Sun 23 Dec 22:22:49 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 2aml-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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/2aml-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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 ============================================================ Sun 23 Dec 22:22:59 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/2aml-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-3.4-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 474 and 0 Target number of residues in the AU: 474 Target solvent content: 0.6261 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-3.4-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: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.65 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: 77.491 3.400 Wilson plot Bfac: 64.20 9931 reflections ( 99.79 % complete ) and 0 restraints for refining 6672 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3101 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3008 (Rfree = 0.000) for 6672 atoms. Found 50 (50 requested) and removed 51 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 6849 seeds are put forward NCS extension: 0 residues added, 6849 seeds are put forward Round 1: 314 peptides, 63 chains. Longest chain 11 peptides. Score 0.327 Round 2: 397 peptides, 67 chains. Longest chain 14 peptides. Score 0.477 Round 3: 424 peptides, 67 chains. Longest chain 15 peptides. Score 0.530 Round 4: 446 peptides, 61 chains. Longest chain 32 peptides. Score 0.616 Round 5: 436 peptides, 64 chains. Longest chain 15 peptides. Score 0.576 Taking the results from Round 4 Chains 72, Residues 385, Estimated correctness of the model 33.8 % 7 chains (77 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11589 restraints for refining 5426 atoms. 9873 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2427 (Rfree = 0.000) for 5426 atoms. Found 27 (40 requested) and removed 48 (20 requested) atoms. Cycle 2: After refmac, R = 0.2221 (Rfree = 0.000) for 5335 atoms. Found 20 (40 requested) and removed 35 (20 requested) atoms. Cycle 3: After refmac, R = 0.2118 (Rfree = 0.000) for 5278 atoms. Found 24 (40 requested) and removed 30 (20 requested) atoms. Cycle 4: After refmac, R = 0.2091 (Rfree = 0.000) for 5249 atoms. Found 29 (39 requested) and removed 27 (19 requested) atoms. Cycle 5: After refmac, R = 0.2010 (Rfree = 0.000) for 5241 atoms. Found 29 (39 requested) and removed 32 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 5465 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5486 seeds are put forward Round 1: 368 peptides, 65 chains. Longest chain 13 peptides. Score 0.433 Round 2: 424 peptides, 62 chains. Longest chain 18 peptides. Score 0.570 Round 3: 428 peptides, 59 chains. Longest chain 15 peptides. Score 0.600 Round 4: 438 peptides, 60 chains. Longest chain 20 peptides. Score 0.610 Round 5: 445 peptides, 58 chains. Longest chain 20 peptides. Score 0.635 Taking the results from Round 5 Chains 60, Residues 387, Estimated correctness of the model 39.7 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11934 restraints for refining 5424 atoms. 10368 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2474 (Rfree = 0.000) for 5424 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 7: After refmac, R = 0.2216 (Rfree = 0.000) for 5391 atoms. Found 38 (41 requested) and removed 33 (20 requested) atoms. Cycle 8: After refmac, R = 0.1877 (Rfree = 0.000) for 5382 atoms. Found 18 (40 requested) and removed 22 (20 requested) atoms. Cycle 9: After refmac, R = 0.1786 (Rfree = 0.000) for 5370 atoms. Found 16 (40 requested) and removed 22 (20 requested) atoms. Cycle 10: After refmac, R = 0.1759 (Rfree = 0.000) for 5354 atoms. Found 6 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 5569 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 5591 seeds are put forward Round 1: 360 peptides, 60 chains. Longest chain 17 peptides. Score 0.462 Round 2: 415 peptides, 63 chains. Longest chain 20 peptides. Score 0.546 Round 3: 440 peptides, 62 chains. Longest chain 29 peptides. Score 0.598 Round 4: 434 peptides, 54 chains. Longest chain 22 peptides. Score 0.646 Round 5: 462 peptides, 62 chains. Longest chain 21 peptides. Score 0.634 Taking the results from Round 4 Chains 56, Residues 380, Estimated correctness of the model 43.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11867 restraints for refining 5427 atoms. 