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 DUD DEOXYURIDINE-5p-DIPHOSPHATE) > (REMARK DUD Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK DUD Extracted from PDB file pdb2yzj.ent) > (REMARK DUD Formula C9 H14 N2 O11 P2) Formula : (DUD C9 H14 N2 O11 P2) > (REMARK DUD Nr of non-hydrogen atoms 24) > (REMARK DUD Eigen-values covariance X/Y/Z 244.9 82.3 25.0) > (REMARK DUD Residue type DUD) > (REMARK DUD Residue name 3243) > (REMARK DUD Original residue name (for O) $A6194) > (REMARK DUD RESOLUTION. 1.66 ANGSTROMS.) > (REMARK DUD occurs in 7 other PDB entries) > (REMARK DUD Also in 1.5-2.0A : 2HR6 1Q5H) > (REMARK DUD Resolution (A) : 1.84 2.00) > (REMARK DUD Also in 2.0-2.5A : 1DUC 2OL0 1DUD) > (REMARK DUD Resolution (A) : 2.05 2.10 2.30) > (REMARK DUD Also in 2.5-3.0A : 1OGK 1SLH) > (REMARK DUD Resolution (A) : 2.85 3.00) > (REMARK DUD) Using residue : (DUD) Identifier : ( 3243) Segment ID : ( ) Using formula : ( C9 H14 N2 O11 P2) Element ? | C| Carbon | 6 9 Element ? | H| Hydrogen | 1 14 Element ? | N| Nitrogen | 7 2 Element ? | O| Oxygen | 8 11 Element ? | P| Phosphorous | 15 2 Atom # 1 = N1 @ -0.011 0.492 3.888 1.00 20.00 Atom # 2 = C2 @ -0.693 -0.664 3.803 1.00 20.00 Atom # 3 = N3 @ -1.692 -0.943 4.662 1.00 20.00 Atom # 4 = C4 @ -2.033 -0.056 5.618 1.00 20.00 Atom # 5 = C5 @ -1.328 1.167 5.715 1.00 20.00 Atom # 6 = C6 @ -0.326 1.418 4.844 1.00 20.00 Atom # 7 = O2 @ -0.397 -1.474 2.946 1.00 20.00 Atom # 8 = O4 @ -2.940 -0.305 6.392 1.00 20.00 Atom # 9 = C1' @ 1.074 0.764 2.943 1.00 20.00 Atom # 10 = C2' @ 2.176 -0.309 3.066 1.00 20.00 Atom # 11 = C3' @ 2.655 -0.525 1.613 1.00 20.00 Atom # 12 = C4' @ 1.784 0.442 0.781 1.00 20.00 Atom # 13 = O4' @ 0.600 0.653 1.583 1.00 20.00 Atom # 14 = O3' @ 4.038 -0.190 1.486 1.00 20.00 Atom # 15 = C5' @ 1.412 -0.186 -0.562 1.00 20.00 Atom # 16 = O5' @ 0.549 0.698 -1.280 1.00 20.00 Atom # 17 = PA @ 0.200 -0.023 -2.676 1.00 20.00 Atom # 18 = O1A @ -0.474 -1.313 -2.409 1.00 20.00 Atom # 19 = O2A @ 1.558 -0.287 -3.498 1.00 20.00 Atom # 20 = O3A @ -0.774 0.923 -3.540 1.00 20.00 Atom # 21 = PB @ -1.081 0.144 -4.915 1.00 20.00 Atom # 22 = O1B @ -1.736 -1.148 -4.614 1.00 20.00 Atom # 23 = O2B @ -2.056 1.038 -5.833 1.00 20.00 Atom # 24 = O3B @ 0.298 -0.123 -5.700 1.00 20.00 > (REMARK DUD ENDHET) Nr of atoms read : ( 24) Nr of extra examples : ( 0) Expected formula : ( C9 H14 N2 O11 P2) Observed formula : (C9 N2 O11 P2) Element | H| Expected 14 | Observed 0 Element | C| Expected 9 | Observed 9 Element | N| Expected 2 | Observed 2 Element | O| Expected 11 | Observed 11 Element | P| Expected 2 | Observed 2 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond N1 - C2 = 1.345 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 N1 - C6 = 1.368 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 N1 - C1' = 1.464 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.48 (devn. 0.02) For: C-N single; range 1.472-1.479 Bond C2 - 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 C2 - O2 = 1.216 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 N3 - C4 = 1.348 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 = 1.415 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.02) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C4 - O4 = 1.218 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 C5 - C6 = 1.351 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.01) For: C-C double or partial triple; range 1.309-1.337 Bond C1' - C2' = 1.543 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C1' - O4' = 1.445 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.01) For: C-O single Bond C2' - C3' = 1.545 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.02) For: C-C single; range 1.49-1.54 Bond C3' - C4' = 1.545 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C3' - O3' = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C4' - O4' = 1.446 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.02) For: C-O single Bond C4' - C5' = 1.529 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.00) For: C-C single; range 1.49-1.54 Bond C5' - O5' = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond O5' - PA = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond PA - O1A = 1.480 A (cutoff : 2.080) Nr of entries in library : ( 2) >>> WARNING - Too far from ideal 1.38 (devn. 0.10) For: O-P double Bond PA - O2A = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond PA - O3A = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond O3A - PB = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond PB - O1B = 1.479 A (cutoff : 2.080) Nr of entries in library : ( 2) >>> WARNING - Too far from ideal 1.38 (devn. 0.10) For: O-P double Bond PB - O2B = 1.610 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Bond PB - O3B = 1.609 A (cutoff : 2.080) Nr of entries in library : ( 2) Closest to 1.63 (devn. 0.02) For: O-P single Nr of bonds found : ( 25) 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 N1 Nbrs: 3 ~Hs: 0 Carbon C2 Nbrs: 3 ~Hs: 0 Nitrogen N3 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 1 Oxygen O2 Nbrs: 1 ~Hs: 0 Oxygen O4 Nbrs: 1 ~Hs: 0 Carbon C1' Nbrs: 3 ~Hs: 1 Carbon C2' Nbrs: 2 ~Hs: 2 Carbon C3' Nbrs: 3 ~Hs: 1 Carbon C4' Nbrs: 3 ~Hs: 1 Oxygen O4' Nbrs: 2 ~Hs: 0 Oxygen O3' Nbrs: 1 ~Hs: 1 Carbon C5' Nbrs: 2 ~Hs: 2 Oxygen O5' Nbrs: 2 ~Hs: 0 Oxygen O1A Nbrs: 1 ~Hs: 1 Oxygen O2A Nbrs: 1 ~Hs: 1 Oxygen O3A Nbrs: 2 ~Hs: 0 Oxygen O1B Nbrs: 1 ~Hs: 1 Oxygen O2B Nbrs: 1 ~Hs: 1 Oxygen O3B Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 16) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 N1 C6 120.62 C2 N1 C1' 119.65 C6 N1 C1' 119.73 N1 C2 N3 120.93 N1 C2 O2 119.59 N3 C2 O2 119.48 C2 N3 C4 120.24 N3 C4 C5 119.43 N3 C4 O4 120.30 C5 C4 O4 120.27 C4 C5 C6 119.07 N1 C6 C5 119.71 N1 C1' C2' 110.40 N1 C1' O4' 110.50 C2' C1' O4' 104.83 C1' C2' C3' 104.10 C2' C3' C4' 104.13 C2' C3' O3' 110.54 C4' C3' O3' 110.56 C3' C4' O4' 104.74 C3' C4' C5' 110.69 O4' C4' C5' 110.37 C1' O4' C4' 105.36 C4' C5' O5' 109.53 C5' O5' PA 106.84 O5' PA O1A 109.44 O5' PA O2A 109.48 O5' PA O3A 109.48 O1A PA O2A 109.48 O1A PA O3A 109.49 O2A PA O3A 109.45 PA O3A PB 106.83 O3A PB O1B 109.46 O3A PB O2B 109.50 O3A PB O3B 109.48 O1B PB O2B 109.44 O1B PB O3B 109.50 O2B PB O3B 109.45 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C6 N1 C2 N3 -0.60 Flat ? C6 N1 C2 O2 -179.99 Flat ? C1' N1 C2 N3 179.73 Flat ? C1' N1 C2 O2 0.35 Flat ? C2 N1 C6 C5 0.28 Flat ? C1' N1 C6 C5 179.94 Flat ? C2 N1 C1' C2' -60.35 C2 N1 C1' O4' 55.15 C6 N1 C1' C2' 119.98 C6 N1 C1' O4' -124.51 N1 C2 N3 C4 0.62 Flat ? O2 C2 N3 C4 -180.00 Flat ? C2 N3 C4 C5 -0.31 Flat ? C2 N3 C4 O4 179.70 Flat ? N3 C4 C5 C6 0.00 Flat ? O4 C4 C5 C6 179.99 Flat ? C4 C5 C6 N1 0.02 Flat ? N1 C1' C2' C3' 142.97 O4' C1' C2' C3' 23.96 N1 C1' O4' C4' -159.33 C2' C1' O4' C4' -40.39 C1' C2' C3' C4' -0.09 Flat ? C1' C2' C3' O3' 118.67 C2' C3' C4' O4' -23.78 C2' C3' C4' C5' -142.73 O3' C3' C4' O4' -142.53 O3' C3' C4' C5' 98.52 C3' C4' O4' C1' 40.28 C5' C4' O4' C1' 159.45 C3' C4' C5' O5' 176.91 Flat ? O4' C4' C5' O5' 61.43 C4' C5' O5' PA 179.98 Flat ? C5' O5' PA O1A 60.00 C5' O5' PA O2A -60.00 C5' O5' PA O3A -179.99 Flat ? O5' PA O3A PB -179.98 Flat ? O1A PA O3A PB -60.00 O2A PA O3A PB 60.01 PA O3A PB O1B 60.01 PA O3A PB O2B 179.98 Flat ? PA O3A PB O3B -60.02 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- N1 C2 C6 C1' 0.20 C2 N1 N3 O2 0.35 C4 N3 C5 O4 0.01 C1' N1 C2' O4' -36.91 C3' C2' C4' O3' -33.59 C4' C3' O4' C5' 34.97 --- Atom with 4 or more non-H neighbours --- PA O5' O1A O2A 35.84 PA O1A O2A O3A -35.85 PA O2A O3A O5' 35.25 PA O3A O5' O1A -34.12 --- Atom with 4 or more non-H neighbours --- PB O3A O1B O2B -35.86 PB O1B O2B O3B 35.85 PB O2B O3B O3A -35.25 PB O3B O3A O1B 34.10 Number of possible flat planes : ( 22) Looking for more planes ... Number of possible flat planes : ( 29) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -6.868E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.020E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.711E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.071E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.225E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.301E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.953E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.143E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.909E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.523E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.027E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.648E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