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ModeRNA (C) 2009 by Magdalena Musielak & Kristian Rother,
Tomasz Puton, Janusz M. Bujnicki
Building RNA 3D models with comparative modeling approach.
support: lenam@amu.edu.pl
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Template loaded from 1QF6_B_tRNA.pdb.
Template sequence:
GCCGAUAUAGCUCAGDDGGDAGAGCAGCGCAUUCGUEAUGCGAAG7UCGUAGGTPCGACUCCUAUUAUCGGCACCA
Alignment loaded from aln_1QF6_E_coli_Tyr2_GUA.fasta:
GGUGGGG4UCCCGAGC-#GCCAAAGGGAGCAGACUQUA*APCUGCCGUCACAGACUUCGAAGGTPCGAAUCCUUCCCCCACCACCA
GCCGAUAUAGCUCAGDDGGD--AGAGCAGCGCAUUCGUEAUGCGAAG--------7UCGUAGGTPCGACUCCUAUUAUCGGCACCA
Checking whether template matches with alignment.
Sequences match:
Seq1: GCCGAUAUAGCUCAGDDGGDAGAGCAGCGCAUUCGUEAUGCGAAG7UCGUAGGTPCGACUCCUAUUAUCGGCACCA
Seq2: GCCGAUAUAGCUCAGDDGGDAGAGCAGCGCAUUCGUEAUGCGAAG7UCGUAGGTPCGACUCCUAUUAUCGGCACCA
Residue 1: residue copied from template to model.
Residue 4: residue copied from template to model.
Residue 11: residue copied from template to model.
Residue 14: residue copied from template to model.
Residue 15: residue copied from template to model.
Residue 19: residue copied from template to model.
Residue 21: residue copied from template to model.
Residue 24: residue copied from template to model.
Residue 26: residue copied from template to model.
Residue 27: residue copied from template to model.
Residue 28: residue copied from template to model.
Residue 31: residue copied from template to model.
Residue 33: residue copied from template to model.
Residue 38: residue copied from template to model.
Residue 42: residue copied from template to model.
Residue 45: residue copied from template to model.
Residue 47: residue copied from template to model.
Residue 48: residue copied from template to model.
Residue 49: residue copied from template to model.
Residue 51: residue copied from template to model.
Residue 52: residue copied from template to model.
Residue 53: residue copied from template to model.
Residue 54: residue copied from template to model.
Residue 55: residue copied from template to model.
Residue 56: residue copied from template to model.
Residue 57: residue copied from template to model.
Residue 58: residue copied from template to model.
Residue 60: residue copied from template to model.
Residue 61: residue copied from template to model.
Residue 62: residue copied from template to model.
Residue 63: residue copied from template to model.
Residue 69: residue copied from template to model.
Residue 72: residue copied from template to model.
Residue 73: residue copied from template to model.
Residue 74: residue copied from template to model.
Residue 75: residue copied from template to model.
Residue 76: residue copied from template to model.
Residue 2: base exchanged (C ---> G), residue added to model.
Residue 3: base exchanged (C ---> U), residue added to model.
Residue 5: base exchanged (A ---> G), residue added to model.
Residue 6: base exchanged (U ---> G), residue added to model.
Residue 7: base exchanged (A ---> G), residue added to model.
Residue 9: base exchanged (A ---> U), residue added to model.
Residue 10: base exchanged (G ---> C), residue added to model.
Residue 12: base exchanged (U ---> C), residue added to model.
Residue 13: base exchanged (C ---> G), residue added to model.
Residue 22: base exchanged (G ---> A), residue added to model.
Residue 23: base exchanged (A ---> G), residue added to model.
Residue 25: base exchanged (C ---> G), residue added to model.
Residue 29: base exchanged (G ---> A), residue added to model.
Residue 30: base exchanged (C ---> G), residue added to model.
Residue 32: base exchanged (U ---> C), residue added to model.
Residue 35: base exchanged (G ---> U), residue added to model.
Residue 36: base exchanged (U ---> A), residue added to model.
Residue 40: base exchanged (G ---> C), residue added to model.
Residue 41: base exchanged (C ---> U), residue added to model.
Residue 43: base exchanged (A ---> C), residue added to model.
Residue 44: base exchanged (A ---> C), residue added to model.
Residue 50: base exchanged (U ---> A), residue added to model.
Residue 59: base exchanged (C ---> A), residue added to model.
Residue 64: base exchanged (A ---> U), residue added to model.
Residue 65: base exchanged (U ---> C), residue added to model.
Residue 66: base exchanged (U ---> C), residue added to model.
