Program parameters : Bond tolerance (A) : ( 0.350) Bond deviation tolerance (A) : ( 0.050) Large range for bond lengths (A) : ( 0.070) Large range for bond angles (d) : ( 8.000) Large range for dihedrals (d) : ( 15.000) Large range for impropers (d) : ( 8.000) Improper deviation tolerance (d) : ( 8.000) Flat improper cut-off (d) : ( 15.000) Max distance to a flat plane (A) : ( 0.050) Reading PDB file ... > (COMPND BRG 8-BROMOGUANINE) > (REMARK BRG Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK BRG Extracted from PDB file pdb1lww.ent) > (REMARK BRG Formula C5 H4 BR N5 O) Formula : (BRG C5 H4 BR N5 O) > (REMARK BRG Nr of non-hydrogen atoms 12) > (REMARK BRG Eigen-values covariance X/Y/Z 49.3 17.5 0.0) > (REMARK BRG Residue type BRG) > (REMARK BRG Residue name 2131) > (REMARK BRG Original residue name (for O) $217) > (REMARK BRG RESOLUTION. 2.10 ANGSTROMS.) > (REMARK BRG occurs in 0 other PDB entries) > (REMARK BRG) Using residue : (BRG) Identifier : ( 2131) Segment ID : ( ) Using formula : ( C5 H4 BR N5 O) Element ? | C| Carbon | 6 5 Element ? | H| Hydrogen | 1 4 Element ? |BR| Bromine | 35 1 Element ? | N| Nitrogen | 7 5 Element ? | O| Oxygen | 8 1 Atom # 1 = N9 @ 1.134 0.000 -0.397 1.00 20.00 Atom # 2 = C4 @ 0.756 0.000 0.892 1.00 20.00 Atom # 3 = N3 @ 1.426 0.000 2.060 1.00 20.00 Atom # 4 = C2 @ 0.787 0.000 3.206 1.00 20.00 Atom # 5 = N2 @ 1.512 0.000 4.373 1.00 20.00 Atom # 6 = N1 @ -0.573 -0.004 3.273 1.00 20.00 Atom # 7 = C6 @ -1.311 0.000 2.140 1.00 20.00 Atom # 8 = O6 @ -2.530 0.001 2.189 1.00 20.00 Atom # 9 = C5 @ -0.642 0.000 0.906 1.00 20.00 Atom # 10 = N7 @ -1.041 0.000 -0.417 1.00 20.00 Atom # 11 = C8 @ 0.079 0.000 -1.169 1.00 20.00 Atom # 12 = BR @ 0.118 0.000 -3.059 1.00 20.00 > (REMARK BRG ENDHET) Nr of atoms read : ( 12) Nr of extra examples : ( 0) Expected formula : ( C5 H4 BR N5 O) Observed formula : (C5 N5 O1 BR1) Element | H| Expected 4 | Observed 0 Element | C| Expected 5 | Observed 5 Element | N| Expected 5 | Observed 5 Element | O| Expected 1 | Observed 1 Element |BR| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond N9 - C4 = 1.343 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.00) For: C-N partial double; range 1.322-1.352 Bond N9 - C8 = 1.307 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Bond C4 - N3 = 1.347 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.01) For: C-N partial double; range 1.322-1.352 Bond C4 - C5 = 1.398 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.01) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond N3 - C2 = 1.312 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Bond C2 - N2 = 1.374 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Bond C2 - N1 = 1.362 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.02) For: C-N partial double; range 1.322-1.352 Bond N1 - C6 = 1.352 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.01) For: C-N partial double; range 1.322-1.352 Bond C6 - O6 = 1.220 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.24 (devn. 0.02) For: C-O double; range 1.23-1.26 Bond C6 - C5 = 1.404 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.01) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C5 - N7 = 1.382 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.04) For: C-N partial double; range 1.322-1.352 Bond N7 - C8 = 1.349 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.01) For: C-N partial double; range 1.322-1.352 Bond C8 - BR = 1.890 A (cutoff : 2.240) Nr of entries in library : ( 3) Closest to 1.87 (devn. 0.02) For: C-Br CH2=CH-Br or C6H5-Br type; range 1.85-1.89 Nr of bonds found : ( 13) Generating neighbour lists ... Trying to guess number of hydrogens ... Minimum C-C single bond (A) : ( 1.480) Minimum C-C double bond (A) : ( 1.280) Minimum C-N single bond (A) : ( 1.400) Minimum C-N double bond (A) : ( 1.200) Minimum C-O single bond (A) : ( 1.300) Minimum C-S single bond (A) : ( 1.770) Nitrogen N9 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 0 Nitrogen N3 Nbrs: 2 ~Hs: 1 Carbon C2 Nbrs: 3 ~Hs: 0 Nitrogen N2 Nbrs: 1 ~Hs: 0 Nitrogen N1 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 3 ~Hs: 0 Oxygen O6 Nbrs: 1 ~Hs: 0 Carbon C5 Nbrs: 3 ~Hs: 0 Nitrogen N7 Nbrs: 2 ~Hs: 1 Carbon C8 Nbrs: 3 ~Hs: 0 Est. total nr of hydrogens : ( 4) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C4 N9 C8 109.85 N9 C4 N3 133.82 N9 C4 C5 106.92 N3 C4 C5 119.27 C4 N3 C2 121.02 N3 C2 N2 119.01 N3 C2 N1 121.96 N2 C2 N1 119.03 C2 N1 C6 120.26 N1 C6 O6 120.78 N1 C6 C5 118.46 O6 C6 C5 120.77 C4 C5 C6 119.04 C4 C5 N7 106.21 C6 C5 N7 134.75 C5 N7 C8 107.10 N9 C8 N7 109.93 N9 C8 BR 125.01 N7 C8 BR 125.06 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C8 N9 C4 N3 180.00 Flat ? C8 N9 C4 C5 0.00 Flat ? C4 N9 C8 N7 0.00 Flat ? C4 N9 C8 BR 180.00 Flat ? N9 C4 N3 C2 180.00 Flat ? C5 C4 N3 C2 0.00 Flat ? N9 C4 C5 C6 180.00 Flat ? N9 C4 C5 N7 0.00 Flat ? N3 C4 C5 C6 0.00 Flat ? N3 C4 C5 N7 180.00 Flat ? C4 N3 C2 N2 180.00 Flat ? C4 N3 C2 N1 0.20 Flat ? N3 C2 N1 C6 -0.40 Flat ? N2 C2 N1 C6 179.80 Flat ? C2 N1 C6 O6 -179.75 Flat ? C2 N1 C6 C5 0.39 Flat ? N1 C6 C5 C4 -0.19 Flat ? N1 C6 C5 N7 179.81 Flat ? O6 C6 C5 C4 179.95 Flat ? O6 C6 C5 N7 -0.05 Flat ? C4 C5 N7 C8 0.00 Flat ? C6 C5 N7 C8 180.00 Flat ? C5 N7 C8 N9 0.00 Flat ? C5 N7 C8 BR 180.00 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C4 N9 N3 C5 0.00 C2 N3 N2 N1 0.11 C6 N1 O6 C5 0.08 C5 C4 C6 N7 0.00 C8 N9 N7 BR 0.00 Number of possible flat planes : ( 29) Looking for more planes ... Number of possible flat planes : ( 33) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -2.694E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.051E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.350E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.732E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.501E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.209E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.788E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.694E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.303E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.276E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.054E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.384E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.825E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.348E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.530E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.054E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.384E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