---------------------------------------------------------------------- Data selection based on individual standard deviations. Stepwise skipping of data Program options: stat_ff -stepcrd -stdev -3.0 ---------------------------------------------------------------------- PDB file names included in the data set ---------------------------------------------------------------------- data/1a02.pdb data/1a74.pdb data/1aay.pdb data/1azq.pdb data/1b3t.pdb data/1ber.pdb data/1bf5.pdb data/1bhm.pdb data/1bl0.pdb data/1c0w.pdb data/1cdw.pdb data/1cf7.pdb data/1cjg.pdb data/1cma.pdb data/1d02.pdb data/1d66.pdb data/1dp7.pdb data/1ecr.pdb data/1fjl.pdb data/1gat.pdb data/1gcc.pdb data/1gdt.pdb data/1hcq.pdb data/1hcr.pdb data/1hdd.pdb data/1hlo.pdb data/1hry.pdb data/1hwt.pdb data/1if1.pdb data/1ign.pdb data/1ihf.pdb data/1lmb.pdb data/1mdy.pdb data/1mey.pdb data/1mhd.pdb data/1mnm.pdb data/1mse.pdb data/1oct.pdb data/1par.pdb data/1pdn.pdb data/1per.pdb data/1pnr.pdb data/1pue.pdb data/1pvi.pdb data/1pyi.pdb data/1rep.pdb data/1srs.pdb data/1svc.pdb data/1tc3.pdb data/1tf3.pdb data/1tro.pdb data/1tsr.pdb data/1ubd.pdb data/1xbr.pdb data/1yrn.pdb data/1ysa.pdb data/1yui.pdb data/2bop.pdb data/2drp.pdb data/2gli.pdb data/2hdc.pdb data/3cro.pdb ---------------------------------------------------------------------- Data selection rules ---------------------------------------------------------------------- 1. Improper base steps are skipped, i.e. - base steps containing a nick, - base steps containing base mismatches. 2. Redundant base steps. 3. Terminal base steps 4. Base steps / coords deviating more than 3. stdev from the average (3. and 4. are sorted out by stat_ff and are listed in a separate file.) 5. Generic base step: Base steps GC, CG, AT, and TA are counted twice in the symmetrized and non-symmetrized data set. ---------------------------------------------------------------------- Data selection coordinate statistics for each bp step / coordinate ---------------------------------------------------------------------- Step N Shift, A Slide, A Rise, A Tilt, deg Roll, deg Twist, deg CG 22 -0.25(1.10) 0.61(0.53) 3.34(0.33) 0.4( 3.8) 3.4( 6.5) 35.1( 6.0) CA 86 -0.03(0.56) 0.42(0.82) 3.33(0.28) -0.2( 3.3) 4.8( 5.5) 36.1( 4.8) TA 62 -0.02(0.56) 0.29(0.87) 3.36(0.29) 0.0( 2.5) 1.2( 6.9) 37.9( 6.3) AG 72 0.07(0.66) -0.41(0.49) 3.36(0.27) -1.6( 3.3) 5.1( 4.7) 31.8( 4.3) GG 78 -0.03(0.65) -0.53(0.77) 3.46(0.29) 0.3( 3.6) 4.3( 4.8) 32.2( 4.8) AA 118 0.00(0.50) -0.17(0.38) 3.28(0.21) -1.0( 3.0) -0.2( 4.6) 35.9( 3.5) GA 68 -0.29(0.47) -0.06(0.59) 3.30(0.23) -1.7( 3.4) 2.2( 4.3) 36.0( 4.7) AT 47 0.15(0.53) -0.63(0.26) 3.25(0.26) 0.3( 2.3) 0.5( 4.6) 30.9( 3.3) AC 91 0.15(0.57) -0.62(0.40) 3.32(0.22) 0.1( 3.4) 0.9( 4.5) 32.0( 3.5) GC 27 0.01(0.82) -0.13(0.62) 3.30(0.20) 0.9( 4.0) 0.6( 5.0) 35.6( 4.3) Generic