Mon 24 Dec 00:57:53 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 2ash-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ash-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.8-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/2ash-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.8-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 00:57:57 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/2ash-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ash-3.8-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 1084 and 0 Target number of residues in the AU: 1084 Target solvent content: 0.6663 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-3.8-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 3.800 Wilson plot Bfac: 89.48 17200 reflections ( 99.72 % complete ) and 0 restraints for refining 13548 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3283 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3076 (Rfree = 0.000) for 13548 atoms. Found 74 (74 requested) and removed 291 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 13553 seeds are put forward NCS extension: 0 residues added, 13553 seeds are put forward Round 1: 485 peptides, 95 chains. Longest chain 10 peptides. Score 0.288 Round 2: 658 peptides, 114 chains. Longest chain 21 peptides. Score 0.379 Round 3: 723 peptides, 118 chains. Longest chain 19 peptides. Score 0.423 Round 4: 711 peptides, 107 chains. Longest chain 18 peptides. Score 0.455 Round 5: 715 peptides, 105 chains. Longest chain 21 peptides. Score 0.466 Taking the results from Round 5 Chains 106, Residues 610, Estimated correctness of the model 0.0 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25780 restraints for refining 11023 atoms. 23291 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2505 (Rfree = 0.000) for 11023 atoms. Found 60 (60 requested) and removed 102 (30 requested) atoms. Cycle 2: After refmac, R = 0.2282 (Rfree = 0.000) for 10834 atoms. Found 43 (60 requested) and removed 71 (30 requested) atoms. Cycle 3: After refmac, R = 0.2183 (Rfree = 0.000) for 10748 atoms. Found 54 (59 requested) and removed 58 (29 requested) atoms. Cycle 4: After refmac, R = 0.2112 (Rfree = 0.000) for 10704 atoms. Found 51 (59 requested) and removed 60 (29 requested) atoms. Cycle 5: After refmac, R = 0.2092 (Rfree = 0.000) for 10662 atoms. Found 58 (58 requested) and removed 63 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.55 Search for helices and strands: 0 residues in 0 chains, 11049 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 11074 seeds are put forward Round 1: 680 peptides, 120 chains. Longest chain 18 peptides. Score 0.376 Round 2: 791 peptides, 116 chains. Longest chain 25 peptides. Score 0.489 Round 3: 821 peptides, 118 chains. Longest chain 20 peptides. Score 0.506 Round 4: 845 peptides, 110 chains. Longest chain 24 peptides. Score 0.552 Round 5: 830 peptides, 108 chains. Longest chain 22 peptides. Score 0.548 Taking the results from Round 4 Chains 111, Residues 735, Estimated correctness of the model 0.0 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 24643 restraints for refining 11025 atoms. 21587 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2176 (Rfree = 0.000) for 11025 atoms. Found 49 (60 requested) and removed 67 (30 requested) atoms. Cycle 7: After refmac, R = 0.2055 (Rfree = 0.000) for 10886 atoms. Found 45 (60 requested) and removed 53 (30 requested) atoms. Cycle 8: After refmac, R = 0.1960 (Rfree = 0.000) for 10823 atoms. Found 34 (59 requested) and removed 58 (29 requested) atoms. Cycle 9: After refmac, R = 0.1675 (Rfree = 0.000) for 10757 atoms. Found 11 (59 requested) and removed 38 (29 requested) atoms. Cycle 10: After refmac, R = 0.1606 (Rfree = 0.000) for 10710 atoms. Found 8 (59 requested) and removed 41 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.59 Search for helices and strands: 0 residues in 0 chains, 11032 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 11056 seeds are put forward Round 1: 704 peptides, 124 chains. Longest chain 17 peptides. Score 0.382 Round 2: 789 peptides, 112 chains. Longest chain 26 peptides. Score 0.502 Round 3: 803 peptides, 111 chains. Longest chain 18 peptides. Score 0.516 Round 4: 781 peptides, 108 chains. Longest chain 18 peptides. Score 0.510 Round 5: 807 peptides, 113 chains. Longest chain 32 peptides. Score 0.513 Taking the results from Round 3 Chains 111, Residues 692, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 24877 restraints for refining 11025 atoms. 