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 BTR 6-BROMO-TRYPTOPHAN) > (REMARK BTR Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK BTR Extracted from PDB file pdb1wct.ent) > (REMARK BTR Formula C11 H11 BR N2 O2) Formula : (BTR C11 H11 BR N2 O2) > (REMARK BTR Nr of non-hydrogen atoms 15) > (REMARK BTR Eigen-values covariance X/Y/Z 83.5 28.5 4.6) > (REMARK BTR Residue type BTR) > (REMARK BTR Residue name 2169) > (REMARK BTR Original residue name (for O) $A7) > (REMARK BTR RESOLUTION. NOT APPLICABLE.) > (REMARK BTR occurs in 0 other PDB entries) > (REMARK BTR) Using residue : (BTR) Identifier : ( 2169) Segment ID : ( ) Using formula : ( C11 H11 BR N2 O2) Element ? | C| Carbon | 6 11 Element ? | H| Hydrogen | 1 11 Element ? |BR| Bromine | 35 1 Element ? | N| Nitrogen | 7 2 Element ? | O| Oxygen | 8 2 Atom # 1 = N @ 0.914 1.286 3.838 1.00 20.00 Atom # 2 = CA @ -0.261 0.455 3.543 1.00 20.00 Atom # 3 = C @ -0.993 0.148 4.824 1.00 20.00 Atom # 4 = O @ -0.383 0.071 5.864 1.00 20.00 Atom # 5 = OXT @ -2.321 -0.040 4.809 1.00 20.00 Atom # 6 = CB @ 0.189 -0.850 2.886 1.00 20.00 Atom # 7 = CG @ 0.921 -0.543 1.605 1.00 20.00 Atom # 8 = CD1 @ 2.239 -0.333 1.470 1.00 20.00 Atom # 9 = NE1 @ 2.540 -0.082 0.159 1.00 20.00 Atom # 10 = CE2 @ 1.392 -0.126 -0.600 1.00 20.00 Atom # 11 = CD2 @ 0.329 -0.423 0.271 1.00 20.00 Atom # 12 = CE3 @ -0.971 -0.524 -0.225 1.00 20.00 Atom # 13 = CZ3 @ -1.203 -0.347 -1.560 1.00 20.00 Atom # 14 = CH2 @ -0.156 -0.059 -2.426 1.00 20.00 Atom # 15 = BR2 @ -0.504 0.180 -4.269 1.00 20.00 Atom # 16 = CZ2 @ 1.134 0.050 -1.955 1.00 20.00 > (REMARK BTR ENDHET) Nr of atoms read : ( 16) Nr of extra examples : ( 0) Expected formula : ( C11 H11 BR N2 O2) Observed formula : (C11 N2 O2 BR1) Element | H| Expected 11 | Observed 0 Element | C| Expected 11 | Observed 11 Element | N| Expected 2 | Observed 2 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 N - CA = 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 = 1.507 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 CA - CB = 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 C - O = 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 C - OXT = 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 CB - CG = 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 CG - CD1 = 1.341 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.00) For: C-C double or partial triple; range 1.309-1.337 Bond CG - CD2 = 1.464 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 CD1 - NE1 = 1.368 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.03) For: C-N partial double; range 1.322-1.352 Bond NE1 - CE2 = 1.377 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.04) For: C-N partial double; range 1.322-1.352 Bond CE2 - CD2 = 1.406 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 CE2 - CZ2 = 1.391 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond CD2 - CE3 = 1.395 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 CE3 - CZ3 = 1.367 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 CZ3 - CH2 = 1.389 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.39 (devn. 0.00) For: C-C aromatic or near two triple bonds; range 1.373-1.395 Bond CH2 - BR2 = 1.891 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 CH2 - CZ2 = 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 Nr of bonds found : ( 17) 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) Nitrogen N Nbrs: 1 ~Hs: 1 Carbon CA Nbrs: 3 ~Hs: 1 Carbon C Nbrs: 3 ~Hs: 0 Oxygen O Nbrs: 1 ~Hs: 0 Oxygen OXT Nbrs: 1 ~Hs: 1 Carbon CB Nbrs: 2 ~Hs: 2 Carbon CG Nbrs: 3 ~Hs: 0 Carbon CD1 Nbrs: 2 ~Hs: 1 Nitrogen NE1 Nbrs: 2 ~Hs: 1 Carbon CE2 Nbrs: 3 ~Hs: 0 Carbon CD2 Nbrs: 3 ~Hs: 0 Carbon CE3 Nbrs: 2 ~Hs: 1 Carbon CZ3 Nbrs: 2 ~Hs: 1 Carbon CH2 Nbrs: 3 ~Hs: 0 Carbon CZ2 Nbrs: 2 ~Hs: 1 Est. total nr of hydrogens : ( 10) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- N CA C 109.45 N CA CB 109.50 C CA CB 109.54 CA C O 119.96 CA C OXT 120.00 O C OXT 120.04 CA CB CG 109.54 CB CG CD1 126.49 CB CG CD2 126.49 CD1 CG CD2 107.02 CG CD1 NE1 109.95 CD1 NE1 CE2 109.81 NE1 CE2 CD2 107.19 NE1 CE2 CZ2 133.46 CD2 CE2 CZ2 119.35 CG CD2 CE2 106.02 CG CD2 CE3 134.00 CE2 CD2 CE3 119.97 CD2 CE3 CZ3 119.75 CE3 CZ3 CH2 120.53 CZ3 CH2 BR2 119.68 CZ3 CH2 CZ2 120.60 BR2 CH2 CZ2 119.71 CE2 CZ2 CH2 119.79 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- N CA C O -30.06 N CA C OXT 149.96 CB CA C O 89.99 CB CA C OXT -89.99 N CA CB CG -59.97 C CA CB CG 180.00 Flat ? CA CB CG CD1 90.00 CA CB CG CD2 -90.28 CB CG CD1 NE1 -179.96 Flat ? CD2 CG CD1 NE1 0.27 Flat ? CB CG CD2 CE2 179.80 Flat ? CB CG CD2 CE3 0.76 Flat ? CD1 CG CD2 CE2 -0.44 Flat ? CD1 CG CD2 CE3 -179.47 Flat ? CG CD1 NE1 CE2 -0.01 Flat ? CD1 NE1 CE2 CD2 -0.28 Flat ? CD1 NE1 CE2 CZ2 -179.89 Flat ? NE1 CE2 CD2 CG 0.43 Flat ? NE1 CE2 CD2 CE3 179.63 Flat ? CZ2 CE2 CD2 CG -179.89 Flat ? CZ2 CE2 CD2 CE3 -0.69 Flat ? NE1 CE2 CZ2 CH2 -179.98 Flat ? CD2 CE2 CZ2 CH2 0.44 Flat ? CG CD2 CE3 CZ3 179.61 Flat ? CE2 CD2 CE3 CZ3 0.68 Flat ? CD2 CE3 CZ3 CH2 -0.41 Flat ? CE3 CZ3 CH2 BR2 179.95 Flat ? CE3 CZ3 CH2 CZ2 0.15 Flat ? CZ3 CH2 CZ2 CE2 -0.17 Flat ? BR2 CH2 CZ2 CE2 -179.97 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- CA N C CB 35.57 C CA O OXT 0.01 CG CB CD1 CD2 -0.16 CE2 NE1 CD2 CZ2 0.18 CD2 CG CE2 CE3 0.43 CH2 CZ3 BR2 CZ2 0.11 Number of possible flat planes : ( 28) Looking for more planes ... Number of possible flat planes : ( 34) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -3.552E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.552E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.125E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.244E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.589E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.498E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.306E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.978E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.006E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.498E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.818E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.590E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.514E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.907E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.415E-09) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.907E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.043E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.989E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.850E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.479E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.647E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.083E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.187E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.989E-09) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.169E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.825E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.131E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.306E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.415E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.715E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.553E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.223E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.071E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.989E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.452E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.807E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.904E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.185E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.942E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.345E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.818E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.113E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.621E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.099E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.871E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.253E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.438E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.096E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.974E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.438E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.181E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.390E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.974E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.289E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.096E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.003E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.327E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.989E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.078E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.438E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.393E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.102E-07) WARNING - Reset negative RMSD in LSQGJK : ( -9.606E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.630E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.794E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.930E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.185E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.393E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.552E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.514E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.038E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.244E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.989E-09) WARNING - Reset negative RMSD in LSQGJK : ( -1.169E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.253E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.567E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.498E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.907E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.981E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.715E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.102E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.418E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.010E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.552E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.745E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.605E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.505E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.032E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.479E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.621E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.818E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.113E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.209E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.320E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.169E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.390E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.989E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.452E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.807E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.140E-07) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) Removing non-unique planes ... Plane nr : ( 24) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) C 0.000 CA 0.000 O 0.000 OXT 0.000 Plane nr : ( 29) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) CB 0.000 CA 0.000 CG 0.000 C 0.000 Plane nr : ( 34) Nr of atoms : ( 11) WARNING - Reset negative RMSD in LSQGJK : ( -8.008E-08) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) CZ2 0.000 CE2 0.001 CH2 0.001 NE1 0.001 CD2 -0.006 CZ3 0.001 BR2 -0.001 CD1 0.000 CG 0.000 CE3 0.001 CB 0.001 ------------------- ----- SUMMARY ----- ------------------- Residue type : (BTR) Identifier : ( 2169) Segment ID : ( ) Nr of atoms : ( 16) List of elements (from file) : ( C11 H11 BR N2 O2) Deduced formula : (C11 N2 O2 BR1) Guestimated total nr of Hs : ( 10) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 17) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 17) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 24) Nr of dihedrals found : ( 30) Nr of atoms with impropers : ( 6) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 3)