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 ASV DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D- VINYLGLYCINE) > (REMARK ASV Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK ASV Extracted from PDB file pdb1odm.ent) > (REMARK ASV Formula C13 H21 N3 O6 S) Formula : (ASV C13 H21 N3 O6 S) > (REMARK ASV Nr of non-hydrogen atoms 23) > (REMARK ASV Eigen-values covariance X/Y/Z 412.1 43.4 30.8) > (REMARK ASV Residue type ASV) > (REMARK ASV Residue name 1742) > (REMARK ASV Original residue name (for O) $A1332) > (REMARK ASV RESOLUTION. 1.15 ANGSTROMS.) > (REMARK ASV occurs in 2 other PDB entries) > (REMARK ASV Also in <1.5A : 1OBN) > (REMARK ASV Resolution (A) : 1.30) > (REMARK ASV) Using residue : (ASV) Identifier : ( 1742) Segment ID : ( ) Using formula : ( C13 H21 N3 O6 S) Element ? | C| Carbon | 6 13 Element ? | H| Hydrogen | 1 21 Element ? | N| Nitrogen | 7 3 Element ? | O| Oxygen | 8 6 Element ? | S| Sulfur | 16 1 Atom # 1 = C1 @ -0.984 -0.194 7.051 1.00 20.00 Atom # 2 = C2 @ -0.459 0.495 5.818 1.00 20.00 Atom # 3 = C3 @ -0.640 -0.420 4.606 1.00 20.00 Atom # 4 = C4 @ -0.107 0.279 3.354 1.00 20.00 Atom # 5 = C7 @ -0.288 -0.636 2.142 1.00 20.00 Atom # 6 = C10 @ 0.235 0.053 0.909 1.00 20.00 Atom # 7 = N11 @ 0.180 -0.567 -0.285 1.00 20.00 Atom # 8 = C12 @ 0.690 0.102 -1.484 1.00 20.00 Atom # 9 = C13 @ -0.082 -0.367 -2.689 1.00 20.00 Atom # 10 = N14 @ 0.966 0.797 5.995 1.00 20.00 Atom # 11 = O15 @ 0.707 1.168 0.991 1.00 20.00 Atom # 12 = C16 @ 2.172 -0.233 -1.665 1.00 20.00 Atom # 13 = S17 @ 3.102 0.332 -0.214 1.00 20.00 Atom # 14 = O18 @ -0.971 -1.182 -2.560 1.00 20.00 Atom # 15 = O19 @ -0.248 -0.883 7.717 1.00 20.00 Atom # 16 = O20 @ -2.268 -0.042 7.410 1.00 20.00 Atom # 17 = N29 @ 0.214 0.117 -3.911 1.00 20.00 Atom # 18 = C30 @ -0.537 -0.339 -5.083 1.00 20.00 Atom # 19 = C31 @ -1.730 0.555 -5.294 1.00 20.00 Atom # 20 = C32 @ 0.350 -0.288 -6.300 1.00 20.00 Atom # 21 = C33 @ 0.600 -1.383 -6.974 1.00 20.00 Atom # 22 = O42 @ -2.736 0.113 -5.797 1.00 20.00 Atom # 23 = O43 @ -1.676 1.845 -4.925 1.00 20.00 > (REMARK ASV ENDHET) Nr of atoms read : ( 23) Nr of extra examples : ( 0) Expected formula : ( C13 H21 N3 O6 S) Observed formula : (C13 N3 O6 S1) Element | H| Expected 21 | Observed 0 Element | C| Expected 13 | Observed 13 Element | N| Expected 3 | Observed 3 Element | O| Expected 6 | Observed 6 Element | S| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 1.507 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 C1 - O19 = 1.208 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.19 (devn. 0.02) For: C-O shortened double; range 1.17-1.207 Bond C1 - O20 = 1.342 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.02) For: C-O partial double Bond C2 - C3 = 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 C2 - N14 = 1.467 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.48 (devn. 0.01) For: C-N single; range 1.472-1.479 Bond C3 - C4 = 1.530 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 C4 - C7 = 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 C7 - C10 = 1.506 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 C10 - N11 = 1.346 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 C10 - O15 = 1.214 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.19 (devn. 0.02) For: C-O shortened double; range 1.17-1.207 Bond N11 - C12 = 1.465 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 C12 - C13 = 1.506 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 C12 - C16 = 1.530 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 C13 - O18 = 1.213 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.19 (devn. 0.02) For: C-O shortened double; range 1.17-1.207 Bond C13 - N29 = 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 C16 - S17 = 1.814 A (cutoff : 2.050) Nr of entries in library : ( 3) Closest to 1.82 (devn. 0.01) For: C-S single Bond N29 - C30 = 1.465 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 C30 - C31 = 1.506 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 C30 - C32 = 1.507 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 C31 - O42 = 1.208 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.19 (devn. 0.02) For: C-O shortened double; range 1.17-1.207 Bond C31 - O43 = 1.343 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.02) For: C-O partial double Bond C32 - C33 = 1.310 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.03) For: C-C double or partial triple; range 1.309-1.337 Nr of bonds found : ( 22) 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: 3 ~Hs: 1 Carbon C3 Nbrs: 2 ~Hs: 2 Carbon C4 Nbrs: 2 ~Hs: 2 Carbon C7 Nbrs: 2 ~Hs: 2 Carbon C10 Nbrs: 3 ~Hs: 0 Nitrogen N11 Nbrs: 2 ~Hs: 1 Carbon C12 Nbrs: 3 ~Hs: 1 Carbon C13 Nbrs: 3 ~Hs: 0 Nitrogen N14 Nbrs: 1 ~Hs: 1 Oxygen O15 Nbrs: 1 ~Hs: 0 Carbon C16 Nbrs: 2 ~Hs: 2 Sulphur S17 Nbrs: 1 ~Hs: 1 Oxygen O18 Nbrs: 1 ~Hs: 0 Oxygen O19 Nbrs: 1 ~Hs: 0 Oxygen O20 Nbrs: 1 ~Hs: 1 Nitrogen N29 Nbrs: 2 ~Hs: 1 Carbon C30 Nbrs: 3 ~Hs: 1 Carbon C31 Nbrs: 3 ~Hs: 0 Carbon C32 Nbrs: 2 ~Hs: 1 Carbon C33 Nbrs: 1 ~Hs: 2 Oxygen O42 Nbrs: 1 ~Hs: 0 Oxygen O43 Nbrs: 1 ~Hs: 1 Est. total nr of hydrogens : ( 20) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 O19 119.97 C2 C1 O20 120.03 O19 C1 O20 120.00 C1 C2 C3 109.49 C1 C2 N14 109.50 C3 C2 N14 109.49 C2 C3 C4 109.51 C3 C4 C7 109.51 C4 C7 C10 109.51 C7 C10 N11 120.07 C7 C10 O15 120.00 N11 C10 O15 119.92 C10 N11 C12 120.09 N11 C12 C13 109.53 N11 C12 C16 109.52 C13 C12 C16 109.49 C12 C13 O18 119.99 C12 C13 N29 120.08 O18 C13 