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 STE STEARIC ACID) > (REMARK STE Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK STE Extracted from PDB file pdb1hmt.ent) > (REMARK STE Formula C18 H36 O2) Formula : (STE C18 H36 O2) > (REMARK STE Nr of non-hydrogen atoms 20) > (REMARK STE Eigen-values covariance X/Y/Z 156.4 109.2 22.9) > (REMARK STE Residue type STE) > (REMARK STE Residue name 7004) > (REMARK STE Original residue name (for O) $133) > (REMARK STE RESOLUTION. 1.40 ANGSTROMS.) > (REMARK STE occurs in 7 other PDB entries) > (REMARK STE Also in 1.5-2.0A : 1LIF 1FK4 1XXS 1K4W 1UVC) > (REMARK STE Resolution (A) : 1.60 1.80 1.80 1.90 2.00) > (REMARK STE Also in >3.0A : 2FVA) > (REMARK STE Resolution (A) : 9.99) > (REMARK STE) Using residue : (STE) Identifier : ( 7004) Segment ID : ( ) Using formula : ( C18 H36 O2) Element ? | C| Carbon | 6 18 Element ? | H| Hydrogen | 1 36 Element ? | O| Oxygen | 8 2 Atom # 1 = C1 @ 0.160 0.001 -9.422 1.00 20.00 Atom # 2 = O1 @ 1.365 0.014 -9.335 1.00 20.00 Atom # 3 = O2 @ -0.425 -0.004 -10.629 1.00 20.00 Atom # 4 = C2 @ -0.684 -0.007 -8.174 1.00 20.00 Atom # 5 = C3 @ 0.223 0.002 -6.943 1.00 20.00 Atom # 6 = C4 @ -0.634 -0.006 -5.676 1.00 20.00 Atom # 7 = C5 @ 0.274 0.003 -4.445 1.00 20.00 Atom # 8 = C6 @ -0.584 -0.006 -3.178 1.00 20.00 Atom # 9 = C7 @ 0.324 0.003 -1.947 1.00 20.00 Atom # 10 = C8 @ -0.533 -0.005 -0.680 1.00 20.00 Atom # 11 = C9 @ 0.374 0.004 0.550 1.00 20.00 Atom # 12 = C10 @ -0.483 -0.005 1.817 1.00 20.00 Atom # 13 = C11 @ 0.424 0.004 3.048 1.00 20.00 Atom # 14 = C12 @ -0.433 -0.004 4.315 1.00 20.00 Atom # 15 = C13 @ 0.475 0.005 5.546 1.00 20.00 Atom # 16 = C14 @ -0.382 -0.004 6.813 1.00 20.00 Atom # 17 = C15 @ 0.525 0.005 8.044 1.00 20.00 Atom # 18 = C16 @ -0.332 -0.003 9.311 1.00 20.00 Atom # 19 = C17 @ 0.575 0.006 10.542 1.00 20.00 Atom # 20 = C18 @ -0.282 -0.003 11.809 1.00 20.00 > (REMARK STE ENDHET) Nr of atoms read : ( 20) Nr of extra examples : ( 0) Expected formula : ( C18 H36 O2) Observed formula : (C18 O2) Element | H| Expected 36 | Observed 0 Element | C| Expected 18 | Observed 18 Element | O| Expected 2 | Observed 2 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - O1 = 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 - O2 = 1.341 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.02) For: C-O partial double 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 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 = 1.530 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 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 = 1.530 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 C7 - C8 = 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 C8 - C9 = 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 C9 - C10 = 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 C10 - C11 = 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 C11 - C12 = 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 C12 - C13 = 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 - C14 = 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 C14 - C15 = 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 C15 - 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 C16 - C17 = 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 C17 - C18 = 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 Nr of bonds found : ( 19) 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 Oxygen O1 Nbrs: 1 ~Hs: 0 Oxygen O2 Nbrs: 1 ~Hs: 1 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: 2 ~Hs: 2 Carbon C9 Nbrs: 2 ~Hs: 2 Carbon C10 Nbrs: 2 ~Hs: 2 Carbon C11 Nbrs: 2 ~Hs: 2 Carbon C12 Nbrs: 2 ~Hs: 2 Carbon C13 Nbrs: 2 ~Hs: 2 Carbon C14 Nbrs: 2 ~Hs: 2 Carbon C15 Nbrs: 2 ~Hs: 2 Carbon C16 Nbrs: 2 ~Hs: 2 Carbon C17 Nbrs: 2 ~Hs: 2 Carbon C18 Nbrs: 1 ~Hs: 3 Est. total nr of hydrogens : ( 36) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- O1 C1 O2 119.99 O1 C1 C2 119.94 O2 C1 C2 120.07 C1 C2 C3 109.54 C2 C3 C4 109.54 C3 C4 C5 109.51 C4 C5 C6 109.48 C5 C6 C7 109.48 C6 C7 C8 109.51 C7 C8 C9 109.52 C8 C9 C10 109.52 C9 C10 C11 109.54 C10 C11 C12 109.54 C11 C12 C13 109.51 C12 C13 C14 109.51 C13 C14 C15 109.54 C14 C15 C16 109.54 C15 C16 C17 109.54 C16 C17 C18 109.54 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- O1 C1 C2 C3 -0.07 Flat ? O2 C1 C2 C3 -179.96 Flat ? C1 C2 C3 C4 180.00 Flat ? C2 C3 C4 C5 180.00 Flat ? C3 C4 C5 C6 -179.96 Flat ? C4 C5 C6 C7 180.00 Flat ? C5 C6 C7 C8 179.96 Flat ? C6 C7 C8 C9 -180.00 Flat ? C7 C8 C9 C10 -179.96 Flat ? C8 C9 C10 C11 180.00 Flat ? C9 C10 C11 C12 179.96 Flat ? C10 C11 C12 C13 180.00 Flat ? C11 C12 C13 C14 -179.96 Flat ? C12 C13 C14 C15 -180.00 Flat ? C13 C14 C15 C16 179.96 Flat ? C14 C15 C16 C17 180.00 Flat ? C15 C16 C17 C18 -179.96 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 O1 O2 C2 0.07 Number of possible flat planes : ( 18) Looking for more planes ... Number of possible flat planes : ( 34) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -7.716E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.962E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.576E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.716E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.932E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.962E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.576E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.962E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.576E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.165E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.869E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.869E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.100E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.733E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.308E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.196E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.308E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.974E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.985E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.196E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.974E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.267E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.810E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.469E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.265E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.267E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.280E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.070E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.157E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.557E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.267E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.152E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.280E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.007E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.070E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.726E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.564E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.005E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.267E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.152E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.232E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.007E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.198E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.726E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.005E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.232E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.198E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.939E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.746E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.491E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.175E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.939E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.939E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.746E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.491E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.175E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.939E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.344E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.346E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.062E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.265E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.344E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.092E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.346E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.062E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.265E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.085E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.092E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.538E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.346E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.062E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.085E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.092E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.538E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.346E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.062E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.340E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.701E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.092E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.538E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.346E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.062E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.379E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.957E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.716E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.962E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.576E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.716E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.962E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.576E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.703E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.143E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.113E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.165E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.667E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.557E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.491E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.555E-08) Removing non-unique planes ... Plane nr : ( 19) Nr of atoms : ( 20) WARNING - Reset negative RMSD in LSQGJK : ( -4.369E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C2 0.000 C1 -0.001 C3 0.000 O1 0.000 O2 0.000 C4 0.000 C5 0.000 C6 0.000 C7 0.000 C8 0.000 C9 0.000 C10 0.000 C11 0.000 C12 0.000 C13 0.000 C14 0.000 C15 0.000 C16 0.000 C17 0.000 C18 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (STE) Identifier : ( 7004) Segment ID : ( ) Nr of atoms : ( 20) List of elements (from file) : ( C18 H36 O2) Deduced formula : (C18 O2) Guestimated total nr of Hs : ( 36) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 19) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 19) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 19) Nr of dihedrals found : ( 17) Nr of atoms with impropers : ( 1) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 1)