.631E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.571E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.586E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.341E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.647E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.438E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.498E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.058E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.792E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.043E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.884E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.058E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.300E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.493E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.857E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.358E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.121E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.020E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.951E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.973E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.357E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.084E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.186E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.806E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.576E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.228E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.055E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.042E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.148E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.391E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.711E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.480E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.454E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.626E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.820E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.323E-09) WARNING - Reset negative RMSD in LSQGJK : ( -7.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.515E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.301E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.027E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.940E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.934E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.041E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.752E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.616E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.107E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.046E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.338E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.059E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.857E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.200E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.095E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.602E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.996E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.391E-08) Removing non-unique planes ... Plane nr : ( 25) Nr of atoms : ( 9) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C6 -0.001 N1 0.001 C5 -0.001 C2 -0.003 C1' 0.001 C4 0.000 N3 0.003 O2 -0.001 O4 0.000 Plane nr : ( 26) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.005E-07) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C2' -0.001 C1' 0.000 C3' 0.001 C4' 0.000 Plane nr : ( 27) Nr of atoms : ( 8) RMSD to least-squares plane (A): ( 0.020) Atom Dist (A) C5' -0.025 C4' -0.016 O5' -0.004 C3' 0.039 PA -0.015 O3A 0.007 PB -0.004 O2B 0.018 ------------------- ----- SUMMARY ----- ------------------- Residue type : (DUD) Identifier : ( 3243) Segment ID : ( ) Nr of atoms : ( 24) List of elements (from file) : ( C9 H14 N2 O11 P2) Deduced formula : (C9 N2 O11 P2) Guestimated total nr of Hs : ( 16) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 25) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 23) ... bonds far from ideal value : ( 2) -"- % : ( 8.000) Nr of angles found : ( 38) Nr of dihedrals found : ( 41) Nr of atoms with impropers : ( 8) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 3)