22083 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2085 (Rfree = 0.000) for 11025 atoms. Found 60 (60 requested) and removed 67 (30 requested) atoms. Cycle 12: After refmac, R = 0.1943 (Rfree = 0.000) for 10954 atoms. Found 45 (60 requested) and removed 55 (30 requested) atoms. Cycle 13: After refmac, R = 0.1918 (Rfree = 0.000) for 10918 atoms. Found 51 (60 requested) and removed 45 (30 requested) atoms. Cycle 14: After refmac, R = 0.1930 (Rfree = 0.000) for 10901 atoms. Found 55 (60 requested) and removed 43 (30 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1828 (Rfree = 0.000) for 10891 atoms. Found 48 (60 requested) and removed 44 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.58 Search for helices and strands: 0 residues in 0 chains, 11265 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11281 seeds are put forward Round 1: 659 peptides, 113 chains. Longest chain 22 peptides. Score 0.384 Round 2: 742 peptides, 113 chains. Longest chain 16 peptides. Score 0.459 Round 3: 755 peptides, 119 chains. Longest chain 17 peptides. Score 0.447 Round 4: 778 peptides, 107 chains. Longest chain 17 peptides. Score 0.511 Round 5: 752 peptides, 111 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 4 Chains 108, Residues 671, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25866 restraints for refining 11026 atoms. 23251 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2177 (Rfree = 0.000) for 11026 atoms. Found 59 (60 requested) and removed 48 (30 requested) atoms. Cycle 17: After refmac, R = 0.1991 (Rfree = 0.000) for 10956 atoms. Found 60 (60 requested) and removed 50 (30 requested) atoms. Cycle 18: After refmac, R = 0.2024 (Rfree = 0.000) for 10926 atoms. Found 60 (60 requested) and removed 51 (30 requested) atoms. Cycle 19: After refmac, R = 0.1912 (Rfree = 0.000) for 10915 atoms. Found 60 (60 requested) and removed 54 (30 requested) atoms. Cycle 20: After refmac, R = 0.1593 (Rfree = 0.000) for 10894 atoms. Found 19 (60 requested) and removed 39 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.58 Search for helices and strands: 0 residues in 0 chains, 11241 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11257 seeds are put forward Round 1: 655 peptides, 124 chains. Longest chain 12 peptides. Score 0.335 Round 2: 718 peptides, 110 chains. Longest chain 15 peptides. Score 0.450 Round 3: 742 peptides, 113 chains. Longest chain 17 peptides. Score 0.459 Round 4: 759 peptides, 108 chains. Longest chain 21 peptides. Score 0.492 Round 5: 768 peptides, 105 chains. Longest chain 26 peptides. Score 0.510 Taking the results from Round 5 Chains 107, Residues 663, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 25484 restraints for refining 11025 atoms. 22886 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2155 (Rfree = 0.000) for 11025 atoms. Found 60 (60 requested) and removed 54 (30 requested) atoms. Cycle 22: After refmac, R = 0.2019 (Rfree = 0.000) for 10974 atoms. Found 56 (60 requested) and removed 53 (30 requested) atoms. Cycle 23: After refmac, R = 0.1905 (Rfree = 0.000) for 10947 atoms. Found 47 (60 requested) and removed 47 (30 requested) atoms. Cycle 24: After refmac, R = 0.1948 (Rfree = 0.000) for 10927 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Cycle 25: After refmac, R = 0.1849 (Rfree = 0.000) for 10922 atoms. Found 54 (60 requested) and removed 42 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.57 Search for helices and strands: 0 residues in 0 chains, 11306 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11321 seeds are put forward Round 1: 606 peptides, 114 chains. Longest chain 13 peptides. Score 0.329 Round 2: 676 peptides, 108 chains. Longest chain 26 peptides. Score 0.420 Round 3: 673 peptides, 109 chains. Longest chain 14 peptides. Score 0.413 Round 4: 713 peptides, 110 chains. Longest chain 19 peptides. Score 0.445 Round 5: 726 peptides, 108 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 5 Chains 110, Residues 618, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26071 restraints for refining 11027 atoms. 23673 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2083 (Rfree = 0.000) for 11027 atoms. Found 60 (60 requested) and removed 50 (30 requested) atoms. Cycle 27: After refmac, R = 0.2000 (Rfree = 0.000) for 10981 atoms. Found 59 (60 requested) and removed 40 (30 requested) atoms. Cycle 28: After refmac, R = 0.1947 (Rfree = 0.000) for 10952 atoms. Found 56 (60 requested) and removed 36 (30 requested) atoms. Cycle 29: After refmac, R = 0.1600 (Rfree = 0.000) for 10940 atoms. Found 15 (60 requested) and removed 32 (30 requested) atoms. Cycle 30: After refmac, R = 0.1533 (Rfree = 0.000) for 10908 atoms. Found 7 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.58 Search for helices and strands: 0 residues in 0 chains, 11223 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 11240 seeds are put forward Round 1: 582 peptides, 121 chains. Longest chain 10 peptides. Score 0.274 Round 2: 683 peptides, 112 chains. Longest chain 20 peptides. Score 0.411 Round 3: 650 peptides, 106 chains. Longest chain 15 peptides. Score 0.404 Round 4: 662 peptides, 109 chains. Longest chain 18 peptides. Score 0.403 Round 5: 660 peptides, 105 chains. Longest chain 20 peptides. Score 0.418 Taking the results from Round 5 Chains 106, Residues 555, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26211 restraints for refining 11024 atoms. 