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 4BF 4-BROMO-L-PHENYLALANINE; P-BROMO-L-PHENYLALANINE) > (REMARK 4BF Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK 4BF Extracted from PDB file pdb2ag6.ent) > (REMARK 4BF Formula C9 H10 BR N O2) Formula : (4BF C9 H10 BR N O2) > (REMARK 4BF Nr of non-hydrogen atoms 13) > (REMARK 4BF Eigen-values covariance X/Y/Z 98.2 7.1 5.5) > (REMARK 4BF Residue type 4BF) > (REMARK 4BF Residue name 808) > (REMARK 4BF Original residue name (for O) $246) > (REMARK 4BF RESOLUTION. 1.90 ANGSTROMS.) > (REMARK 4BF occurs in 0 other PDB entries) > (REMARK 4BF) Using residue : (4BF) Identifier : ( 808) Segment ID : ( ) Using formula : ( C9 H10 BR N O2) Element ? | C| Carbon | 6 9 Element ? | H| Hydrogen | 1 10 Element ? |BR| Bromine | 35 1 Element ? | N| Nitrogen | 7 1 Element ? | O| Oxygen | 8 2 Atom # 1 = CD1 @ -0.128 -1.327 0.190 1.00 20.00 Atom # 2 = CE1 @ 1.232 -1.261 -0.051 1.00 20.00 Atom # 3 = CZ @ 1.909 -0.069 0.129 1.00 20.00 Atom # 4 = BR @ 3.771 0.019 -0.193 1.00 20.00 Atom # 5 = CE2 @ 1.225 1.059 0.547 1.00 20.00 Atom # 6 = CD2 @ -0.135 0.994 0.783 1.00 20.00 Atom # 7 = CG @ -0.812 -0.198 0.602 1.00 20.00 Atom # 8 = CB @ -2.295 -0.268 0.860 1.00 20.00 Atom # 9 = CA @ -3.052 0.061 -0.428 1.00 20.00 Atom # 10 = N @ -2.790 1.456 -0.807 1.00 20.00 Atom # 11 = C @ -4.531 -0.128 -0.204 1.00 20.00 Atom # 12 = OXT @ -5.063 -1.359 -0.246 1.00 20.00 Atom # 13 = O @ -5.236 0.828 0.013 1.00 20.00 > (REMARK 4BF ENDHET) Nr of atoms read : ( 13) Nr of extra examples : ( 0) Expected formula : ( C9 H10 BR N O2) Observed formula : (C9 N1 O2 BR1) Element | H| Expected 10 | Observed 0 Element | C| Expected 9 | Observed 9 Element | N| Expected 1 | Observed 1 Element | O| Expected 2 | Observed 2 Element |BR| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond CD1 - CE1 = 1.383 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 CD1 - CG = 1.383 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 CE1 - CZ = 1.383 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 CZ - BR = 1.892 A (cutoff : 2.240) Nr of entries in library : ( 3) Closest to 1.87 (devn. 0.02) For: C-Br CH2=CH-Br or C6H5-Br type; range 1.85-1.89 Bond CZ - CE2 = 1.384 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 CE2 - CD2 = 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 CD2 - CG = 1.383 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 CG - CB = 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 CB - CA = 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 CA - N = 1.469 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 CA - C = 1.508 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 C - OXT = 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 C - O = 1.207 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 Nr of bonds found : ( 13) 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 CD1 Nbrs: 2 ~Hs: 1 Carbon CE1 Nbrs: 2 ~Hs: 1 Carbon CZ Nbrs: 3 ~Hs: 0 Carbon CE2 Nbrs: 2 ~Hs: 1 Carbon CD2 Nbrs: 2 ~Hs: 1 Carbon CG Nbrs: 3 ~Hs: 0 Carbon CB Nbrs: 2 ~Hs: 2 Carbon CA Nbrs: 3 ~Hs: 1 Nitrogen N Nbrs: 1 ~Hs: 1 Carbon C Nbrs: 3 ~Hs: 0 Oxygen OXT Nbrs: 1 ~Hs: 1 Oxygen O Nbrs: 1 ~Hs: 0 Est. total nr of hydrogens : ( 9) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- CE1 CD1 CG 119.96 CD1 CE1 CZ 120.00 CE1 CZ BR 119.99 CE1 CZ CE2 120.00 BR CZ CE2 120.00 CZ CE2 CD2 119.98 CE2 CD2 CG 120.00 CD1 CG CD2 120.04 CD1 CG CB 119.99 CD2 CG CB 119.97 CG CB CA 109.44 CB CA N 109.46 CB CA C 109.47 N CA C 109.41 CA C OXT 119.95 CA C O 120.01 OXT C O 120.03 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- CG CD1 CE1 CZ 0.45 Flat ? CE1 CD1 CG CD2 -0.50 Flat ? CE1 CD1 CG CB 179.78 Flat ? CD1 CE1 CZ BR 179.71 Flat ? CD1 CE1 CZ CE2 -0.17 Flat ? CE1 CZ CE2 CD2 -0.07 Flat ? BR CZ CE2 CD2 -179.95 Flat ? CZ CE2 CD2 CG 0.03 Flat ? CE2 CD2 CG CD1 0.26 Flat ? CE2 CD2 CG CB 179.98 Flat ? CD1 CG CB CA -90.22 CD2 CG CB CA 90.06 CG CB CA N -65.08 CG CB CA C 175.01 Flat ? CB CA C OXT -80.05 CB CA C O 99.96 N CA C OXT 160.00 N CA C O -19.99 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- CZ CE1 BR CE2 0.06 CG CD1 CD2 CB 0.17 CA CB N C 35.39 C CA OXT O 0.00 Number of possible flat planes : ( 14) Looking for more planes ... Number of possible flat planes : ( 19) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -4.734E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.842E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.011E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.725E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.085E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.817E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.224E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.964E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.258E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.683E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.144E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.271E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.258E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.038E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.085E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.510E-09) WARNING - Reset negative RMSD in LSQGJK : ( -9.450E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.888E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.595E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.195E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.174E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.725E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.449E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.174E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.224E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.674E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.258E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.465E-09) WARNING - Reset negative RMSD in LSQGJK : ( -9.449E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.174E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.449E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.823E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.391E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.271E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.735E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.271E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.669E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.085E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.069E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.595E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.195E-08) Removing non-unique planes ... Plane nr : ( 14) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C 0.000 CA 0.000 OXT 0.000 O 0.000 Plane nr : ( 18) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -9.449E-09) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) CD2 0.001 CE2 0.001 CG -0.001 CZ -0.001 CD1 0.003 CB -0.001 CE1 -0.002 BR 0.000 Plane nr : ( 19) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.469E-07) RMSD to least-squares plane (A): ( 0.031) Atom Dist (A) CB -0.031 CG 0.031 CA -0.031 C 0.031 ------------------- ----- SUMMARY ----- ------------------- Residue type : (4BF) Identifier : ( 808) Segment ID : ( ) Nr of atoms : ( 13) List of elements (from file) : ( C9 H10 BR N O2) Deduced formula : (C9 N1 O2 BR1) Guestimated total nr of Hs : ( 9) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 13) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 13) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 17) Nr of dihedrals found : ( 18) Nr of atoms with impropers : ( 4) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 3)