Mon 24 Dec 07:27:31 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aml-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aml-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-parrot-noncs ############### 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 07:27:35 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/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-3.2-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.60 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 6628 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3230 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2778 (Rfree = 0.000) for 6628 atoms. Found 59 (59 requested) and removed 93 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 6748 seeds are put forward NCS extension: 0 residues added, 6748 seeds are put forward Round 1: 326 peptides, 64 chains. Longest chain 10 peptides. Score 0.346 Round 2: 382 peptides, 68 chains. Longest chain 16 peptides. Score 0.436 Round 3: 423 peptides, 71 chains. Longest chain 16 peptides. Score 0.495 Round 4: 413 peptides, 64 chains. Longest chain 18 peptides. Score 0.534 Round 5: 437 peptides, 64 chains. Longest chain 17 peptides. Score 0.578 Taking the results from Round 5 Chains 64, Residues 373, Estimated correctness of the model 35.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12083 restraints for refining 5443 atoms. 10623 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2309 (Rfree = 0.000) for 5443 atoms. Found 36 (48 requested) and removed 42 (24 requested) atoms. Cycle 2: After refmac, R = 0.2115 (Rfree = 0.000) for 5385 atoms. Found 25 (48 requested) and removed 28 (24 requested) atoms. Cycle 3: After refmac, R = 0.1990 (Rfree = 0.000) for 5372 atoms. Found 13 (48 requested) and removed 28 (24 requested) atoms. Cycle 4: After refmac, R = 0.1952 (Rfree = 0.000) for 5350 atoms. Found 16 (48 requested) and removed 26 (24 requested) atoms. Cycle 5: After refmac, R = 0.1891 (Rfree = 0.000) for 5337 atoms. Found 14 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5593 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5607 seeds are put forward Round 1: 375 peptides, 63 chains. Longest chain 18 peptides. Score 0.466 Round 2: 407 peptides, 55 chains. Longest chain 17 peptides. Score 0.595 Round 3: 427 peptides, 55 chains. Longest chain 16 peptides. Score 0.628 Round 4: 433 peptides, 59 chains. Longest chain 20 peptides. Score 0.609 Round 5: 428 peptides, 55 chains. Longest chain 21 peptides. Score 0.630 Taking the results from Round 5 Chains 55, Residues 373, Estimated correctness of the model 48.9 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12241 restraints for refining 5446 atoms. 10742 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2163 (Rfree = 0.000) for 5446 atoms. Found 41 (48 requested) and removed 28 (24 requested) atoms. Cycle 7: After refmac, R = 0.2067 (Rfree = 0.000) for 5447 atoms. Found 19 (48 requested) and removed 28 (24 requested) atoms. Cycle 8: After refmac, R = 0.1964 (Rfree = 0.000) for 5432 atoms. Found 14 (48 requested) and removed 24 (24 requested) atoms. Cycle 9: After refmac, R = 0.1924 (Rfree = 0.000) for 5411 atoms. Found 18 (48 requested) and removed 24 (24 requested) atoms. Cycle 10: After refmac, R = 0.1898 (Rfree = 0.000) for 5398 atoms. Found 19 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 5604 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 5620 seeds are put forward Round 1: 366 peptides, 56 chains. Longest chain 18 peptides. Score 0.510 Round 2: 396 peptides, 54 chains. Longest chain 25 peptides. Score 0.583 Round 3: 422 peptides, 53 chains. Longest chain 23 peptides. Score 0.634 Round 4: 404 peptides, 50 chains. Longest chain 26 peptides. Score 0.627 Round 5: 384 peptides, 52 chains. Longest chain 20 peptides. Score 0.578 Taking the results from Round 3 Chains 55, Residues 369, Estimated correctness of the model 49.9 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11744 restraints for refining 5448 atoms. 