null 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 2pgc-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-4.0-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/2pgc-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-4.0-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/2pgc-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-4.0-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 708 and 0 Target number of residues in the AU: 708 Target solvent content: 0.6719 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-4.0-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 8280 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: 98.043 4.000 Wilson plot Bfac: 93.78 10366 reflections ( 99.41 % complete ) and 0 restraints for refining 9194 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3505 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3342 (Rfree = 0.000) for 9194 atoms. Found 43 (43 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.95 3.85 Search for helices and strands: 0 residues in 0 chains, 9361 seeds are put forward NCS extension: 0 residues added, 9361 seeds are put forward Round 1: 299 peptides, 64 chains. Longest chain 10 peptides. Score 0.243 Round 2: 407 peptides, 67 chains. Longest chain 17 peptides. Score 0.391 Round 3: 437 peptides, 66 chains. Longest chain 21 peptides. Score 0.438 Round 4: 447 peptides, 68 chains. Longest chain 20 peptides. Score 0.440 Round 5: 485 peptides, 69 chains. Longest chain 26 peptides. Score 0.483 Taking the results from Round 5 Chains 69, Residues 416, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17752 restraints for refining 7473 atoms. 16134 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3101 (Rfree = 0.000) for 7473 atoms. Found 25 (35 requested) and removed 31 (17 requested) atoms. Cycle 2: After refmac, R = 0.2703 (Rfree = 0.000) for 7302 atoms. Found 17 (35 requested) and removed 28 (17 requested) atoms. Cycle 3: After refmac, R = 0.2494 (Rfree = 0.000) for 7175 atoms. Found 16 (34 requested) and removed 25 (17 requested) atoms. Cycle 4: After refmac, R = 0.2125 (Rfree = 0.000) for 7107 atoms. Found 7 (34 requested) and removed 20 (17 requested) atoms. Cycle 5: After refmac, R = 0.2206 (Rfree = 0.000) for 7048 atoms. Found 13 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7256 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7281 seeds are put forward Round 1: 366 peptides, 74 chains. Longest chain 11 peptides. Score 0.284 Round 2: 448 peptides, 73 chains. Longest chain 12 peptides. Score 0.411 Round 3: 478 peptides, 78 chains. Longest chain 15 peptides. Score 0.422 Round 4: 474 peptides, 75 chains. Longest chain 19 peptides. Score 0.434 Round 5: 489 peptides, 76 chains. Longest chain 17 peptides. Score 0.448 Taking the results from Round 5 Chains 76, Residues 413, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 16614 restraints for refining 7108 atoms. 15038 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2195 (Rfree = 0.000) for 7108 atoms. Found 24 (33 requested) and removed 43 (16 requested) atoms. Cycle 7: After refmac, R = 0.1889 (Rfree = 0.000) for 7026 atoms. Found 13 (33 requested) and removed 23 (16 requested) atoms. Cycle 8: After refmac, R = 0.1822 (Rfree = 0.000) for 6995 atoms. Found 8 (33 requested) and removed 20 (16 requested) atoms. Cycle 9: After refmac, R = 0.1803 (Rfree = 0.000) for 6980 atoms. Found 3 (33 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.1761 (Rfree = 0.000) for 6963 atoms. Found 4 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7127 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7151 seeds are put forward Round 1: 436 peptides, 85 chains. Longest chain 11 peptides. Score 0.320 Round 2: 484 peptides, 83 chains. Longest chain 13 peptides. Score 0.401 Round 3: 477 peptides, 72 chains. Longest chain 19 peptides. Score 0.456 Round 4: 476 peptides, 69 chains. Longest chain 16 peptides. Score 0.472 Round 5: 478 peptides, 71 chains. Longest chain 16 peptides. Score 0.463 Taking the results from Round 4 Chains 69, Residues 407, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17287 restraints for refining 7410 atoms. 