Mon 24 Dec 00:37:06 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 2aml-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-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/2aml-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-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 ============================================================ Mon 24 Dec 00:37:10 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/2aml-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-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 492 and 0 Target number of residues in the AU: 492 Target solvent content: 0.6119 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-3.2-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: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.2-parrot-mrncs.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 3.200 Wilson plot Bfac: 57.53 11884 reflections ( 99.82 % complete ) and 0 restraints for refining 6569 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3053 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2665 (Rfree = 0.000) for 6569 atoms. Found 58 (58 requested) and removed 51 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.51 Search for helices and strands: 0 residues in 0 chains, 6732 seeds are put forward NCS extension: 0 residues added, 6732 seeds are put forward Round 1: 337 peptides, 65 chains. Longest chain 16 peptides. Score 0.363 Round 2: 441 peptides, 68 chains. Longest chain 15 peptides. Score 0.554 Round 3: 471 peptides, 63 chains. Longest chain 20 peptides. Score 0.641 Round 4: 496 peptides, 60 chains. Longest chain 36 peptides. Score 0.696 Round 5: 504 peptides, 61 chains. Longest chain 22 peptides. Score 0.701 Taking the results from Round 5 Chains 70, Residues 443, Estimated correctness of the model 65.4 % 8 chains (80 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 B and 222 B 68 chains (443 residues) following loop building 7 chains (88 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11095 restraints for refining 5447 atoms. 9120 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2506 (Rfree = 0.000) for 5447 atoms. Found 45 (48 requested) and removed 50 (24 requested) atoms. Cycle 2: After refmac, R = 0.2293 (Rfree = 0.000) for 5387 atoms. Found 28 (47 requested) and removed 36 (24 requested) atoms. Cycle 3: After refmac, R = 0.2250 (Rfree = 0.000) for 5361 atoms. Found 24 (46 requested) and removed 31 (24 requested) atoms. Cycle 4: After refmac, R = 0.2176 (Rfree = 0.000) for 5345 atoms. Found 27 (45 requested) and removed 35 (24 requested) atoms. Cycle 5: After refmac, R = 0.2063 (Rfree = 0.000) for 5324 atoms. Found 7 (43 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5554 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5574 seeds are put forward Round 1: 417 peptides, 64 chains. Longest chain 22 peptides. Score 0.542 Round 2: 467 peptides, 58 chains. Longest chain 21 peptides. Score 0.669 Round 3: 481 peptides, 51 chains. Longest chain 23 peptides. Score 0.730 Round 4: 496 peptides, 50 chains. Longest chain 28 peptides. Score 0.753 Round 5: 496 peptides, 49 chains. Longest chain 28 peptides. Score 0.758 Taking the results from Round 5 Chains 55, Residues 447, Estimated correctness of the model 76.5 % 8 chains (104 residues) have been docked in sequence Building loops using Loopy2018 55 chains (447 residues) following loop building 8 chains (104 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 10934 restraints for refining 5448 atoms. 8788 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2318 (Rfree = 0.000) for 5448 atoms. Found 38 (43 requested) and removed 42 (24 requested) atoms. Cycle 7: After refmac, R = 0.2209 (Rfree = 0.000) for 5421 atoms. Found 15 (42 requested) and removed 30 (24 requested) atoms. Cycle 8: After refmac, R = 0.2081 (Rfree = 0.000) for 5396 atoms. Found 10 (41 requested) and removed 26 (24 requested) atoms. Cycle 9: After refmac, R = 0.1996 (Rfree = 0.000) for 5376 atoms. Found 6 (40 requested) and removed 26 (24 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 5354 atoms. Found 15 (39 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5542 seeds are put forward NCS extension: 27 residues added (7 deleted due to clashes), 5569 seeds are put forward Round 1: 411 peptides, 56 chains. Longest chain 18 peptides. Score 0.594 Round 2: 473 peptides, 49 chains. Longest chain 28 peptides. Score 0.731 Round 3: 476 peptides, 51 chains. Longest chain 51 peptides. Score 0.724 Round 4: 465 peptides, 49 chains. Longest chain 54 peptides. Score 0.721 Round 5: 463 peptides, 46 chains. Longest chain 29 peptides. Score 0.736 Taking the results from Round 5 Chains 52, Residues 417, Estimated correctness of the model 72.4 % 7 chains (98 residues) have been docked in sequence Building loops using Loopy2018 52 chains (417 residues) following loop building 7 chains (98 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11219 restraints for refining 5448 atoms. 