24068 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2171 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2140 (Rfree = 0.000) for 10959 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 33: After refmac, R = 0.2061 (Rfree = 0.000) for 10916 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 34: After refmac, R = 0.1646 (Rfree = 0.000) for 10901 atoms. Found 30 (60 requested) and removed 37 (30 requested) atoms. Cycle 35: After refmac, R = 0.1544 (Rfree = 0.000) for 10861 atoms. Found 15 (59 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.62 Search for helices and strands: 0 residues in 0 chains, 11175 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11196 seeds are put forward Round 1: 548 peptides, 114 chains. Longest chain 14 peptides. Score 0.269 Round 2: 647 peptides, 116 chains. Longest chain 17 peptides. Score 0.361 Round 3: 627 peptides, 108 chains. Longest chain 12 peptides. Score 0.375 Round 4: 638 peptides, 103 chains. Longest chain 14 peptides. Score 0.405 Round 5: 630 peptides, 102 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 4 Chains 103, Residues 535, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26276 restraints for refining 11026 atoms. 24222 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2015 (Rfree = 0.000) for 11026 atoms. Found 60 (60 requested) and removed 57 (30 requested) atoms. Cycle 37: After refmac, R = 0.2024 (Rfree = 0.000) for 10985 atoms. Found 60 (60 requested) and removed 36 (30 requested) atoms. Cycle 38: After refmac, R = 0.1944 (Rfree = 0.000) for 10975 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 39: After refmac, R = 0.1526 (Rfree = 0.000) for 10951 atoms. Found 15 (60 requested) and removed 40 (30 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1449 (Rfree = 0.000) for 10906 atoms. Found 15 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.60 Search for helices and strands: 0 residues in 0 chains, 11287 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 11298 seeds are put forward Round 1: 486 peptides, 102 chains. Longest chain 13 peptides. Score 0.257 Round 2: 614 peptides, 111 chains. Longest chain 14 peptides. Score 0.349 Round 3: 617 peptides, 103 chains. Longest chain 18 peptides. Score 0.386 Round 4: 650 peptides, 104 chains. Longest chain 22 peptides. Score 0.412 Round 5: 637 peptides, 96 chains. Longest chain 21 peptides. Score 0.433 Taking the results from Round 5 Chains 96, Residues 541, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17200 reflections ( 99.72 % complete ) and 26254 restraints for refining 11024 atoms. 24186 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1989 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Cycle 42: After refmac, R = 0.1960 (Rfree = 0.000) for 10977 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 43: After refmac, R = 0.1876 (Rfree = 0.000) for 10959 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 44: After refmac, R = 0.1442 (Rfree = 0.000) for 10936 atoms. Found 20 (60 requested) and removed 35 (30 requested) atoms. Cycle 45: After refmac, R = 0.1380 (Rfree = 0.000) for 10894 atoms. Found 16 (60 requested) and removed 31 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.76 3.61 Search for helices and strands: 0 residues in 0 chains, 11269 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 11283 seeds are put forward Round 1: 460 peptides, 98 chains. Longest chain 10 peptides. Score 0.247 Round 2: 522 peptides, 89 chains. Longest chain 12 peptides. Score 0.353 Round 3: 559 peptides, 94 chains. Longest chain 14 peptides. Score 0.368 Round 4: 581 peptides, 100 chains. Longest chain 13 peptides. Score 0.364 Round 5: 567 peptides, 95 chains. Longest chain 15 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 96, Residues 472, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 96 chains (472 residues) following loop building 4 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17200 reflections ( 99.72 % complete ) and 26312 restraints for refining 11027 atoms. 24450 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1899 (Rfree = 0.000) for 11027 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.1888 (Rfree = 0.000) for 10947 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.1479 (Rfree = 0.000) for 10900 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.1411 (Rfree = 0.000) for 10857 atoms. TimeTaking 122.4