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 OCT N-OCTANE) > (REMARK OCT Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK OCT Extracted from PDB file pdb2euk.ent) > (REMARK OCT Formula C8 H18) Formula : (OCT C8 H18) > (REMARK OCT Nr of non-hydrogen atoms 8) > (REMARK OCT Eigen-values covariance X/Y/Z 49.8 5.7 0.9) > (REMARK OCT Residue type OCT) > (REMARK OCT Residue name 5783) > (REMARK OCT Original residue name (for O) $303) > (REMARK OCT RESOLUTION. 1.85 ANGSTROMS.) > (REMARK OCT occurs in 20 other PDB entries) > (REMARK OCT Also in 1.5-2.0A : 2GFC 1SX6 2VDF 1APM 2EVD) > (REMARK OCT Resolution (A) : 1.87 1.95 1.95 2.00 2.00) > (REMARK OCT Also in 2.0-2.5A : 1RE8 2GSK 1JBP 1XJI 2EVL 1CWQ 1JLU 2J58 1Y5M 2EUM) > (REMARK OCT Resolution (A) : 2.10 2.10 2.20 2.20 2.20 2.25 2.25 2.25 2.30 2.30) > (REMARK OCT Also in 2.5-3.0A : 1BRR 1KPL) > (REMARK OCT Resolution (A) : 2.90 3.00) > (REMARK OCT Also in >3.0A : 1IEK 1IEY 1K9Q) > (REMARK OCT Resolution (A) : 9.99 9.99 9.99) > (REMARK OCT) Using residue : (OCT) Identifier : ( 5783) Segment ID : ( ) Using formula : ( C8 H18) Element ? | C| Carbon | 6 8 Element ? | H| Hydrogen | 1 18 Atom # 1 = C1 @ -0.277 0.000 4.385 1.00 20.00 Atom # 2 = C2 @ 0.558 0.000 3.104 1.00 20.00 Atom # 3 = C3 @ -0.371 0.000 1.889 1.00 20.00 Atom # 4 = C4 @ 0.464 0.000 0.607 1.00 20.00 Atom # 5 = C5 @ -0.464 0.000 -0.607 1.00 20.00 Atom # 6 = C6 @ 0.371 0.000 -1.889 1.00 20.00 Atom # 7 = C7 @ -0.558 0.000 -3.104 1.00 20.00 Atom # 8 = C8 @ 0.277 0.000 -4.385 1.00 20.00 > (REMARK OCT ENDHET) Nr of atoms read : ( 8) Nr of extra examples : ( 0) Expected formula : ( C8 H18) Observed formula : (C8) Element | H| Expected 18 | Observed 0 Element | C| Expected 8 | Observed 8 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 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 - 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 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 - C5 = 1.528 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 - C6 = 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 C6 - 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 - C8 = 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 Nr of bonds found : ( 7) 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: 1 ~Hs: 3 Carbon C2 Nbrs: 2 ~Hs: 2 Carbon C3 Nbrs: 2 ~Hs: 2 Carbon C4 Nbrs: 2 ~Hs: 2 Carbon C5 Nbrs: 2 ~Hs: 2 Carbon C6 Nbrs: 2 ~Hs: 2 Carbon C7 Nbrs: 2 ~Hs: 2 Carbon C8 Nbrs: 1 ~Hs: 3 Est. total nr of hydrogens : ( 18) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C1 C2 C3 109.50 C2 C3 C4 109.52 C3 C4 C5 109.53 C4 C5 C6 109.53 C5 C6 C7 109.52 C6 C7 C8 109.50 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C1 C2 C3 C4 180.00 Flat ? C2 C3 C4 C5 180.00 Flat ? C3 C4 C5 C6 180.00 Flat ? C4 C5 C6 C7 180.00 Flat ? C5 C6 C7 C8 180.00 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- Number of possible flat planes : ( 5) Looking for more planes ... Number of possible flat planes : ( 11) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.005E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.020E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) Removing non-unique planes ... Plane nr : ( 11) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -9.250E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C7 0.000 C6 0.000 C8 0.000 C5 0.000 C4 0.000 C3 0.000 C2 0.000 C1 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (OCT) Identifier : ( 5783) Segment ID : ( ) Nr of atoms : ( 8) List of elements (from file) : ( C8 H18) Deduced formula : (C8) Guestimated total nr of Hs : ( 18) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 7) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 7) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 6) Nr of dihedrals found : ( 5) Nr of atoms with impropers : ( 0) Nr of flat planes : ( 1)