270 (Rfree = 0.000) for 6398 atoms. Found 34 (41 requested) and removed 35 (20 requested) atoms. Cycle 3: After refmac, R = 0.2110 (Rfree = 0.000) for 6369 atoms. Found 37 (41 requested) and removed 31 (20 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2107 (Rfree = 0.000) for 6351 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1824 (Rfree = 0.000) for 6334 atoms. Found 9 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6560 seeds are put forward Round 1: 346 peptides, 66 chains. Longest chain 13 peptides. Score 0.324 Round 2: 383 peptides, 65 chains. Longest chain 17 peptides. Score 0.395 Round 3: 430 peptides, 65 chains. Longest chain 15 peptides. Score 0.469 Round 4: 432 peptides, 65 chains. Longest chain 19 peptides. Score 0.472 Round 5: 428 peptides, 59 chains. Longest chain 17 peptides. Score 0.505 Taking the results from Round 5 Chains 60, Residues 369, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10697 reflections ( 89.31 % complete ) and 15030 restraints for refining 6453 atoms. 13559 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2210 (Rfree = 0.000) for 6453 atoms. Found 27 (41 requested) and removed 47 (20 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2101 (Rfree = 0.000) for 6401 atoms. Found 26 (41 requested) and removed 33 (20 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2056 (Rfree = 0.000) for 6374 atoms. Found 39 (41 requested) and removed 35 (20 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2025 (Rfree = 0.000) for 6360 atoms. Found 20 (40 requested) and removed 36 (20 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1947 (Rfree = 0.000) for 6322 atoms. Found 35 (40 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 6530 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6551 seeds are put forward Round 1: 380 peptides, 77 chains. Longest chain 9 peptides. Score 0.302 Round 2: 396 peptides, 66 chains. Longest chain 14 peptides. Score 0.409 Round 3: 418 peptides, 68 chains. Longest chain 15 peptides. Score 0.430 Round 4: 402 peptides, 67 chains. Longest chain 13 peptides. Score 0.412 Round 5: 402 peptides, 60 chains. Longest chain 18 peptides. Score 0.460 Taking the results from Round 5 Chains 62, Residues 342, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14851 restraints for refining 6454 atoms. 13429 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2118 (Rfree = 0.000) for 6454 atoms. Found 28 (41 requested) and removed 51 (20 requested) atoms. Cycle 12: After refmac, R = 0.2041 (Rfree = 0.000) for 6401 atoms. Found 21 (41 requested) and removed 30 (20 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1998 (Rfree = 0.000) for 6374 atoms. Found 18 (41 requested) and removed 39 (20 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1905 (Rfree = 0.000) for 6345 atoms. Found 21 (40 requested) and removed 29 (20 requested) atoms. Cycle 15: After refmac, R = 0.1992 (Rfree = 0.000) for 6324 atoms. Found 27 (40 requested) and removed 28 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 6544 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6568 seeds are put forward Round 1: 392 peptides, 76 chains. Longest chain 13 peptides. Score 0.330 Round 2: 433 peptides, 65 chains. Longest chain 16 peptides. Score 0.474 Round 3: 443 peptides, 66 chains. Longest chain 21 peptides. Score 0.482 Round 4: 439 peptides, 66 chains. Longest chain 20 peptides. Score 0.476 Round 5: 429 peptides, 65 chains. Longest chain 18 peptides. Score 0.468 Taking the results from Round 3 Chains 69, Residues 377, Estimated correctness of the model 0.0 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10697 reflections ( 89.31 % complete ) and 14348 restraints for refining 6453 atoms. 