.974E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.765E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.237E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.483E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.314E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.837E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.853E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.210E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.129E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.809E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.158E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.100E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.903E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.158E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.054E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.749E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.314E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.731E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.578E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.645E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.229E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.438E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.358E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.200E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.648E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.275E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.705E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.168E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.935E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.833E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.180E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.858E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.180E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.439E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.935E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.262E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.210E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.609E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.973E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.887E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.249E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.472E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.629E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.347E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.777E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.081E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.488E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.645E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.527E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.081E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.507E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.475E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.553E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.303E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.141E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.231E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.209E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.788E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.629E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.507E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.141E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.303E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.743E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.903E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.084E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.303E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.797E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.895E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.527E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.231E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.797E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.895E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.527E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.731E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.200E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.660E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.229E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.065E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.158E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.438E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.903E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.276E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.463E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.765E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.080E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.209E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.469E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.627E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.694E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.051E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.051E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.483E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.163E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.551E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.609E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.858E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.084E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.231E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.209E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.469E-08) Removing non-unique planes ... Plane nr : ( 33) Nr of atoms : ( 12) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) N7 0.000 C5 0.000 C8 0.000 C4 0.000 C6 0.000 N9 0.000 BR 0.000 N3 0.000 N1 -0.003 O6 0.001 C2 0.001 N2 0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (BRG) Identifier : ( 2131) Segment ID : ( ) Nr of atoms : ( 12) List of elements (from file) : ( C5 H4 BR N5 O) Deduced formula : (C5 N5 O1 BR1) Guestimated total nr of Hs : ( 4) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 13) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 13) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 19) Nr of dihedrals found : ( 24) Nr of atoms with impropers : ( 5) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 1)