9247 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2130 (Rfree = 0.000) for 5448 atoms. Found 28 (38 requested) and removed 39 (24 requested) atoms. Cycle 12: After refmac, R = 0.2077 (Rfree = 0.000) for 5430 atoms. Found 21 (37 requested) and removed 27 (24 requested) atoms. Cycle 13: After refmac, R = 0.2010 (Rfree = 0.000) for 5415 atoms. Found 13 (36 requested) and removed 27 (24 requested) atoms. Cycle 14: After refmac, R = 0.1980 (Rfree = 0.000) for 5393 atoms. Found 26 (36 requested) and removed 26 (24 requested) atoms. Cycle 15: After refmac, R = 0.1905 (Rfree = 0.000) for 5388 atoms. Found 14 (35 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5572 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 5589 seeds are put forward Round 1: 422 peptides, 64 chains. Longest chain 21 peptides. Score 0.551 Round 2: 465 peptides, 58 chains. Longest chain 24 peptides. Score 0.666 Round 3: 467 peptides, 56 chains. Longest chain 23 peptides. Score 0.681 Round 4: 472 peptides, 59 chains. Longest chain 24 peptides. Score 0.669 Round 5: 471 peptides, 56 chains. Longest chain 27 peptides. Score 0.687 Taking the results from Round 5 Chains 61, Residues 415, Estimated correctness of the model 62.4 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11482 restraints for refining 5448 atoms. 9615 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2128 (Rfree = 0.000) for 5448 atoms. Found 34 (34 requested) and removed 33 (24 requested) atoms. Cycle 17: After refmac, R = 0.1951 (Rfree = 0.000) for 5439 atoms. Found 9 (34 requested) and removed 26 (24 requested) atoms. Cycle 18: After refmac, R = 0.1924 (Rfree = 0.000) for 5417 atoms. Found 8 (34 requested) and removed 25 (24 requested) atoms. Cycle 19: After refmac, R = 0.1899 (Rfree = 0.000) for 5399 atoms. Found 10 (34 requested) and removed 24 (24 requested) atoms. Cycle 20: After refmac, R = 0.1912 (Rfree = 0.000) for 5381 atoms. Found 16 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5590 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5609 seeds are put forward Round 1: 387 peptides, 60 chains. Longest chain 25 peptides. Score 0.517 Round 2: 430 peptides, 54 chains. Longest chain 34 peptides. Score 0.640 Round 3: 437 peptides, 53 chains. Longest chain 26 peptides. Score 0.658 Round 4: 455 peptides, 53 chains. Longest chain 27 peptides. Score 0.684 Round 5: 446 peptides, 54 chains. Longest chain 33 peptides. Score 0.664 Taking the results from Round 4 Chains 59, Residues 402, Estimated correctness of the model 61.7 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11646 restraints for refining 5447 atoms. 9882 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2145 (Rfree = 0.000) for 5447 atoms. Found 34 (34 requested) and removed 32 (24 requested) atoms. Cycle 22: After refmac, R = 0.2015 (Rfree = 0.000) for 5442 atoms. Found 18 (34 requested) and removed 25 (24 requested) atoms. Cycle 23: After refmac, R = 0.1967 (Rfree = 0.000) for 5430 atoms. Found 17 (34 requested) and removed 24 (24 requested) atoms. Cycle 24: After refmac, R = 0.1902 (Rfree = 0.000) for 5420 atoms. Found 15 (34 requested) and removed 26 (24 requested) atoms. Cycle 25: After refmac, R = 0.1874 (Rfree = 0.000) for 5404 atoms. Found 12 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5596 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5614 seeds are put forward Round 1: 380 peptides, 59 chains. Longest chain 20 peptides. Score 0.512 Round 2: 430 peptides, 57 chains. Longest chain 30 peptides. Score 0.619 Round 3: 433 peptides, 61 chains. Longest chain 18 peptides. Score 0.594 Round 4: 425 peptides, 53 chains. Longest chain 30 peptides. Score 0.639 Round 5: 418 peptides, 58 chains. Longest chain 20 peptides. Score 0.591 Taking the results from Round 4 Chains 56, Residues 372, Estimated correctness of the model 51.1 % 5 chains (68 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11706 restraints for refining 5448 atoms. 10039 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2087 (Rfree = 0.000) for 5448 atoms. Found 33 (34 requested) and removed 30 (24 requested) atoms. Cycle 27: After refmac, R = 0.1983 (Rfree = 0.000) for 5436 atoms. Found 22 (34 requested) and removed 24 (24 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 5426 atoms. Found 13 (34 requested) and removed 25 (24 requested) atoms. Cycle 29: After refmac, R = 0.1999 (Rfree = 0.000) for 5409 atoms. Found 26 (34 requested) and removed 24 (24 requested) atoms. Cycle 30: After refmac, R = 0.1956 (Rfree = 0.000) for 5402 atoms. Found 24 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5591 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 5607 seeds are put forward Round 1: 365 peptides, 61 chains. Longest chain 16 peptides. Score 0.463 Round 2: 396 peptides, 55 chains. Longest chain 18 peptides. Score 0.575 Round 3: 395 peptides, 52 chains. Longest chain 22 peptides. Score 0.597 Round 4: 421 peptides, 57 chains. Longest chain 32 peptides. Score 0.603 Round 5: 410 peptides, 55 chains. Longest chain 20 peptides. Score 0.600 Taking the results from Round 4 Chains 57, Residues 364, Estimated correctness of the model 41.9 % 2 chains (45 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11748 restraints for refining 5448 atoms. 