12707 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2133 (Rfree = 0.000) for 6453 atoms. Found 27 (41 requested) and removed 36 (20 requested) atoms. Cycle 17: After refmac, R = 0.2040 (Rfree = 0.000) for 6415 atoms. Found 33 (41 requested) and removed 30 (20 requested) atoms. Cycle 18: After refmac, R = 0.2064 (Rfree = 0.000) for 6394 atoms. Found 37 (41 requested) and removed 35 (20 requested) atoms. Cycle 19: After refmac, R = 0.1957 (Rfree = 0.000) for 6370 atoms. Found 35 (41 requested) and removed 30 (20 requested) atoms. Cycle 20: After refmac, R = 0.1948 (Rfree = 0.000) for 6355 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 6572 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6591 seeds are put forward Round 1: 327 peptides, 64 chains. Longest chain 11 peptides. Score 0.305 Round 2: 360 peptides, 63 chains. Longest chain 13 peptides. Score 0.371 Round 3: 388 peptides, 69 chains. Longest chain 16 peptides. Score 0.374 Round 4: 398 peptides, 64 chains. Longest chain 19 peptides. Score 0.426 Round 5: 392 peptides, 69 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 4 Chains 68, Residues 334, Estimated correctness of the model 0.0 % 7 chains (48 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 14853 restraints for refining 6454 atoms. 13443 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2149 (Rfree = 0.000) for 6454 atoms. Found 40 (41 requested) and removed 43 (20 requested) atoms. Cycle 22: After refmac, R = 0.2025 (Rfree = 0.000) for 6408 atoms. Found 41 (41 requested) and removed 39 (20 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1942 (Rfree = 0.000) for 6390 atoms. Found 38 (41 requested) and removed 33 (20 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1831 (Rfree = 0.000) for 6384 atoms. Found 23 (41 requested) and removed 29 (20 requested) atoms. Cycle 25: After refmac, R = 0.1852 (Rfree = 0.000) for 6371 atoms. Found 28 (40 requested) and removed 30 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 6545 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6561 seeds are put forward Round 1: 346 peptides, 70 chains. Longest chain 10 peptides. Score 0.294 Round 2: 361 peptides, 61 chains. Longest chain 15 peptides. Score 0.387 Round 3: 369 peptides, 62 chains. Longest chain 13 peptides. Score 0.393 Round 4: 382 peptides, 58 chains. Longest chain 19 peptides. Score 0.443 Round 5: 388 peptides, 60 chains. Longest chain 15 peptides. Score 0.438 Taking the results from Round 4 Chains 59, Residues 324, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10697 reflections ( 89.31 % complete ) and 14938 restraints for refining 6454 atoms. 13584 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2031 (Rfree = 0.000) for 6454 atoms. Found 28 (41 requested) and removed 42 (20 requested) atoms. Cycle 27: After refmac, R = 0.1976 (Rfree = 0.000) for 6412 atoms. Found 28 (41 requested) and removed 32 (20 requested) atoms. Cycle 28: After refmac, R = 0.1838 (Rfree = 0.000) for 6392 atoms. Found 29 (41 requested) and removed 27 (20 requested) atoms. Cycle 29: After refmac, R = 0.1813 (Rfree = 0.000) for 6379 atoms. Found 39 (41 requested) and removed 27 (20 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 6378 atoms. Found 29 (41 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 6556 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6573 seeds are put forward Round 1: 298 peptides, 59 chains. Longest chain 9 peptides. Score 0.291 Round 2: 346 peptides, 60 chains. Longest chain 12 peptides. Score 0.369 Round 3: 370 peptides, 62 chains. Longest chain 19 peptides. Score 0.395 Round 4: 379 peptides, 60 chains. Longest chain 22 peptides. Score 0.424 Round 5: 360 peptides, 56 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 60, Residues 319, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10697 reflections ( 89.31 % complete ) and 15162 restraints for refining 6452 atoms. 