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 1vr0-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-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/1vr0-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-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/1vr0-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.2-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 523 and 0 Target number of residues in the AU: 523 Target solvent content: 0.6136 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.2-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5928 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: 226.759 3.200 Wilson plot Bfac: 58.25 12698 reflections ( 99.73 % complete ) and 0 restraints for refining 6526 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3096 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2485 (Rfree = 0.000) for 6526 atoms. Found 58 (58 requested) and removed 77 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 6640 seeds are put forward NCS extension: 0 residues added, 6640 seeds are put forward Round 1: 361 peptides, 66 chains. Longest chain 14 peptides. Score 0.396 Round 2: 435 peptides, 65 chains. Longest chain 16 peptides. Score 0.549 Round 3: 457 peptides, 58 chains. Longest chain 27 peptides. Score 0.635 Round 4: 464 peptides, 52 chains. Longest chain 26 peptides. Score 0.683 Round 5: 480 peptides, 57 chains. Longest chain 22 peptides. Score 0.674 Taking the results from Round 4 Chains 55, Residues 412, Estimated correctness of the model 61.5 % 5 chains (65 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11153 restraints for refining 5410 atoms. 9303 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2372 (Rfree = 0.000) for 5410 atoms. Found 40 (48 requested) and removed 44 (24 requested) atoms. Cycle 2: After refmac, R = 0.2217 (Rfree = 0.000) for 5350 atoms. Found 14 (48 requested) and removed 31 (24 requested) atoms. Cycle 3: After refmac, R = 0.2190 (Rfree = 0.000) for 5306 atoms. Found 20 (47 requested) and removed 24 (23 requested) atoms. Cycle 4: After refmac, R = 0.2156 (Rfree = 0.000) for 5287 atoms. Found 9 (47 requested) and removed 23 (23 requested) atoms. Cycle 5: After refmac, R = 0.2137 (Rfree = 0.000) for 5264 atoms. Found 9 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 5411 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 5427 seeds are put forward Round 1: 429 peptides, 61 chains. Longest chain 19 peptides. Score 0.569 Round 2: 486 peptides, 56 chains. Longest chain 40 peptides. Score 0.688 Round 3: 487 peptides, 59 chains. Longest chain 24 peptides. Score 0.671 Round 4: 484 peptides, 54 chains. Longest chain 18 peptides. Score 0.697 Round 5: 494 peptides, 51 chains. Longest chain 34 peptides. Score 0.726 Taking the results from Round 5 Chains 52, Residues 443, Estimated correctness of the model 70.5 % 6 chains (89 residues) have been docked in sequence Building loops using Loopy2018 52 chains (443 residues) following loop building 6 chains (89 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11072 restraints for refining 5395 atoms. 9046 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2547 (Rfree = 0.000) for 5395 atoms. Found 28 (48 requested) and removed 49 (24 requested) atoms. Cycle 7: After refmac, R = 0.2346 (Rfree = 0.000) for 5355 atoms. Found 19 (47 requested) and removed 28 (24 requested) atoms. Cycle 8: After refmac, R = 0.2243 (Rfree = 0.000) for 5336 atoms. Found 13 (45 requested) and removed 26 (23 requested) atoms. Cycle 9: After refmac, R = 0.2162 (Rfree = 0.000) for 5318 atoms. Found 7 (44 requested) and removed 24 (23 requested) atoms. Cycle 10: After refmac, R = 0.2134 (Rfree = 0.000) for 5296 atoms. Found 6 (43 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 5447 seeds are put forward NCS extension: 25 residues added (28 deleted due to clashes), 5472 seeds are put forward Round 1: 440 peptides, 57 chains. Longest chain 22 peptides. Score 0.616 Round 2: 479 peptides, 47 chains. Longest chain 29 peptides. Score 0.730 Round 3: 483 peptides, 47 chains. Longest chain 29 peptides. Score 0.735 Round 4: 484 peptides, 49 chains. Longest chain 26 peptides. Score 0.725 Round 5: 477 peptides, 47 chains. Longest chain 26 peptides. Score 0.728 Taking the results from Round 3 Chains 48, Residues 436, Estimated correctness of the model 72.3 % 3 chains (40 residues) have been docked in sequence Building loops using Loopy2018 48 chains (436 residues) following loop building 3 chains (40 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11485 restraints for refining 5373 atoms. 