10273 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2337 (Rfree = 0.000) for 5427 atoms. Found 27 (40 requested) and removed 44 (20 requested) atoms. Cycle 12: After refmac, R = 0.2220 (Rfree = 0.000) for 5392 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. Cycle 13: After refmac, R = 0.2096 (Rfree = 0.000) for 5387 atoms. Found 38 (40 requested) and removed 27 (20 requested) atoms. Cycle 14: After refmac, R = 0.1983 (Rfree = 0.000) for 5383 atoms. Found 26 (40 requested) and removed 24 (20 requested) atoms. Cycle 15: After refmac, R = 0.1979 (Rfree = 0.000) for 5375 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 5585 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5604 seeds are put forward Round 1: 347 peptides, 62 chains. Longest chain 16 peptides. Score 0.415 Round 2: 396 peptides, 59 chains. Longest chain 23 peptides. Score 0.543 Round 3: 411 peptides, 56 chains. Longest chain 28 peptides. Score 0.594 Round 4: 405 peptides, 57 chains. Longest chain 22 peptides. Score 0.576 Round 5: 423 peptides, 55 chains. Longest chain 22 peptides. Score 0.622 Taking the results from Round 5 Chains 56, Residues 368, Estimated correctness of the model 35.7 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11870 restraints for refining 5426 atoms. 10333 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2368 (Rfree = 0.000) for 5426 atoms. Found 32 (40 requested) and removed 38 (20 requested) atoms. Cycle 17: After refmac, R = 0.2203 (Rfree = 0.000) for 5395 atoms. Found 40 (40 requested) and removed 36 (20 requested) atoms. Cycle 18: After refmac, R = 0.2034 (Rfree = 0.000) for 5377 atoms. Found 40 (40 requested) and removed 27 (20 requested) atoms. Cycle 19: After refmac, R = 0.1909 (Rfree = 0.000) for 5383 atoms. Found 40 (40 requested) and removed 23 (20 requested) atoms. Cycle 20: After refmac, R = 0.1535 (Rfree = 0.000) for 5388 atoms. Found 16 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 5637 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5655 seeds are put forward Round 1: 317 peptides, 61 chains. Longest chain 12 peptides. Score 0.355 Round 2: 372 peptides, 56 chains. Longest chain 19 peptides. Score 0.522 Round 3: 392 peptides, 56 chains. Longest chain 18 peptides. Score 0.560 Round 4: 389 peptides, 54 chains. Longest chain 32 peptides. Score 0.571 Round 5: 382 peptides, 53 chains. Longest chain 23 peptides. Score 0.566 Taking the results from Round 4 Chains 56, Residues 335, Estimated correctness of the model 18.9 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 11942 restraints for refining 5427 atoms. 10502 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2106 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1893 (Rfree = 0.000) for 5417 atoms. Found 35 (41 requested) and removed 26 (20 requested) atoms. Cycle 23: After refmac, R = 0.1868 (Rfree = 0.000) for 5408 atoms. Found 35 (40 requested) and removed 25 (20 requested) atoms. Cycle 24: After refmac, R = 0.1861 (Rfree = 0.000) for 5413 atoms. Found 40 (40 requested) and removed 24 (20 requested) atoms. Cycle 25: After refmac, R = 0.1787 (Rfree = 0.000) for 5418 atoms. Found 40 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 5648 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5666 seeds are put forward Round 1: 302 peptides, 55 chains. Longest chain 18 peptides. Score 0.380 Round 2: 363 peptides, 53 chains. Longest chain 25 peptides. Score 0.530 Round 3: 354 peptides, 52 chains. Longest chain 20 peptides. Score 0.521 Round 4: 361 peptides, 49 chains. Longest chain 18 peptides. Score 0.560 Round 5: 350 peptides, 48 chains. Longest chain 23 peptides. Score 0.547 Taking the results from Round 4 Chains 50, Residues 312, Estimated correctness of the model 15.1 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12470 restraints for refining 5427 atoms. 11243 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2028 (Rfree = 0.000) for 5427 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 27: After refmac, R = 0.1975 (Rfree = 0.000) for 5428 atoms. Found 41 (41 requested) and removed 24 (20 requested) atoms. Cycle 28: After refmac, R = 0.1783 (Rfree = 0.000) for 5431 atoms. Found 34 (41 requested) and removed 25 (20 requested) atoms. Cycle 29: After refmac, R = 0.1661 (Rfree = 0.000) for 5436 atoms. Found 37 (41 requested) and removed 21 (20 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1355 (Rfree = 0.000) for 5448 atoms. Found 10 (41 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 5639 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 5663 seeds are put forward Round 1: 315 peptides, 58 chains. Longest chain 24 peptides. Score 0.380 Round 2: 333 peptides, 50 chains. Longest chain 25 peptides. Score 0.496 Round 3: 347 peptides, 51 chains. Longest chain 20 peptides. Score 0.516 Round 4: 359 peptides, 52 chains. Longest chain 25 peptides. Score 0.531 Round 5: 352 peptides, 53 chains. Longest chain 17 peptides. Score 0.508 Taking the results from Round 4 Chains 53, Residues 307, Estimated correctness of the model 4.6 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12328 restraints for refining 5425 atoms. 