Residue 67: base exchanged (A ---> C), residue added to model.
Residue 68: base exchanged (U ---> C), residue added to model.
Residue 70: base exchanged (G ---> A), residue added to model.
Residue 71: base exchanged (G ---> C), residue added to model.
Residue 16: modification removed (D ---> C).
Residue 20: modification removed (D ---> C).
Residue 46: modification removed (m7G ---> U).
Residue 8: modification added (U ---> s4U).
Residue 18: modification added (G ---> Gm).
Residue 34: modification added (C ---> QtRNA).
Residue 37: modification added (m6t6A ---> ms2i6A).
Residue 39: modification added (U ---> Y).
Searching loop between residue 19 and residue 22.
Best loop fragment:
Fragment instance:
-stem residues: 19,22
-sequence: CCAA
-residue identifiers: ['5', '4', '7', '6', '9', '8']
Residue 5 ---> renumbered to 19A
Residue 6 ---> renumbered to 19B
Residue 7 ---> renumbered to 19C
Residue 8 ---> renumbered to 19D
Residue 4 ---> renumbered to 19
Residue 9 ---> renumbered to 22
Residues in fragment:
19 A,19A C,19B C,19C A,19D A,22 A
Residue 19 ---> renumbered to 19
Residue 22 ---> renumbered to 22
Residue 19A ---> renumbered to 20
Residue 19D ---> renumbered to 21
Residue 19B ---> renumbered to 20A
Residue 19C ---> renumbered to 20B
The backbone between residues 19 and 20 is interrupted after loop insertion.
Rebuilding P and O5.
... failed. The structure needs to be refined.
The backbone between residues 21 and 22 is interrupted after loop insertion.
Rebuilding P and O5.
... failed. The structure needs to be refined.
Fragment inserted between residues 19 and residue 22.
Fragment is 6 residues long.
Searching loop between residue 44 and residue 47.
Best loop fragment:
Fragment instance:
-stem residues: 44,47
-sequence: GUCACAGACU
-residue identifiers: ['1986', '1987', '1984', '1985', '1982', '1979', '1980', '1981', '1977', '1976', '1978', '1983']
Residue 1977 ---> renumbered to 44A
Residue 1978 ---> renumbered to 44B
Residue 1979 ---> renumbered to 44C
Residue 1980 ---> renumbered to 44D
Residue 1981 ---> renumbered to 44E
Residue 1982 ---> renumbered to 44F
Residue 1983 ---> renumbered to 44G
Residue 1984 ---> renumbered to 44H
Residue 1985 ---> renumbered to 44I
Residue 1986 ---> renumbered to 44J
Residue 1976 ---> renumbered to 44
Residue 1987 ---> renumbered to 47
Residues in fragment:
44 G,44A G,44B U,44C C,44D A,44E C,44F A,44G G,44H A,44I C,44J U,47 C
Residue 44 ---> renumbered to 44
Residue 47 ---> renumbered to 47
Residue 44A ---> renumbered to 45
Residue 44J ---> renumbered to 46
Residue 44B ---> renumbered to 45A
Residue 44C ---> renumbered to 45B
Residue 44D ---> renumbered to 45C
Residue 44E ---> renumbered to 45D
Residue 44F ---> renumbered to 45E
Residue 44G ---> renumbered to 45F
Residue 44H ---> renumbered to 45G
Residue 44I ---> renumbered to 45H
Fragment inserted between residues 44 and residue 47.
Fragment is 12 residues long.
Searching loop between residue 15 and residue 19.
Best loop fragment:
Fragment instance:
-stem residues: 15,19
-sequence: C#
-residue identifiers: ['19', '18', '15', '16']
Residue 16 ---> renumbered to 15A
Residue 18 ---> renumbered to 15B
Residue 15 ---> renumbered to 15
Residue 19 ---> renumbered to 19
Residues in fragment:
15 G,15A C,15B Gm,19 G
Residue 15 ---> renumbered to 15
Residue 19 ---> renumbered to 19
Residue 15A ---> renumbered to 16
Residue 15B ---> renumbered to 18
Fragment inserted between residues 15 and residue 19.
Fragment is 4 residues long.
Checking whether alignment matches with model.
Sequences match:
Seq1: GGUGGGG4UCCCGAGC#GCCAAAGGGAGCAGACUQUA*APCUGCCGUCACAGACUUCGAAGGTPCGAAUCCUUCCCCCACCACCA
Seq2: GGUGGGG4UCCCGAGC#GCCAAAGGGAGCAGACUQUA*APCUGCCGUCACAGACUUCGAAGGTPCGAAUCCUUCCCCCACCACCA