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 MGR MALACHITE GREEN) > (REMARK MGR Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK MGR Extracted from PDB file pdb1jup.ent) > (REMARK MGR Formula C23 H25 N2 1+) Formula : (MGR C23 H25 N2 1+) > (REMARK MGR Nr of non-hydrogen atoms 25) > (REMARK MGR Eigen-values covariance X/Y/Z 290.8 141.0 9.6) > (REMARK MGR Residue type MGR) > (REMARK MGR Residue name 5152) > (REMARK MGR Original residue name (for O) $200) > (REMARK MGR RESOLUTION. 2.95 ANGSTROMS.) > (REMARK MGR occurs in 1 other PDB entries) > (REMARK MGR Also in >3.0A : 1Q8N) > (REMARK MGR Resolution (A) : 9.99) > (REMARK MGR) Using residue : (MGR) Identifier : ( 5152) Segment ID : ( ) Using formula : ( C23 H25 N2 1+) Element ? | C| Carbon | 6 23 Element ? | H| Hydrogen | 1 25 Element ? | N| Nitrogen | 7 2 ERROR --- While reading integer from input string Element ? | 1| ??? | -1 -1 Atom # 1 = C1 @ -0.023 0.781 0.021 1.00 20.00 Atom # 2 = C2 @ -0.065 2.252 0.060 1.00 20.00 Atom # 3 = C3 @ -0.616 2.911 1.165 1.00 20.00 Atom # 4 = C4 @ -0.652 4.288 1.194 1.00 20.00 Atom # 5 = C5 @ -0.144 5.020 0.134 1.00 20.00 Atom # 6 = C6 @ 0.403 4.376 -0.963 1.00 20.00 Atom # 7 = C7 @ 0.452 2.999 -1.005 1.00 20.00 Atom # 8 = C8 @ 1.225 0.107 0.026 1.00 20.00 Atom # 9 = C9 @ 2.110 0.255 -1.058 1.00 20.00 Atom # 10 = C10 @ 3.307 -0.392 -1.051 1.00 20.00 Atom # 11 = C11 @ 3.659 -1.207 0.036 1.00 20.00 Atom # 12 = C12 @ 2.775 -1.360 1.116 1.00 20.00 Atom # 13 = C13 @ 1.580 -0.710 1.115 1.00 20.00 Atom # 14 = C14 @ -1.230 0.038 -0.022 1.00 20.00 Atom # 15 = C15 @ -2.468 0.706 -0.027 1.00 20.00 Atom # 16 = C16 @ -3.625 -0.009 -0.068 1.00 20.00 Atom # 17 = C17 @ -3.584 -1.411 -0.106 1.00 20.00 Atom # 18 = C18 @ -2.350 -2.079 -0.101 1.00 20.00 Atom # 19 = C19 @ -1.190 -1.368 -0.065 1.00 20.00 Atom # 20 = C22 @ 5.776 -1.699 -1.088 1.00 20.00 Atom # 21 = C23 @ 5.224 -2.704 1.175 1.00 20.00 Atom # 22 = C24 @ -6.029 -1.437 -0.019 1.00 20.00 Atom # 23 = C25 @ -4.700 -3.578 -0.318 1.00 20.00 Atom # 24 = N2 @ 4.855 -1.853 0.041 1.00 20.00 Atom # 25 = N3 @ -4.741 -2.124 -0.146 1.00 20.00 > (REMARK MGR ENDHET) Nr of atoms read : ( 25) Nr of extra examples : ( 0) Expected formula : ( C23 H25 N2 1+) Observed formula : (C23 N2) Element | H| Expected 25 | Observed 0 Element | C| Expected 23 | Observed 23 Element | N| Expected 2 | Observed 2 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 1.472 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.03) For: C-C single shortened; range 1.421-1.46 Bond C1 - C8 = 1.418 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.02) For: C-C single shortened; range 1.421-1.46 Bond C1 - C14 = 1.418 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.02) For: C-C single shortened; range 1.421-1.46 Bond C2 - C3 = 1.400 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 C2 - C7 = 1.400 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 = 1.378 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 C4 - C5 = 1.385 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 C5 - C6 = 1.385 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 C6 - C7 = 1.379 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 C8 - C9 = 1.407 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 C8 - C13 = 1.407 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 C9 - C10 = 1.361 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.02) For: C-C double or partial triple; range 1.309-1.337 Bond C10 - C11 = 1.403 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 C11 - C12 = 1.404 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 C11 - N2 = 1.359 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.02) For: C-N partial double; range 1.322-1.352 Bond C12 - C13 = 1.360 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.02) For: C-C double or partial triple; range 1.309-1.337 Bond C14 - C15 = 1.407 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 C14 - C19 = 1.407 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 C15 - C16 = 1.361 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.02) For: C-C double or partial triple; range 1.309-1.337 Bond C16 - C17 = 1.403 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 C17 - C18 = 1.403 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 C17 - N3 = 1.360 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.02) For: C-N partial double; range 1.322-1.352 Bond C18 - C19 = 1.361 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.02) For: C-C double or partial triple; range 1.309-1.337 Bond C22 - N2 = 1.465 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 C23 - N2 = 1.465 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 C24 - N3 = 1.465 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 C25 - N3 = 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 Nr of bonds found : ( 27) 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: 0 Carbon C3 Nbrs: 2 ~Hs: 1 Carbon C4 Nbrs: 2 ~Hs: 1 Carbon C5 Nbrs: 2 ~Hs: 1 Carbon C6 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 2 ~Hs: 1 Carbon C8 Nbrs: 3 ~Hs: 0 Carbon C9 Nbrs: 2 ~Hs: 1 Carbon C10 Nbrs: 2 ~Hs: 1 Carbon C11 Nbrs: 3 ~Hs: 0 Carbon C12 Nbrs: 2 ~Hs: 1 Carbon C13 Nbrs: 2 ~Hs: 1 Carbon C14 Nbrs: 3 ~Hs: 0 Carbon C15 Nbrs: 2 ~Hs: 1 Carbon C16 Nbrs: 2 ~Hs: 1 Carbon C17 Nbrs: 3 ~Hs: 0 Carbon C18 Nbrs: 2 ~Hs: 1 Carbon C19 Nbrs: 2 ~Hs: 1 Carbon C22 Nbrs: 1 ~Hs: 3 Carbon C23 Nbrs: 1 ~Hs: 3 Carbon C24 Nbrs: 1 ~Hs: 3 Carbon C25 Nbrs: 1 ~Hs: 3 Nitrogen N2 Nbrs: 3 ~Hs: 0 Nitrogen N3 Nbrs: 3 ~Hs: 0 Est. total nr of hydrogens : ( 25) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 C8 119.99 C2 C1 C14 120.01 C8 C1 C14 120.00 C1 C2 C3 120.17 C1 C2 C7 120.17 C3 C2 C7 119.66 C2 C3 C4 119.83 C3 C4 C5 120.17 C4 C5 C6 120.37 C5 C6 C7 120.18 C2 C7 C6 119.78 C1 C8 C9 120.04 C1 C8 C13 120.05 C9 C8 C13 119.91 C8 C9 C10 119.95 C9 C10 C11 120.05 C10 C11 C12 120.08 C10 C11 N2 119.97 C12 C11 N2 119.96 C11 C12 C13 120.03 C8 C13 C12 119.98 C1 C14 C15 120.03 C1 C14 C19 120.02 C15 C14 C19 119.96 C14 C15 C16 119.93 C15 C16 C17 120.07 C16 C17 C18 120.08 C16 C17 N3 119.99 C18 C17 N3 119.92 C17 C18 C19 120.06 C14 C19 C18 119.90 C11 N2 C22 120.02 C11 N2 C23 120.03 C22 N2 C23 119.95 C17 N3 C24 119.97 C17 N3 C25 120.01 C24 N3 C25 120.01 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C8 C1 C2 C3 -114.97 C8 C1 C2 C7 64.71 C14 C1 C2 C3 65.05 C14 C1 C2 C7 -115.27 C2 C1 C8 C9 -64.99 C2 C1 C8 