10176 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2092 (Rfree = 0.000) for 5448 atoms. Found 30 (48 requested) and removed 31 (24 requested) atoms. Cycle 12: After refmac, R = 0.1991 (Rfree = 0.000) for 5435 atoms. Found 19 (48 requested) and removed 24 (24 requested) atoms. Cycle 13: After refmac, R = 0.1956 (Rfree = 0.000) for 5423 atoms. Found 18 (48 requested) and removed 24 (24 requested) atoms. Cycle 14: After refmac, R = 0.2139 (Rfree = 0.000) for 5413 atoms. Found 37 (48 requested) and removed 24 (24 requested) atoms. Cycle 15: After refmac, R = 0.1916 (Rfree = 0.000) for 5421 atoms. Found 16 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 5629 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5646 seeds are put forward Round 1: 365 peptides, 56 chains. Longest chain 17 peptides. Score 0.508 Round 2: 417 peptides, 53 chains. Longest chain 26 peptides. Score 0.626 Round 3: 397 peptides, 54 chains. Longest chain 19 peptides. Score 0.585 Round 4: 401 peptides, 52 chains. Longest chain 17 peptides. Score 0.607 Round 5: 404 peptides, 52 chains. Longest chain 22 peptides. Score 0.612 Taking the results from Round 2 Chains 55, Residues 364, Estimated correctness of the model 47.9 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12148 restraints for refining 5447 atoms. 10676 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1965 (Rfree = 0.000) for 5447 atoms. Found 36 (48 requested) and removed 27 (24 requested) atoms. Cycle 17: After refmac, R = 0.1937 (Rfree = 0.000) for 5450 atoms. Found 17 (48 requested) and removed 24 (24 requested) atoms. Cycle 18: After refmac, R = 0.1873 (Rfree = 0.000) for 5443 atoms. Found 18 (48 requested) and removed 25 (24 requested) atoms. Cycle 19: After refmac, R = 0.2283 (Rfree = 0.000) for 5433 atoms. Found 48 (48 requested) and removed 26 (24 requested) atoms. Cycle 20: After refmac, R = 0.1822 (Rfree = 0.000) for 5448 atoms. Found 19 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5651 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 5670 seeds are put forward Round 1: 389 peptides, 61 chains. Longest chain 20 peptides. Score 0.513 Round 2: 411 peptides, 55 chains. Longest chain 29 peptides. Score 0.602 Round 3: 418 peptides, 54 chains. Longest chain 24 peptides. Score 0.621 Round 4: 390 peptides, 48 chains. Longest chain 26 peptides. Score 0.619 Round 5: 389 peptides, 48 chains. Longest chain 26 peptides. Score 0.617 Taking the results from Round 3 Chains 55, Residues 364, Estimated correctness of the model 46.6 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12198 restraints for refining 5448 atoms. 10746 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1979 (Rfree = 0.000) for 5448 atoms. Found 42 (48 requested) and removed 28 (24 requested) atoms. Cycle 22: After refmac, R = 0.1831 (Rfree = 0.000) for 5455 atoms. Found 16 (49 requested) and removed 24 (24 requested) atoms. Cycle 23: After refmac, R = 0.1808 (Rfree = 0.000) for 5446 atoms. Found 20 (48 requested) and removed 24 (24 requested) atoms. Cycle 24: After refmac, R = 0.1781 (Rfree = 0.000) for 5440 atoms. Found 14 (48 requested) and removed 24 (24 requested) atoms. Cycle 25: After refmac, R = 0.1763 (Rfree = 0.000) for 5428 atoms. Found 19 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5633 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 5661 seeds are put forward Round 1: 372 peptides, 56 chains. Longest chain 24 peptides. Score 0.522 Round 2: 406 peptides, 51 chains. Longest chain 26 peptides. Score 0.623 Round 3: 407 peptides, 48 chains. Longest chain 26 peptides. Score 0.646 Round 4: 388 peptides, 45 chains. Longest chain 28 peptides. Score 0.638 Round 5: 402 peptides, 48 chains. Longest chain 33 peptides. Score 0.639 Taking the results from Round 3 Chains 53, Residues 359, Estimated correctness of the model 52.9 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11582 restraints for refining 5446 atoms. 10007 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2029 (Rfree = 0.000) for 5446 atoms. Found 45 (48 requested) and removed 35 (24 requested) atoms. Cycle 27: After refmac, R = 0.1850 (Rfree = 0.000) for 5444 atoms. Found 17 (48 requested) and removed 25 (24 requested) atoms. Cycle 28: After refmac, R = 0.1798 (Rfree = 0.000) for 5430 atoms. Found 16 (48 requested) and removed 24 (24 requested) atoms. Cycle 29: After refmac, R = 0.1750 (Rfree = 0.000) for 5418 atoms. Found 23 (48 requested) and removed 24 (24 requested) atoms. Cycle 30: After refmac, R = 0.1728 (Rfree = 0.000) for 5414 atoms. Found 14 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 5608 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5628 seeds are put forward Round 1: 358 peptides, 55 chains. Longest chain 18 peptides. Score 0.503 Round 2: 393 peptides, 52 chains. Longest chain 27 peptides. Score 0.594 Round 3: 409 peptides, 52 chains. Longest chain 19 peptides. Score 0.621 Round 4: 377 peptides, 51 chains. Longest chain 29 peptides. Score 0.573 Round 5: 368 peptides, 50 chains. Longest chain 17 peptides. Score 0.565 Taking the results from Round 3 Chains 56, Residues 357, Estimated correctness of the model 46.6 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12004 restraints for refining 5448 atoms. 