N29 119.93 C12 C16 S17 109.50 C13 N29 C30 120.08 N29 C30 C31 109.48 N29 C30 C32 109.51 C31 C30 C32 109.46 C30 C31 O42 120.05 C30 C31 O43 120.00 O42 C31 O43 119.95 C30 C32 C33 119.98 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- O19 C1 C2 C3 90.08 O19 C1 C2 N14 -29.98 O20 C1 C2 C3 -89.97 O20 C1 C2 N14 149.98 C1 C2 C3 C4 -179.99 Flat ? N14 C2 C3 C4 -59.94 C2 C3 C4 C7 180.00 Flat ? C3 C4 C7 C10 179.92 Flat ? C4 C7 C10 N11 179.98 Flat ? C4 C7 C10 O15 0.00 Flat ? C7 C10 N11 C12 -179.92 Flat ? O15 C10 N11 C12 0.05 Flat ? C10 N11 C12 C13 -150.01 C10 N11 C12 C16 89.90 N11 C12 C13 O18 -0.08 Flat ? N11 C12 C13 N29 179.96 Flat ? C16 C12 C13 O18 120.03 C16 C12 C13 N29 -59.93 N11 C12 C16 S17 -59.90 C13 C12 C16 S17 179.99 Flat ? C12 C13 N29 C30 -179.99 Flat ? O18 C13 N29 C30 0.05 Flat ? C13 N29 C30 C31 89.94 C13 N29 C30 C32 -150.05 N29 C30 C31 O42 -150.00 N29 C30 C31 O43 30.10 C32 C30 C31 O42 89.96 C32 C30 C31 O43 -89.94 N29 C30 C32 C33 119.92 C31 C30 C32 C33 -120.05 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 O19 O20 -0.03 C2 C1 C3 N14 34.77 C10 C7 N11 O15 0.01 C12 N11 C13 C16 35.61 C13 C12 O18 N29 0.02 C30 N29 C31 C32 -35.45 C31 C30 O42 O43 0.06 Number of possible flat planes : ( 16) Looking for more planes ... Number of possible flat planes : ( 22) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -1.583E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.430E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.132E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.115E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.330E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.924E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.902E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.272E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.184E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.061E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.524E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.184E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.383E-09) WARNING - Reset negative RMSD in LSQGJK : ( -9.061E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.278E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.481E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.257E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.562E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.883E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.383E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.257E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.259E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.055E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.890E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.383E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.257E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.753E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.715E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.304E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.304E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.193E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.783E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.383E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.304E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.673E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.223E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.028E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.330E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.583E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.924E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.902E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.184E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.316E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.796E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.319E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.589E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.319E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.257E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.304E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.080E-08) Removing non-unique planes ... Plane nr : ( 13) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C1 0.000 C2 0.000 O19 0.000 O20 0.000 Plane nr : ( 16) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C31 0.000 C30 0.000 O42 0.000 O43 0.000 Plane nr : ( 20) Nr of atoms : ( 9) WARNING - Reset negative RMSD in LSQGJK : ( -3.257E-08) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) N11 0.000 C10 0.000 C12 0.000 C7 0.000 O15 0.001 C4 -0.001 C3 0.000 C2 0.000 C1 0.001 Plane nr : ( 21) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C16 0.000 C12 0.000 S17 0.000 C13 0.000 Plane nr : ( 22) Nr of atoms : ( 6) WARNING - Reset negative RMSD in LSQGJK : ( -1.306E-07) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) N29 0.000 C13 0.000 C30 0.000 C12 0.000 O18 0.000 N11 0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (ASV) Identifier : ( 1742) Segment ID : ( ) Nr of atoms : ( 23) List of elements (from file) : ( C13 H21 N3 O6 S) Deduced formula : (C13 N3 O6 S1) Guestimated total nr of Hs : ( 20) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 22) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 22) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 28) Nr of dihedrals found : ( 30) Nr of atoms with impropers : ( 7) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 5)