C13 114.99 C14 C1 C8 C9 114.99 C14 C1 C8 C13 -65.03 C2 C1 C14 C15 -0.02 Flat ? C2 C1 C14 C19 179.73 Flat ? C8 C1 C14 C15 -180.00 Flat ? C8 C1 C14 C19 -0.25 Flat ? C1 C2 C3 C4 -179.98 Flat ? C7 C2 C3 C4 0.33 Flat ? C1 C2 C7 C6 179.70 Flat ? C3 C2 C7 C6 -0.61 Flat ? C2 C3 C4 C5 -0.05 Flat ? C3 C4 C5 C6 0.04 Flat ? C4 C5 C6 C7 -0.33 Flat ? C5 C6 C7 C2 0.61 Flat ? C1 C8 C9 C10 179.97 Flat ? C13 C8 C9 C10 0.00 Flat ? C1 C8 C13 C12 179.74 Flat ? C9 C8 C13 C12 -0.29 Flat ? C8 C9 C10 C11 0.03 Flat ? C9 C10 C11 C12 0.22 Flat ? C9 C10 C11 N2 179.97 Flat ? C10 C11 C12 C13 -0.51 Flat ? N2 C11 C12 C13 179.74 Flat ? C10 C11 N2 C22 -0.02 Flat ? C10 C11 N2 C23 179.99 Flat ? C12 C11 N2 C22 179.73 Flat ? C12 C11 N2 C23 -0.25 Flat ? C11 C12 C13 C8 0.54 Flat ? C1 C14 C15 C16 -179.99 Flat ? C19 C14 C15 C16 0.26 Flat ? C1 C14 C19 C18 179.75 Flat ? C15 C14 C19 C18 -0.50 Flat ? C14 C15 C16 C17 -0.03 Flat ? C15 C16 C17 C18 0.04 Flat ? C15 C16 C17 N3 179.95 Flat ? C16 C17 C18 C19 -0.28 Flat ? N3 C17 C18 C19 179.81 Flat ? C16 C17 N3 C24 -5.90 Flat ? C16 C17 N3 C25 174.00 Flat ? C18 C17 N3 C24 174.01 Flat ? C18 C17 N3 C25 -6.08 Flat ? C17 C18 C19 C14 0.51 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C1 C2 C8 C14 0.01 C2 C1 C3 C7 -0.18 C8 C1 C9 C13 -0.01 C11 C10 C12 N2 -0.14 C14 C1 C15 C19 -0.14 C17 C16 C18 N3 -0.05 N2 C11 C22 C23 0.01 N3 C17 C24 C25 -0.05 Number of possible flat planes : ( 48) Looking for more planes ... Number of possible flat planes : ( 61) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -4.964E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.543E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.569E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.898E-11) WARNING - Reset negative RMSD in LSQGJK : ( -1.036E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.068E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.604E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.448E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.686E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.806E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.185E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.178E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.031E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.116E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.068E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.609E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.088E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.489E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.324E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.235E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.536E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.289E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.286E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.676E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.031E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.891E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.684E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.238E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.540E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.493E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.559E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.543E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.381E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.943E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.543E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.005E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.653E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.411E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.383E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.943E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.317E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.083E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.331E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.184E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.706E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.881E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.614E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.232E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.146E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.298E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.544E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.133E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.407E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.219E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.717E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.964E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.165E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.562E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.120E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.331E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.063E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.645E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.569E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.036E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.791E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.608E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.019E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.120E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.284E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.063E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.120E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.645E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.562E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.201E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.496E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.987E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.153E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.153E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.935E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.496E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.972E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.411E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.201E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.433E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.030E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.082E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.849E-11) WARNING - Reset negative RMSD in LSQGJK : ( -8.756E-11) WARNING - Reset negative RMSD in LSQGJK : ( -2.071E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.145E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.972E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.842E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.232E-13) WARNING - Reset negative RMSD in LSQGJK : ( -1.863E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.846E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.118E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.456E-10) WARNING - Reset negative RMSD in LSQGJK : ( -5.020E-10) WARNING - Reset negative RMSD in LSQGJK : ( -3.752E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.846E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.314E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.846E-11) WARNING - Reset negative RMSD in LSQGJK : ( -6.373E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.359E-09) WARNING - Reset negative RMSD in LSQGJK : ( -7.935E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.453E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.645E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.075E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.068E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.324E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.574E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.543E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.368E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.368E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.791E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.120E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.645E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.168E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.334E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.396E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.731E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.383E-10) WARNING - Reset negative RMSD in LSQGJK : ( -9.193E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.088E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.713E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.256E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.030E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.088E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.874E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.589E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.068E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.105E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.686E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.088E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.289E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.238E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.339E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.536E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.675E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.493E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.235E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.887E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.197E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.383E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.623E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.881E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.286E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.187E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.165E-10) WARNING - Reset negative RMSD in LSQGJK : ( -4.562E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.964E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.120E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.201E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.562E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.359E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.496E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.715E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.756E-11) WARNING - Reset negative RMSD in LSQGJK : ( -1.153E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.935E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.145E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.972E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.569E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.120E-09) Removing non-unique planes ... Plane nr : ( 33) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -5.732E-08) RMSD to least-squares plane (A): ( 0.049) Atom Dist (A) C15 -0.040 C16 -0.047 C17 0.006 N3 0.001 C14 0.020 C18 0.067 C24 0.070 C25 -0.077 Plane nr : ( 35) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -2.695E-08) RMSD to least-squares plane (A): ( 0.049) Atom Dist (A) N3 0.000 C17 -0.007 C18 0.048 C19 0.037 C24 0.076 C25 -0.070 C16 -0.067 C14 -0.018 Plane nr : ( 46) Nr of atoms : ( 7) WARNING - Reset negative RMSD in LSQGJK : ( -4.772E-09) RMSD to least-squares plane (A): ( 0.032) Atom Dist (A) C17 -0.022 C16 -0.024 C18 0.007 N3 -0.047 C15 0.002 C19 0.028 C24 0.055 Plane nr : ( 53) Nr of atoms : ( 7) WARNING - Reset negative RMSD in LSQGJK : ( -6.088E-08) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C7 0.004 C2 -0.001 C6 -0.002 C1 -0.001 C3 0.001 C5 -0.001 C4 0.001 Plane nr : ( 57) Nr of atoms : ( 10) WARNING - Reset negative RMSD in LSQGJK : ( -3.567E-07) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C13 -0.002 C8 0.000 C12 0.004 C1 0.000 C9 0.000 C11 -0.001 C10 0.000 N2 -0.001 C22 0.001 C23 -0.001 Plane nr : ( 61) Nr of atoms : ( 10) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C19 -0.004 C14 0.001 C18 0.001 C1 0.001 C15 0.000 C17 0.000 C2 -0.001 C8 0.002 C16 0.000 N3 0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (MGR) Identifier : ( 5152) Segment ID : ( ) Nr of atoms : ( 25) List of elements (from file) : ( C23 H25 N2 1+) Deduced formula : (C23 N2) Guestimated total nr of Hs : ( 25) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 27) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 27) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 37) Nr of dihedrals found : ( 48) Nr of atoms with impropers : ( 8) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 6)