13903 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1969 (Rfree = 0.000) for 6452 atoms. Found 26 (41 requested) and removed 30 (20 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1900 (Rfree = 0.000) for 6429 atoms. Found 19 (41 requested) and removed 25 (20 requested) atoms. Cycle 33: After refmac, R = 0.1848 (Rfree = 0.000) for 6416 atoms. Found 31 (41 requested) and removed 29 (20 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1795 (Rfree = 0.000) for 6408 atoms. Found 31 (41 requested) and removed 30 (20 requested) atoms. Cycle 35: After refmac, R = 0.1768 (Rfree = 0.000) for 6404 atoms. Found 21 (41 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.45 Search for helices and strands: 0 residues in 0 chains, 6588 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 6621 seeds are put forward Round 1: 302 peptides, 61 chains. Longest chain 9 peptides. Score 0.283 Round 2: 325 peptides, 60 chains. Longest chain 10 peptides. Score 0.332 Round 3: 328 peptides, 57 chains. Longest chain 10 peptides. Score 0.361 Round 4: 352 peptides, 58 chains. Longest chain 19 peptides. Score 0.394 Round 5: 344 peptides, 57 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 4 Chains 59, Residues 294, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15252 restraints for refining 6454 atoms. 14072 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1964 (Rfree = 0.000) for 6454 atoms. Found 29 (41 requested) and removed 30 (20 requested) atoms. Cycle 37: After refmac, R = 0.1894 (Rfree = 0.000) for 6431 atoms. Found 32 (41 requested) and removed 28 (20 requested) atoms. Cycle 38: After refmac, R = 0.1826 (Rfree = 0.000) for 6420 atoms. Found 40 (41 requested) and removed 23 (20 requested) atoms. Cycle 39: After refmac, R = 0.1780 (Rfree = 0.000) for 6422 atoms. Found 36 (41 requested) and removed 25 (20 requested) atoms. Cycle 40: After refmac, R = 0.1774 (Rfree = 0.000) for 6423 atoms. Found 32 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 6603 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6617 seeds are put forward Round 1: 260 peptides, 56 chains. Longest chain 9 peptides. Score 0.242 Round 2: 314 peptides, 60 chains. Longest chain 14 peptides. Score 0.313 Round 3: 303 peptides, 57 chains. Longest chain 8 peptides. Score 0.316 Round 4: 310 peptides, 58 chains. Longest chain 13 peptides. Score 0.321 Round 5: 321 peptides, 55 chains. Longest chain 14 peptides. Score 0.364 Taking the results from Round 5 Chains 55, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10697 reflections ( 89.31 % complete ) and 15600 restraints for refining 6453 atoms. 14591 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1888 (Rfree = 0.000) for 6453 atoms. Found 40 (41 requested) and removed 23 (20 requested) atoms. Cycle 42: After refmac, R = 0.1889 (Rfree = 0.000) for 6460 atoms. Found 41 (41 requested) and removed 24 (20 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 6471 atoms. Found 37 (41 requested) and removed 21 (20 requested) atoms. Cycle 44: After refmac, R = 0.1721 (Rfree = 0.000) for 6475 atoms. Found 31 (41 requested) and removed 26 (20 requested) atoms. Cycle 45: After refmac, R = 0.1472 (Rfree = 0.000) for 6475 atoms. Found 8 (41 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 6641 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6656 seeds are put forward Round 1: 239 peptides, 53 chains. Longest chain 9 peptides. Score 0.225 Round 2: 289 peptides, 52 chains. Longest chain 11 peptides. Score 0.330 Round 3: 283 peptides, 49 chains. Longest chain 13 peptides. Score 0.343 Round 4: 300 peptides, 48 chains. Longest chain 12 peptides. Score 0.381 Round 5: 302 peptides, 50 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 252, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (252 residues) following loop building 4 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10697 reflections ( 89.31 % complete ) and 15363 restraints for refining 6452 atoms. 14365 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1937 (Rfree = 0.000) for 6452 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1897 (Rfree = 0.000) for 6412 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1821 (Rfree = 0.000) for 6379 atoms. Found 0 (41 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1837 (Rfree = 0.000) for 6351 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:58:13 GMT 2018 Job finished. TimeTaking 90.27