15655 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2118 (Rfree = 0.000) for 7410 atoms. Found 17 (35 requested) and removed 47 (17 requested) atoms. Cycle 12: After refmac, R = 0.1971 (Rfree = 0.000) for 7331 atoms. Found 9 (35 requested) and removed 24 (17 requested) atoms. Cycle 13: After refmac, R = 0.1940 (Rfree = 0.000) for 7303 atoms. Found 3 (34 requested) and removed 20 (17 requested) atoms. Cycle 14: After refmac, R = 0.1906 (Rfree = 0.000) for 7281 atoms. Found 3 (34 requested) and removed 18 (17 requested) atoms. Cycle 15: After refmac, R = 0.1897 (Rfree = 0.000) for 7261 atoms. Found 1 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 7450 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 7461 seeds are put forward Round 1: 404 peptides, 80 chains. Longest chain 12 peptides. Score 0.304 Round 2: 473 peptides, 74 chains. Longest chain 17 peptides. Score 0.439 Round 3: 464 peptides, 73 chains. Longest chain 14 peptides. Score 0.433 Round 4: 458 peptides, 71 chains. Longest chain 18 peptides. Score 0.437 Round 5: 459 peptides, 73 chains. Longest chain 16 peptides. Score 0.426 Taking the results from Round 2 Chains 74, Residues 399, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17409 restraints for refining 7432 atoms. 15851 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2114 (Rfree = 0.000) for 7432 atoms. Found 19 (35 requested) and removed 31 (17 requested) atoms. Cycle 17: After refmac, R = 0.1922 (Rfree = 0.000) for 7375 atoms. Found 8 (35 requested) and removed 28 (17 requested) atoms. Cycle 18: After refmac, R = 0.1956 (Rfree = 0.000) for 7341 atoms. Found 5 (34 requested) and removed 20 (17 requested) atoms. Cycle 19: After refmac, R = 0.1920 (Rfree = 0.000) for 7322 atoms. Found 4 (34 requested) and removed 23 (17 requested) atoms. Cycle 20: After refmac, R = 0.1910 (Rfree = 0.000) for 7299 atoms. Found 2 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 7490 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7503 seeds are put forward Round 1: 413 peptides, 83 chains. Longest chain 12 peptides. Score 0.298 Round 2: 459 peptides, 76 chains. Longest chain 15 peptides. Score 0.408 Round 3: 458 peptides, 77 chains. Longest chain 12 peptides. Score 0.401 Round 4: 444 peptides, 65 chains. Longest chain 24 peptides. Score 0.453 Round 5: 472 peptides, 74 chains. Longest chain 19 peptides. Score 0.438 Taking the results from Round 4 Chains 65, Residues 379, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17837 restraints for refining 7477 atoms. 16347 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 7477 atoms. Found 30 (35 requested) and removed 30 (17 requested) atoms. Cycle 22: After refmac, R = 0.2145 (Rfree = 0.000) for 7448 atoms. Found 10 (35 requested) and removed 19 (17 requested) atoms. Cycle 23: After refmac, R = 0.2011 (Rfree = 0.000) for 7431 atoms. Found 5 (35 requested) and removed 20 (17 requested) atoms. Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 7412 atoms. Found 3 (35 requested) and removed 19 (17 requested) atoms. Cycle 25: After refmac, R = 0.2030 (Rfree = 0.000) for 7390 atoms. Found 17 (35 requested) and removed 114 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 7446 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7463 seeds are put forward Round 1: 368 peptides, 78 chains. Longest chain 10 peptides. Score 0.261 Round 2: 401 peptides, 69 chains. Longest chain 12 peptides. Score 0.369 Round 3: 402 peptides, 67 chains. Longest chain 13 peptides. Score 0.384 Round 4: 418 peptides, 64 chains. Longest chain 19 peptides. Score 0.424 Round 5: 426 peptides, 65 chains. Longest chain 22 peptides. Score 0.429 Taking the results from Round 5 Chains 65, Residues 361, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17810 restraints for refining 7478 atoms. 16343 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2157 (Rfree = 0.000) for 7478 atoms. Found 15 (35 requested) and removed 39 (17 requested) atoms. Cycle 27: After refmac, R = 0.2319 (Rfree = 0.000) for 7397 atoms. Found 35 (35 requested) and removed 34 (17 requested) atoms. Cycle 28: After refmac, R = 0.1893 (Rfree = 0.000) for 7335 atoms. Found 17 (35 requested) and removed 23 (17 requested) atoms. Cycle 29: After refmac, R = 0.1779 (Rfree = 0.000) for 7291 atoms. Found 13 (34 requested) and removed 22 (17 requested) atoms. Cycle 30: After refmac, R = 0.1576 (Rfree = 0.000) for 7261 atoms. Found 1 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 7425 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 7462 seeds are put forward Round 1: 353 peptides, 77 chains. Longest chain 8 peptides. Score 0.243 Round 2: 406 peptides, 75 chains. Longest chain 13 peptides. Score 0.339 Round 3: 402 peptides, 72 chains. Longest chain 12 peptides. Score 0.352 Round 4: 428 peptides, 72 chains. Longest chain 13 peptides. Score 0.389 Round 5: 428 peptides, 74 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 4 Chains 72, Residues 356, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17625 restraints for refining 7427 atoms. 