base step (applying above described selection rules) XX 590 -0.01(0.65) -0.12(0.76) 3.33(0.26) -0.2( 3.3) 1.8( 5.7) 34.6( 5.4) ---------------------------------------------------------------------- Effective ff matrix for each base step ---------------------------------------------------------------------- Shift Slide Rise Tilt Roll Twist CG Number of data: 22 Shift 1.43 -0.05 -0.31 -0.29 -0.04 0.04 Slide -0.05 3.73 1.26 0.03 0.02 0.04 Rise -0.31 1.26 10.70 0.35 0.02 -0.04 Tilt -0.29 0.03 0.35 0.15 0.03 -0.01 Roll -0.04 0.02 0.02 0.03 0.03 0.01 Twist 0.04 0.04 -0.04 -0.01 0.01 0.03 CA Number of data: 86 Shift 3.81 0.38 -0.53 -0.20 -0.02 -0.09 Slide 0.38 2.32 1.86 0.07 0.02 -0.21 Rise -0.53 1.86 15.04 0.33 0.01 -0.25 Tilt -0.20 0.07 0.33 0.11 0.01 -0.01 Roll -0.02 0.02 0.01 0.01 0.04 0.02 Twist -0.09 -0.21 -0.25 -0.01 0.02 0.07 TA Number of data: 62 Shift 3.51 -0.32 -1.96 -0.11 0.06 0.04 Slide -0.32 2.15 3.10 0.07 -0.07 -0.20 Rise -1.96 3.10 19.27 -0.06 -0.34 -0.59 Tilt -0.11 0.07 -0.06 0.17 0.00 0.01 Roll 0.06 -0.07 -0.34 0.00 0.04 0.03 Twist 0.04 -0.20 -0.59 0.01 0.03 0.06 AG Number of data: 72 Shift 2.99 0.65 2.31 -0.23 0.02 0.04 Slide 0.65 4.57 2.18 -0.03 -0.11 -0.06 Rise 2.31 2.18 23.17 -0.72 -0.26 -0.65 Tilt -0.23 -0.03 -0.72 0.12 0.00 0.01 Roll 0.02 -0.11 -0.26 0.00 0.06 0.03 Twist 0.04 -0.06 -0.65 0.01 0.03 0.09 GG Number of data: 78 Shift 3.71 -0.05 -0.78 -0.29 0.07 0.18 Slide -0.05 2.02 0.51 0.11 0.05 -0.08 Rise -0.78 0.51 16.44 -0.57 0.04 -0.16 Tilt -0.29 0.11 -0.57 0.13 0.00 -0.02 Roll 0.07 0.05 0.04 0.00 0.05 0.01 Twist 0.18 -0.08 -0.16 -0.02 0.01 0.06 AA Number of data: 118 Shift 6.05 2.05 5.88 -0.33 -0.01 0.15 Slide 2.05 8.08 1.57 -0.06 -0.14 -0.14 Rise 5.88 1.57 31.12 -0.79 0.22 0.14 Tilt -0.33 -0.06 -0.79 0.14 0.01 0.00 Roll -0.01 -0.14 0.22 0.01 0.06 0.03 Twist 0.15 -0.14 0.14 0.00 0.03 0.10 GA Number of data: 68 Shift 6.34 1.43 -0.56 -0.22 0.06 0.20 Slide 1.43 3.78 -0.81 0.09 -0.10 -0.14 Rise -0.56 -0.81 24.69 -0.77 -0.12 -0.30 Tilt -0.22 0.09 -0.77 0.12 -0.01 -0.01 Roll 0.06 -0.10 -0.12 -0.01 0.09 0.05 Twist 0.20 -0.14 -0.30 -0.01 0.05 0.09 AT Number of data: 47 Shift 3.71 0.62 -0.20 -0.13 -0.01 0.03 Slide 0.62 15.44 0.99 0.23 0.16 0.05 Rise -0.20 0.99 17.97 0.12 -0.26 -0.55 Tilt -0.13 0.23 0.12 0.20 0.02 0.00 Roll -0.01 0.16 -0.26 0.02 0.06 0.03 Twist 0.03 0.05 -0.55 0.00 0.03 0.12 AC Number of data: 91 Shift 3.28 0.22 -1.68 -0.10 -0.01 0.01 Slide 0.22 6.78 3.43 0.01 0.04 -0.03 Rise -1.68 3.43 24.35 0.13 0.06 -0.23 Tilt -0.10 0.01 0.13 0.09 0.01 0.00 Roll -0.01 0.04 0.06 0.01 0.06 0.03 Twist 0.01 -0.03 -0.23 0.00 0.03 0.10 GC Number of data: 27 Shift 2.78 0.59 -6.96 -0.36 0.00 0.12 Slide 0.59 5.01 3.45 -0.04 0.32 -0.19 Rise -6.96 3.45 58.89 1.83 0.78 -0.64 Tilt -0.36 -0.04 1.83 0.13 0.03 0.00 Roll 0.00 0.32 0.78 0.03 0.09 0.03 Twist 0.12 -0.19 -0.64 0.00 0.03 0.10