10139 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2146 (Rfree = 0.000) for 5448 atoms. Found 34 (34 requested) and removed 32 (24 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 5434 atoms. Found 22 (34 requested) and removed 25 (24 requested) atoms. Cycle 33: After refmac, R = 0.1933 (Rfree = 0.000) for 5420 atoms. Found 13 (34 requested) and removed 24 (24 requested) atoms. Cycle 34: After refmac, R = 0.1971 (Rfree = 0.000) for 5398 atoms. Found 33 (34 requested) and removed 27 (24 requested) atoms. Cycle 35: After refmac, R = 0.1809 (Rfree = 0.000) for 5392 atoms. Found 12 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 5580 seeds are put forward NCS extension: 39 residues added (6 deleted due to clashes), 5619 seeds are put forward Round 1: 342 peptides, 55 chains. Longest chain 18 peptides. Score 0.469 Round 2: 388 peptides, 53 chains. Longest chain 17 peptides. Score 0.577 Round 3: 395 peptides, 52 chains. Longest chain 28 peptides. Score 0.597 Round 4: 398 peptides, 48 chains. Longest chain 21 peptides. Score 0.632 Round 5: 407 peptides, 50 chains. Longest chain 32 peptides. Score 0.632 Taking the results from Round 5 Chains 54, Residues 357, Estimated correctness of the model 49.4 % 4 chains (72 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11484 restraints for refining 5448 atoms. 9797 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2091 (Rfree = 0.000) for 5448 atoms. Found 26 (34 requested) and removed 35 (24 requested) atoms. Cycle 37: After refmac, R = 0.1994 (Rfree = 0.000) for 5430 atoms. Found 20 (34 requested) and removed 25 (24 requested) atoms. Cycle 38: After refmac, R = 0.1944 (Rfree = 0.000) for 5421 atoms. Found 16 (34 requested) and removed 24 (24 requested) atoms. Cycle 39: After refmac, R = 0.1926 (Rfree = 0.000) for 5408 atoms. Found 11 (34 requested) and removed 24 (24 requested) atoms. Cycle 40: After refmac, R = 0.1872 (Rfree = 0.000) for 5389 atoms. Found 11 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5558 seeds are put forward NCS extension: 44 residues added (5 deleted due to clashes), 5602 seeds are put forward Round 1: 334 peptides, 53 chains. Longest chain 17 peptides. Score 0.471 Round 2: 382 peptides, 55 chains. Longest chain 18 peptides. Score 0.550 Round 3: 386 peptides, 56 chains. Longest chain 17 peptides. Score 0.549 Round 4: 382 peptides, 50 chains. Longest chain 19 peptides. Score 0.590 Round 5: 370 peptides, 52 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 4 Chains 53, Residues 332, Estimated correctness of the model 38.3 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12158 restraints for refining 5448 atoms. 10778 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2024 (Rfree = 0.000) for 5448 atoms. Found 26 (34 requested) and removed 26 (24 requested) atoms. Cycle 42: After refmac, R = 0.1914 (Rfree = 0.000) for 5446 atoms. Found 18 (34 requested) and removed 26 (24 requested) atoms. Cycle 43: After refmac, R = 0.1860 (Rfree = 0.000) for 5435 atoms. Found 17 (34 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.1794 (Rfree = 0.000) for 5426 atoms. Found 20 (34 requested) and removed 24 (24 requested) atoms. Cycle 45: After refmac, R = 0.1768 (Rfree = 0.000) for 5419 atoms. Found 21 (34 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5590 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5609 seeds are put forward Round 1: 291 peptides, 49 chains. Longest chain 16 peptides. Score 0.414 Round 2: 338 peptides, 44 chains. Longest chain 24 peptides. Score 0.559 Round 3: 336 peptides, 40 chains. Longest chain 24 peptides. Score 0.589 Round 4: 341 peptides, 47 chains. Longest chain 22 peptides. Score 0.539 Round 5: 338 peptides, 44 chains. Longest chain 21 peptides. Score 0.559 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 296, Estimated correctness of the model 38.1 % 4 chains (59 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 70 A and 84 A 39 chains (304 residues) following loop building 3 chains (72 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11884 reflections ( 99.82 % complete ) and 11714 restraints for refining 5448 atoms. 10224 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2015 (Rfree = 0.000) for 5448 atoms. Found 0 (34 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1966 (Rfree = 0.000) for 5409 atoms. Found 0 (34 requested) and removed 19 (24 requested) atoms. Cycle 48: After refmac, R = 0.1910 (Rfree = 0.000) for 5386 atoms. Found 0 (34 requested) and removed 12 (24 requested) atoms. Cycle 49: After refmac, R = 0.1874 (Rfree = 0.000) for 5371 atoms. Found 0 (34 requested) and removed 11 (24 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 54.92