16273 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2128 (Rfree = 0.000) for 7427 atoms. Found 31 (35 requested) and removed 71 (17 requested) atoms. Cycle 32: After refmac, R = 0.1825 (Rfree = 0.000) for 7319 atoms. Found 13 (35 requested) and removed 32 (17 requested) atoms. Cycle 33: After refmac, R = 0.1547 (Rfree = 0.000) for 7259 atoms. Found 7 (34 requested) and removed 24 (17 requested) atoms. Cycle 34: After refmac, R = 0.1445 (Rfree = 0.000) for 7221 atoms. Found 6 (34 requested) and removed 25 (17 requested) atoms. Cycle 35: After refmac, R = 0.1420 (Rfree = 0.000) for 7191 atoms. Found 6 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7355 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7373 seeds are put forward Round 1: 309 peptides, 64 chains. Longest chain 9 peptides. Score 0.260 Round 2: 375 peptides, 68 chains. Longest chain 18 peptides. Score 0.337 Round 3: 396 peptides, 67 chains. Longest chain 18 peptides. Score 0.375 Round 4: 415 peptides, 67 chains. Longest chain 17 peptides. Score 0.402 Round 5: 399 peptides, 66 chains. Longest chain 17 peptides. Score 0.385 Taking the results from Round 4 Chains 67, Residues 348, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17327 restraints for refining 7405 atoms. 15966 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2147 (Rfree = 0.000) for 7405 atoms. Found 35 (35 requested) and removed 46 (17 requested) atoms. Cycle 37: After refmac, R = 0.2011 (Rfree = 0.000) for 7342 atoms. Found 35 (35 requested) and removed 43 (17 requested) atoms. Cycle 38: After refmac, R = 0.1829 (Rfree = 0.000) for 7273 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 39: After refmac, R = 0.1592 (Rfree = 0.000) for 7262 atoms. Found 15 (34 requested) and removed 24 (17 requested) atoms. Cycle 40: After refmac, R = 0.1371 (Rfree = 0.000) for 7237 atoms. Found 2 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 7402 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7420 seeds are put forward Round 1: 291 peptides, 64 chains. Longest chain 10 peptides. Score 0.230 Round 2: 361 peptides, 68 chains. Longest chain 14 peptides. Score 0.316 Round 3: 382 peptides, 68 chains. Longest chain 15 peptides. Score 0.348 Round 4: 377 peptides, 71 chains. Longest chain 10 peptides. Score 0.321 Round 5: 377 peptides, 68 chains. Longest chain 11 peptides. Score 0.340 Taking the results from Round 3 Chains 68, Residues 314, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17416 restraints for refining 7368 atoms. 16228 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1781 (Rfree = 0.000) for 7368 atoms. Found 16 (35 requested) and removed 27 (17 requested) atoms. Cycle 42: After refmac, R = 0.1605 (Rfree = 0.000) for 7311 atoms. Found 8 (34 requested) and removed 19 (17 requested) atoms. Cycle 43: After refmac, R = 0.1615 (Rfree = 0.000) for 7287 atoms. Found 7 (34 requested) and removed 20 (17 requested) atoms. Cycle 44: After refmac, R = 0.1597 (Rfree = 0.000) for 7272 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1618 (Rfree = 0.000) for 7261 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 7407 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 7436 seeds are put forward Round 1: 327 peptides, 70 chains. Longest chain 10 peptides. Score 0.248 Round 2: 371 peptides, 68 chains. Longest chain 13 peptides. Score 0.331 Round 3: 379 peptides, 68 chains. Longest chain 13 peptides. Score 0.343 Round 4: 382 peptides, 69 chains. Longest chain 13 peptides. Score 0.341 Round 5: 385 peptides, 65 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 320, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2pgc-4_warpNtrace.pdb as input Building loops using Loopy2018 65 chains (320 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10366 reflections ( 99.41 % complete ) and 17764 restraints for refining 7478 atoms. 16535 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1995 (Rfree = 0.000) for 7478 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1756 (Rfree = 0.000) for 7411 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1765 (Rfree = 0.000) for 7386 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1781 (Rfree = 0.000) for 7369 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:11:16 GMT 2018 Job finished. TimeTaking 103.32 Used memory is bytes: 20564536