10548 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1918 (Rfree = 0.000) for 5448 atoms. Found 45 (48 requested) and removed 25 (24 requested) atoms. Cycle 32: After refmac, R = 0.1813 (Rfree = 0.000) for 5463 atoms. Found 17 (49 requested) and removed 25 (24 requested) atoms. Cycle 33: After refmac, R = 0.1760 (Rfree = 0.000) for 5452 atoms. Found 14 (48 requested) and removed 25 (24 requested) atoms. Cycle 34: After refmac, R = 0.1739 (Rfree = 0.000) for 5434 atoms. Found 14 (48 requested) and removed 24 (24 requested) atoms. Cycle 35: After refmac, R = 0.1718 (Rfree = 0.000) for 5420 atoms. Found 16 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5603 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 5628 seeds are put forward Round 1: 328 peptides, 53 chains. Longest chain 18 peptides. Score 0.458 Round 2: 379 peptides, 54 chains. Longest chain 27 peptides. Score 0.552 Round 3: 375 peptides, 52 chains. Longest chain 27 peptides. Score 0.561 Round 4: 377 peptides, 52 chains. Longest chain 27 peptides. Score 0.565 Round 5: 373 peptides, 53 chains. Longest chain 27 peptides. Score 0.549 Taking the results from Round 4 Chains 55, Residues 325, Estimated correctness of the model 31.3 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11993 restraints for refining 5448 atoms. 10605 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1979 (Rfree = 0.000) for 5448 atoms. Found 48 (48 requested) and removed 31 (24 requested) atoms. Cycle 37: After refmac, R = 0.1870 (Rfree = 0.000) for 5458 atoms. Found 21 (49 requested) and removed 26 (24 requested) atoms. Cycle 38: After refmac, R = 0.1854 (Rfree = 0.000) for 5449 atoms. Found 24 (48 requested) and removed 25 (24 requested) atoms. Cycle 39: After refmac, R = 0.1880 (Rfree = 0.000) for 5445 atoms. Found 19 (48 requested) and removed 27 (24 requested) atoms. Cycle 40: After refmac, R = 0.1877 (Rfree = 0.000) for 5437 atoms. Found 26 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5655 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5675 seeds are put forward Round 1: 312 peptides, 49 chains. Longest chain 19 peptides. Score 0.461 Round 2: 344 peptides, 50 chains. Longest chain 21 peptides. Score 0.518 Round 3: 349 peptides, 46 chains. Longest chain 22 peptides. Score 0.563 Round 4: 368 peptides, 50 chains. Longest chain 22 peptides. Score 0.565 Round 5: 351 peptides, 49 chains. Longest chain 24 peptides. Score 0.541 Taking the results from Round 4 Chains 52, Residues 318, Estimated correctness of the model 31.3 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 12340 restraints for refining 5448 atoms. 11043 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2009 (Rfree = 0.000) for 5448 atoms. Found 47 (48 requested) and removed 28 (24 requested) atoms. Cycle 42: After refmac, R = 0.1911 (Rfree = 0.000) for 5462 atoms. Found 22 (49 requested) and removed 26 (24 requested) atoms. Cycle 43: After refmac, R = 0.1906 (Rfree = 0.000) for 5455 atoms. Found 20 (48 requested) and removed 27 (24 requested) atoms. Cycle 44: After refmac, R = 0.1874 (Rfree = 0.000) for 5442 atoms. Found 18 (48 requested) and removed 25 (24 requested) atoms. Cycle 45: After refmac, R = 0.1860 (Rfree = 0.000) for 5430 atoms. Found 21 (48 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5635 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 5651 seeds are put forward Round 1: 299 peptides, 57 chains. Longest chain 10 peptides. Score 0.352 Round 2: 321 peptides, 51 chains. Longest chain 16 peptides. Score 0.462 Round 3: 326 peptides, 50 chains. Longest chain 24 peptides. Score 0.482 Round 4: 342 peptides, 53 chains. Longest chain 24 peptides. Score 0.488 Round 5: 332 peptides, 50 chains. Longest chain 21 peptides. Score 0.494 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 282, Estimated correctness of the model 9.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11884 reflections ( 99.82 % complete ) and 12649 restraints for refining 5448 atoms. 11571 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1983 (Rfree = 0.000) for 5448 atoms. Found 0 (48 requested) and removed 8 (24 requested) atoms. Cycle 47: After refmac, R = 0.1993 (Rfree = 0.000) for 5438 atoms. Found 0 (48 requested) and removed 5 (24 requested) atoms. Cycle 48: After refmac, R = 0.1922 (Rfree = 0.000) for 5431 atoms. Found 0 (48 requested) and removed 3 (24 requested) atoms. Cycle 49: After refmac, R = 0.2015 (Rfree = 0.000) for 5426 atoms. Found 0 (48 requested) and removed 11 (24 requested) atoms. Writing output files ... TimeTaking 53.92