11092 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1838 (Rfree = 0.000) for 5425 atoms. Found 40 (40 requested) and removed 24 (20 requested) atoms. Cycle 32: After refmac, R = 0.1743 (Rfree = 0.000) for 5433 atoms. Found 35 (41 requested) and removed 22 (20 requested) atoms. Cycle 33: After refmac, R = 0.1674 (Rfree = 0.000) for 5434 atoms. Found 36 (41 requested) and removed 20 (20 requested) atoms. Cycle 34: After refmac, R = 0.1835 (Rfree = 0.000) for 5443 atoms. Found 41 (41 requested) and removed 25 (20 requested) atoms. Cycle 35: After refmac, R = 0.1579 (Rfree = 0.000) for 5447 atoms. Found 32 (41 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 5670 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 5701 seeds are put forward Round 1: 276 peptides, 49 chains. Longest chain 13 peptides. Score 0.379 Round 2: 314 peptides, 46 chains. Longest chain 16 peptides. Score 0.493 Round 3: 323 peptides, 46 chains. Longest chain 24 peptides. Score 0.512 Round 4: 308 peptides, 48 chains. Longest chain 19 peptides. Score 0.462 Round 5: 324 peptides, 45 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 5 Chains 45, Residues 279, Estimated correctness of the model 1.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12771 restraints for refining 5427 atoms. 11700 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1973 (Rfree = 0.000) for 5427 atoms. Found 34 (40 requested) and removed 28 (20 requested) atoms. Cycle 37: After refmac, R = 0.1998 (Rfree = 0.000) for 5424 atoms. Found 41 (41 requested) and removed 23 (20 requested) atoms. Cycle 38: After refmac, R = 0.1904 (Rfree = 0.000) for 5427 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 39: After refmac, R = 0.2042 (Rfree = 0.000) for 5437 atoms. Found 41 (41 requested) and removed 30 (20 requested) atoms. Cycle 40: After refmac, R = 0.2440 (Rfree = 0.000) for 5442 atoms. Found 41 (41 requested) and removed 33 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.71 Search for helices and strands: 0 residues in 0 chains, 5662 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5684 seeds are put forward Round 1: 260 peptides, 50 chains. Longest chain 13 peptides. Score 0.329 Round 2: 287 peptides, 47 chains. Longest chain 15 peptides. Score 0.425 Round 3: 273 peptides, 44 chains. Longest chain 13 peptides. Score 0.423 Round 4: 283 peptides, 44 chains. Longest chain 14 peptides. Score 0.445 Round 5: 290 peptides, 47 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 4 Chains 46, Residues 239, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9931 reflections ( 99.79 % complete ) and 12711 restraints for refining 5425 atoms. 11763 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2024 (Rfree = 0.000) for 5425 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 42: After refmac, R = 0.1874 (Rfree = 0.000) for 5420 atoms. Found 41 (41 requested) and removed 27 (20 requested) atoms. Cycle 43: After refmac, R = 0.1862 (Rfree = 0.000) for 5424 atoms. Found 41 (41 requested) and removed 24 (20 requested) atoms. Cycle 44: After refmac, R = 0.1483 (Rfree = 0.000) for 5431 atoms. Found 12 (41 requested) and removed 20 (20 requested) atoms. Cycle 45: After refmac, R = 0.1429 (Rfree = 0.000) for 5418 atoms. Found 23 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 5578 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5590 seeds are put forward Round 1: 241 peptides, 47 chains. Longest chain 12 peptides. Score 0.313 Round 2: 291 peptides, 49 chains. Longest chain 12 peptides. Score 0.414 Round 3: 297 peptides, 49 chains. Longest chain 16 peptides. Score 0.428 Round 4: 300 peptides, 49 chains. Longest chain 14 peptides. Score 0.434 Round 5: 277 peptides, 45 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 251, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (251 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9931 reflections ( 99.79 % complete ) and 12436 restraints for refining 5427 atoms. 11431 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2307 (Rfree = 0.000) for 5427 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.2359 (Rfree = 0.000) for 5382 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1948 (Rfree = 0.000) for 5348 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2190 (Rfree = 0.000) for 5311 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... TimeTaking 73.68