9632 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2288 (Rfree = 0.000) for 5373 atoms. Found 28 (43 requested) and removed 31 (24 requested) atoms. Cycle 12: After refmac, R = 0.2109 (Rfree = 0.000) for 5355 atoms. Found 7 (42 requested) and removed 25 (24 requested) atoms. Cycle 13: After refmac, R = 0.2068 (Rfree = 0.000) for 5332 atoms. Found 11 (40 requested) and removed 23 (23 requested) atoms. Cycle 14: After refmac, R = 0.2002 (Rfree = 0.000) for 5316 atoms. Found 5 (39 requested) and removed 23 (23 requested) atoms. Cycle 15: After refmac, R = 0.1968 (Rfree = 0.000) for 5297 atoms. Found 2 (39 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 5469 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 5513 seeds are put forward Round 1: 404 peptides, 55 chains. Longest chain 16 peptides. Score 0.571 Round 2: 449 peptides, 53 chains. Longest chain 23 peptides. Score 0.656 Round 3: 448 peptides, 52 chains. Longest chain 31 peptides. Score 0.661 Round 4: 455 peptides, 46 chains. Longest chain 24 peptides. Score 0.707 Round 5: 450 peptides, 50 chains. Longest chain 23 peptides. Score 0.676 Taking the results from Round 4 Chains 49, Residues 409, Estimated correctness of the model 66.7 % 4 chains (48 residues) have been docked in sequence Building loops using Loopy2018 49 chains (409 residues) following loop building 4 chains (48 residues) in sequence following loop building ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11614 restraints for refining 5411 atoms. 9824 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2271 (Rfree = 0.000) for 5411 atoms. Found 37 (38 requested) and removed 27 (24 requested) atoms. Cycle 17: After refmac, R = 0.2100 (Rfree = 0.000) for 5405 atoms. Found 13 (37 requested) and removed 26 (24 requested) atoms. Cycle 18: After refmac, R = 0.2061 (Rfree = 0.000) for 5384 atoms. Found 8 (36 requested) and removed 25 (24 requested) atoms. Cycle 19: After refmac, R = 0.2003 (Rfree = 0.000) for 5360 atoms. Found 7 (36 requested) and removed 24 (24 requested) atoms. Cycle 20: After refmac, R = 0.1977 (Rfree = 0.000) for 5337 atoms. Found 5 (34 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 5490 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 5500 seeds are put forward Round 1: 411 peptides, 58 chains. Longest chain 20 peptides. Score 0.561 Round 2: 441 peptides, 59 chains. Longest chain 20 peptides. Score 0.603 Round 3: 447 peptides, 51 chains. Longest chain 30 peptides. Score 0.666 Round 4: 436 peptides, 49 chains. Longest chain 45 peptides. Score 0.663 Round 5: 440 peptides, 56 chains. Longest chain 27 peptides. Score 0.623 Taking the results from Round 3 Chains 52, Residues 396, Estimated correctness of the model 57.6 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11691 restraints for refining 5412 atoms. 9974 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2119 (Rfree = 0.000) for 5412 atoms. Found 33 (34 requested) and removed 34 (24 requested) atoms. Cycle 22: After refmac, R = 0.1964 (Rfree = 0.000) for 5403 atoms. Found 7 (34 requested) and removed 25 (24 requested) atoms. Cycle 23: After refmac, R = 0.1930 (Rfree = 0.000) for 5380 atoms. Found 6 (34 requested) and removed 24 (24 requested) atoms. Cycle 24: After refmac, R = 0.1866 (Rfree = 0.000) for 5360 atoms. Found 8 (34 requested) and removed 24 (24 requested) atoms. Cycle 25: After refmac, R = 0.1836 (Rfree = 0.000) for 5337 atoms. Found 5 (33 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 5516 seeds are put forward NCS extension: 32 residues added (4 deleted due to clashes), 5548 seeds are put forward Round 1: 394 peptides, 54 chains. Longest chain 24 peptides. Score 0.562 Round 2: 426 peptides, 50 chains. Longest chain 31 peptides. Score 0.642 Round 3: 448 peptides, 49 chains. Longest chain 40 peptides. Score 0.680 Round 4: 453 peptides, 51 chains. Longest chain 31 peptides. Score 0.674 Round 5: 437 peptides, 51 chains. Longest chain 31 peptides. Score 0.652 Taking the results from Round 3 Chains 51, Residues 399, Estimated correctness of the model 60.8 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11484 restraints for refining 5412 atoms. 9737 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2069 (Rfree = 0.000) for 5412 atoms. Found 34 (34 requested) and removed 35 (24 requested) atoms. Cycle 27: After refmac, R = 0.1937 (Rfree = 0.000) for 5400 atoms. Found 17 (34 requested) and removed 25 (24 requested) atoms. Cycle 28: After refmac, R = 0.1867 (Rfree = 0.000) for 5389 atoms. Found 8 (34 requested) and removed 25 (24 requested) atoms. Cycle 29: After refmac, R = 0.1826 (Rfree = 0.000) for 5368 atoms. Found 10 (34 requested) and removed 24 (24 requested) atoms. Cycle 30: After refmac, R = 0.1819 (Rfree = 0.000) for 5350 atoms. Found 17 (34 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 5551 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 5581 seeds are put forward Round 1: 367 peptides, 54 chains. Longest chain 20 peptides. Score 0.513 Round 2: 426 peptides, 53 chains. Longest chain 25 peptides. Score 0.622 Round 3: 432 peptides, 47 chains. Longest chain 24 peptides. Score 0.671 Round 4: 435 peptides, 49 chains. Longest chain 31 peptides. Score 0.662 Round 5: 402 peptides, 51 chains. Longest chain 38 peptides. Score 0.598 Taking the results from Round 3 Chains 48, Residues 385, Estimated correctness of the model 58.8 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11623 restraints for refining 5412 atoms. 