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 EUG 2-METHOXY-4-VINYL-PHENOL) > (REMARK EUG Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK EUG Extracted from PDB file pdb2qu9.ent) > (REMARK EUG Formula C9 H10 O2) Formula : (EUG C9 H10 O2) > (REMARK EUG Nr of non-hydrogen atoms 11) > (REMARK EUG Eigen-values covariance X/Y/Z 39.9 19.1 1.2) > (REMARK EUG Residue type EUG) > (REMARK EUG Residue name 3433) > (REMARK EUG Original residue name (for O) $A302) > (REMARK EUG RESOLUTION. 2.08 ANGSTROMS.) > (REMARK EUG occurs in 7 other PDB entries) > (REMARK EUG Also in 2.0-2.5A : 1QLU) > (REMARK EUG Resolution (A) : 2.40) > (REMARK EUG Also in 2.5-3.0A : 1W1K 1W1J 1W1L 1DZN 2VAO 1W1M) > (REMARK EUG Resolution (A) : 2.55 2.70 2.70 2.80 2.80 3.00) > (REMARK EUG) Using residue : (EUG) Identifier : ( 3433) Segment ID : ( ) Using formula : ( C9 H10 O2) Element ? | C| Carbon | 6 9 Element ? | H| Hydrogen | 1 10 Element ? | O| Oxygen | 8 2 Atom # 1 = C1 @ 0.180 0.000 -1.363 1.00 20.00 Atom # 2 = C2 @ 0.921 0.000 -0.181 1.00 20.00 Atom # 3 = C3 @ 0.270 0.009 1.038 1.00 20.00 Atom # 4 = C4 @ -1.121 0.014 1.085 1.00 20.00 Atom # 5 = C5 @ -1.857 0.020 -0.089 1.00 20.00 Atom # 6 = C6 @ -1.214 0.010 -1.310 1.00 20.00 Atom # 7 = C7 @ 0.870 -0.011 -2.670 1.00 20.00 Atom # 8 = C8 @ 0.165 -0.011 -3.793 1.00 20.00 Atom # 9 = C9 @ 2.369 -0.001 1.820 1.00 20.00 Atom # 10 = O3 @ 0.990 0.009 2.193 1.00 20.00 Atom # 11 = O4 @ -1.759 0.024 2.286 1.00 20.00 > (REMARK EUG ENDHET) Nr of atoms read : ( 11) Nr of extra examples : ( 0) Expected formula : ( C9 H10 O2) Observed formula : (C9 O2) Element | H| Expected 10 | Observed 0 Element | C| Expected 9 | Observed 9 Element | O| Expected 2 | Observed 2 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 1.395 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 C1 - C6 = 1.395 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 C1 - C7 = 1.478 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.04) For: C-C single shortened; range 1.421-1.46 Bond C2 - C3 = 1.382 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 C3 - C4 = 1.392 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C3 - O3 = 1.361 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.00) For: C-O partial double Bond C4 - C5 = 1.386 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond C4 - O4 = 1.360 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.00) For: C-O partial double Bond C5 - C6 = 1.380 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 C7 - C8 = 1.326 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 C9 - O3 = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Nr of bonds found : ( 11) 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) Carbon C1 Nbrs: 3 ~Hs: 0 Carbon C2 Nbrs: 2 ~Hs: 1 Carbon C3 Nbrs: 3 ~Hs: 0 Carbon C4 Nbrs: 3 ~Hs: 0 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 2 ~Hs: 1 Carbon C8 Nbrs: 1 ~Hs: 2 Carbon C9 Nbrs: 1 ~Hs: 3 Oxygen O3 Nbrs: 2 ~Hs: 0 Oxygen O4 Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 10) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 C6 119.91 C2 C1 C7 120.08 C6 C1 C7 120.01 C1 C2 C3 119.81 C2 C3 C4 120.04 C2 C3 O3 119.96 C4 C3 O3 120.00 C3 C4 C5 120.15 C3 C4 O4 119.91 C5 C4 O4 119.93 C4 C5 C6 120.14 C1 C6 C5 119.95 C1 C7 C8 120.05 C3 O3 C9 106.80 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C6 C1 C2 C3 0.04 Flat ? C7 C1 C2 C3 -179.94 Flat ? C2 C1 C6 C5 0.01 Flat ? C7 C1 C6 C5 179.99 Flat ? C2 C1 C7 C8 180.00 Flat ? C6 C1 C7 C8 0.02 Flat ? C1 C2 C3 C4 0.19 Flat ? C1 C2 C3 O3 180.00 Flat ? C2 C3 C4 C5 -0.48 Flat ? C2 C3 C4 O4 -179.94 Flat ? O3 C3 C4 C5 179.71 Flat ? O3 C3 C4 O4 0.25 Flat ? C2 C3 O3 C9 0.01 Flat ? C4 C3 O3 C9 179.82 Flat ? C3 C4 C5 C6 0.53 Flat ? O4 C4 C5 C6 180.00 Flat ? C4 C5 C6 C1 -0.29 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 C6 C7 0.01 C3 C2 C4 O3 -0.11 C4 C3 C5 O4 0.31 Number of possible flat planes : ( 20) Looking for more planes ... Number of possible flat planes : ( 25) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -3.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.841E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.751E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.010E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.970E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.996E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.737E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.303E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.778E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.088E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.778E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.135E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.797E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.970E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.121E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.389E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.121E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.075E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.797E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.132E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.841E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.996E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.366E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.050E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.030E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.789E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.622E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.464E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.047E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.075E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.275E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.480E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.789E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.514E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.038E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.132E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.059E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.688E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.132E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.785E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.943E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.842E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.583E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.880E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.059E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.943E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.085E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.132E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.038E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.430E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.132E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.286E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.078E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.778E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.972E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.082E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.286E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.702E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.789E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.943E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.622E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.132E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.632E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.841E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.751E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.688E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.010E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.778E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.088E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.021E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.121E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.970E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.389E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.797E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.702E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.943E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.785E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.458E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.583E-08) Removing non-unique planes ... Plane nr : ( 25) Nr of atoms : ( 11) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) O3 0.001 C3 0.001 C9 0.000 C2 0.000 C4 -0.003 C1 0.000 C5 0.003 O4 -0.002 C6 0.002 C7 -0.001 C8 -0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (EUG) Identifier : ( 3433) Segment ID : ( ) Nr of atoms : ( 11) List of elements (from file) : ( C9 H10 O2) Deduced formula : (C9 O2) Guestimated total nr of Hs : ( 10) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 11) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 11) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 14) Nr of dihedrals found : ( 17) Nr of atoms with impropers : ( 3) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 1)