9964 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2037 (Rfree = 0.000) for 5412 atoms. Found 34 (34 requested) and removed 27 (24 requested) atoms. Cycle 32: After refmac, R = 0.1881 (Rfree = 0.000) for 5413 atoms. Found 17 (34 requested) and removed 24 (24 requested) atoms. Cycle 33: After refmac, R = 0.1943 (Rfree = 0.000) for 5401 atoms. Found 16 (34 requested) and removed 27 (24 requested) atoms. Cycle 34: After refmac, R = 0.1853 (Rfree = 0.000) for 5384 atoms. Found 18 (34 requested) and removed 24 (24 requested) atoms. Cycle 35: After refmac, R = 0.1816 (Rfree = 0.000) for 5376 atoms. Found 7 (34 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.29 Search for helices and strands: 0 residues in 0 chains, 5550 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5571 seeds are put forward Round 1: 370 peptides, 53 chains. Longest chain 18 peptides. Score 0.527 Round 2: 407 peptides, 52 chains. Longest chain 23 peptides. Score 0.599 Round 3: 411 peptides, 50 chains. Longest chain 51 peptides. Score 0.619 Round 4: 407 peptides, 51 chains. Longest chain 16 peptides. Score 0.606 Round 5: 407 peptides, 48 chains. Longest chain 21 peptides. Score 0.627 Taking the results from Round 5 Chains 50, Residues 359, Estimated correctness of the model 48.1 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11864 restraints for refining 5412 atoms. 10301 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2119 (Rfree = 0.000) for 5412 atoms. Found 34 (34 requested) and removed 29 (24 requested) atoms. Cycle 37: After refmac, R = 0.1962 (Rfree = 0.000) for 5408 atoms. Found 21 (34 requested) and removed 24 (24 requested) atoms. Cycle 38: After refmac, R = 0.1924 (Rfree = 0.000) for 5401 atoms. Found 18 (34 requested) and removed 24 (24 requested) atoms. Cycle 39: After refmac, R = 0.1885 (Rfree = 0.000) for 5385 atoms. Found 17 (34 requested) and removed 25 (24 requested) atoms. Cycle 40: After refmac, R = 0.1824 (Rfree = 0.000) for 5374 atoms. Found 11 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 5521 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 5536 seeds are put forward Round 1: 350 peptides, 55 chains. Longest chain 21 peptides. Score 0.471 Round 2: 388 peptides, 49 chains. Longest chain 31 peptides. Score 0.590 Round 3: 379 peptides, 47 chains. Longest chain 19 peptides. Score 0.590 Round 4: 375 peptides, 47 chains. Longest chain 22 peptides. Score 0.583 Round 5: 396 peptides, 43 chains. Longest chain 30 peptides. Score 0.646 Taking the results from Round 5 Chains 44, Residues 353, Estimated correctness of the model 52.9 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ 12698 reflections ( 99.73 % complete ) and 11798 restraints for refining 5411 atoms. 10195 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2082 (Rfree = 0.000) for 5411 atoms. Found 34 (34 requested) and removed 36 (24 requested) atoms. Cycle 42: After refmac, R = 0.1908 (Rfree = 0.000) for 5401 atoms. Found 18 (34 requested) and removed 24 (24 requested) atoms. Cycle 43: After refmac, R = 0.1845 (Rfree = 0.000) for 5393 atoms. Found 9 (34 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.1800 (Rfree = 0.000) for 5373 atoms. Found 9 (34 requested) and removed 25 (24 requested) atoms. Cycle 45: After refmac, R = 0.1770 (Rfree = 0.000) for 5356 atoms. Found 7 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 3.27 Search for helices and strands: 0 residues in 0 chains, 5524 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5550 seeds are put forward Round 1: 356 peptides, 55 chains. Longest chain 21 peptides. Score 0.483 Round 2: 372 peptides, 51 chains. Longest chain 18 peptides. Score 0.547 Round 3: 401 peptides, 51 chains. Longest chain 28 peptides. Score 0.596 Round 4: 386 peptides, 47 chains. Longest chain 26 peptides. Score 0.601 Round 5: 388 peptides, 49 chains. Longest chain 25 peptides. Score 0.590 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 339, Estimated correctness of the model 41.3 % 3 chains (40 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input Building loops using Loopy2018 48 chains (339 residues) following loop building 3 chains (40 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12698 reflections ( 99.73 % complete ) and 11940 restraints for refining 5412 atoms. 10469 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2004 (Rfree = 0.000) for 5412 atoms. Found 0 (34 requested) and removed 17 (24 requested) atoms. Cycle 47: After refmac, R = 0.1921 (Rfree = 0.000) for 5386 atoms. Found 0 (34 requested) and removed 2 (24 requested) atoms. Cycle 48: After refmac, R = 0.1862 (Rfree = 0.000) for 5384 atoms. Found 0 (34 requested) and removed 3 (24 requested) atoms. Cycle 49: After refmac, R = 0.1822 (Rfree = 0.000) for 5379 atoms. Found 0 (34 requested) and removed 3 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:56:57 GMT 2018 Job finished. TimeTaking 89 Used memory is bytes: 22440800