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 PH9 (2Z)-2-((1-ADAMANTYLCARBONYL)AMINO)-3-(4-(2- BROMOPHENOXY) PHENYL)PROP-2-ENOIC ACID) > (REMARK PH9 Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK PH9 Extracted from PDB file pdb1z4u.ent) > (REMARK PH9 Formula C26 H28 BR N O4) Formula : (PH9 C26 H28 BR N O4) > (REMARK PH9 Nr of non-hydrogen atoms 32) > (REMARK PH9 Eigen-values covariance X/Y/Z 387.7 197.8 27.1) > (REMARK PH9 Residue type PH9) > (REMARK PH9 Residue name 6142) > (REMARK PH9 Original residue name (for O) $600) > (REMARK PH9 RESOLUTION. 2.80 ANGSTROMS.) > (REMARK PH9 occurs in 0 other PDB entries) > (REMARK PH9) Using residue : (PH9) Identifier : ( 6142) Segment ID : ( ) Using formula : ( C26 H28 BR N O4) Element ? | C| Carbon | 6 26 Element ? | H| Hydrogen | 1 28 Element ? |BR| Bromine | 35 1 Element ? | N| Nitrogen | 7 1 Element ? | O| Oxygen | 8 4 Atom # 1 = CB2 @ 0.143 2.229 -0.156 1.00 20.00 Atom # 2 = CB3 @ -0.738 2.500 0.875 1.00 20.00 Atom # 3 = CB4 @ -1.833 1.684 1.082 1.00 20.00 Atom # 4 = CB6 @ -2.050 0.592 0.254 1.00 20.00 Atom # 5 = CB5 @ -1.165 0.322 -0.780 1.00 20.00 Atom # 6 = CB1 @ -0.074 1.144 -0.986 1.00 20.00 Atom # 7 = C2 @ 2.524 2.597 0.431 1.00 20.00 Atom # 8 = C1 @ 1.336 3.121 -0.379 1.00 20.00 Atom # 9 = N @ 2.921 1.282 -0.080 1.00 20.00 Atom # 10 = C @ 3.562 0.412 0.726 1.00 20.00 Atom # 11 = CO2 @ 3.680 3.555 0.305 1.00 20.00 Atom # 12 = O @ 3.810 0.717 1.873 1.00 20.00 Atom # 13 = OC1 @ 4.728 3.178 -0.163 1.00 20.00 Atom # 14 = OC2 @ 3.545 4.826 0.713 1.00 20.00 Atom # 15 = OAB @ -3.127 -0.212 0.455 1.00 20.00 Atom # 16 = CA1 @ -4.148 0.310 -0.275 1.00 20.00 Atom # 17 = CA2 @ -5.399 -0.290 -0.247 1.00 20.00 Atom # 18 = CA3 @ -6.437 0.246 -0.986 1.00 20.00 Atom # 19 = CA4 @ -6.226 1.371 -1.761 1.00 20.00 Atom # 20 = CA5 @ -4.979 1.967 -1.794 1.00 20.00 Atom # 21 = CA6 @ -3.939 1.439 -1.053 1.00 20.00 Atom # 22 = BRA2 @ -5.688 -1.829 0.813 1.00 20.00 Atom # 23 = CC4 @ 3.847 -3.865 0.317 1.00 20.00 Atom # 24 = CC3 @ 3.142 -3.079 -0.791 1.00 20.00 Atom # 25 = CC5 @ 5.090 -3.099 0.775 1.00 20.00 Atom # 26 = CC2 @ 4.675 -1.726 1.308 1.00 20.00 Atom # 27 = CC6 @ 2.728 -1.706 -0.257 1.00 20.00 Atom # 28 = CC1 @ 3.970 -0.940 0.200 1.00 20.00 Atom # 29 = C10 @ 6.043 -2.919 -0.409 1.00 20.00 Atom # 30 = CC8 @ 5.338 -2.134 -1.516 1.00 20.00 Atom # 31 = CC9 @ 4.095 -2.900 -1.974 1.00 20.00 Atom # 32 = CC7 @ 4.923 -0.761 -0.983 1.00 20.00 > (REMARK PH9 ENDHET) Nr of atoms read : ( 32) Nr of extra examples : ( 0) Expected formula : ( C26 H28 BR N O4) Observed formula : (C26 N1 O4 BR1) Element | H| Expected 28 | Observed 0 Element | C| Expected 26 | Observed 26 Element | N| Expected 1 | Observed 1 Element | O| Expected 4 | Observed 4 Element |BR| Expected 1 | Observed 1 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond CB2 - CB3 = 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 CB2 - CB1 = 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 CB2 - C1 = 1.506 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 CB3 - CB4 = 1.381 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 CB4 - CB6 = 1.387 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 CB6 - CB5 = 1.388 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 CB6 - OAB = 1.359 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.00) For: C-O partial double Bond CB5 - CB1 = 1.381 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 - C1 = 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 C2 - N = 1.466 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 C2 - CO2 = 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 N - C = 1.348 A (cutoff : 1.710) Nr of entries in library : ( 4) Closest to 1.34 (devn. 0.01) For: C-N partial double; range 1.322-1.352 Bond C - O = 1.212 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 - CC1 = 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 CO2 - OC1 = 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 CO2 - OC2 = 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 OAB - CA1 = 1.359 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.36 (devn. 0.00) For: C-O partial double Bond CA1 - CA2 = 1.388 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 CA1 - CA6 = 1.387 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 CA2 - CA3 = 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 CA2 - BRA2 = 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 CA3 - CA4 = 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 CA4 - CA5 = 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 CA5 - CA6 = 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 CC4 - CC3 = 1.531 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 CC4 - CC5 = 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 CC3 - CC6 = 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 CC3 - CC9 = 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 CC5 - CC2 = 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 CC5 - C10 = 1.531 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 CC2 - CC1 = 1.531 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 CC6 - CC1 = 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 CC1 - CC7 = 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 - CC8 = 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 CC8 - CC9 = 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 CC8 - CC7 = 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 : ( 36) 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 CB2 Nbrs: 3 ~Hs: 0 Carbon CB3 Nbrs: 2 ~Hs: 1 Carbon CB4 Nbrs: 2 ~Hs: 1 Carbon CB6 Nbrs: 3 ~Hs: 0 Carbon CB5 Nbrs: 2 ~Hs: 1 Carbon CB1 Nbrs: 2 ~Hs: 1 Carbon C2 Nbrs: 3 ~Hs: 1 Carbon C1 Nbrs: 2 ~Hs: 2 Nitrogen N Nbrs: 2 ~Hs: 1 Carbon C Nbrs: 3 ~Hs: 0 Carbon CO2 Nbrs: 3 ~Hs: 0 Oxygen O Nbrs: 1 ~Hs: 0 Oxygen OC1 Nbrs: 1 ~Hs: 0 Oxygen OC2 Nbrs: 1 ~Hs: 1 Oxygen OAB Nbrs: 2 ~Hs: 0 Carbon CA1 Nbrs: 3 ~Hs: 0 Carbon CA2 Nbrs: 3 ~Hs: 0 Carbon CA3 Nbrs: 2 ~Hs: 1 Carbon CA4 Nbrs: 2 ~Hs: 1 Carbon CA5 Nbrs: 2 ~Hs: 1 Carbon CA6 Nbrs: 2 ~Hs: 1 Carbon CC4 Nbrs: 2 ~Hs: 2 Carbon CC3 Nbrs: 3 ~Hs: 1 Carbon CC5 Nbrs: 3 ~Hs: 1 Carbon CC2 Nbrs: 2 ~Hs: 2 Carbon CC6 Nbrs: 2 ~Hs: 2 Carbon CC1 Nbrs: 4 ~Hs: 0 Carbon C10 Nbrs: 2 ~Hs: 2 Carbon CC8 Nbrs: 3 ~Hs: 1 Carbon CC9 Nbrs: 2 ~Hs: 2 Carbon CC7 Nbrs: 2 ~Hs: 2 Est. total nr of hydrogens : ( 28) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- CB3 CB2 CB1 120.07 CB3 CB2 C1 119.93 CB1 CB2 C1 120.00 CB2 CB3 CB4 120.07 CB3 CB4 CB6 119.97 CB4 CB6 CB5 119.87 CB4 CB6 OAB 120.09 CB5 CB6 OAB 120.04 CB6 CB5 CB1 119.94 CB2 CB1 CB5 120.08 C1 C2 N 109.45 C1 C2 CO2 109.49 N C2 CO2 109.48 CB2 C1 C2 109.49 C2 N C 119.96 N C O 120.03 N C CC1 119.94 O C CC1 120.03 C2 CO2 OC1 119.97 C2 CO2 OC2 119.98 OC1 CO2 OC2 120.05 CB6 OAB CA1 106.78 OAB CA1 CA2 120.02 OAB CA1 CA6 120.04 CA2 CA1 CA6 119.94 CA1 CA2 CA3 119.90 CA1 CA2 BRA2 120.06 CA3 CA2 BRA2 120.03 CA2 CA3 CA4 120.05 CA3 CA4 CA5 120.13 CA4 CA5 CA6 120.09 CA1 CA6 CA5 119.90 CC3 CC4 CC5 109.50 CC4 CC3 CC6 109.44 CC4 CC3 CC9 109.45 CC6 CC3 CC9 109.48 CC4 CC5 CC2 109.46 CC4 CC5 C10 109.46 CC2 CC5 C10 109.44 CC5 CC2 CC1 109.49 CC3 CC6 CC1 109.51 C CC1 CC2 109.44 C CC1 CC6 109.50 C CC1 CC7 109.49 CC2 CC1 CC6 109.47 CC2 CC1 CC7 109.45 CC6 CC1 CC7 109.48 CC5 C10 CC8 109.47 C10 CC8 CC9 109.52 C10 CC8 CC7 109.48 CC9 CC8 CC7 109.46 CC3 CC9 CC8 109.46 CC1 CC7 CC8 109.47 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- CB1 CB2 CB3 CB4 0.31 Flat ? C1 CB2 CB3 CB4 179.99 Flat ? CB3 CB2 CB1 CB5 -0.55 Flat ? C1 CB2 CB1 CB5 179.77 Flat ? CB3 CB2 C1 C2 90.04 CB1 CB2 C1 C2 -90.28 CB2 CB3 CB4 CB6 -0.06 Flat ? CB3 CB4 CB6 CB5 0.05 Flat ? CB3 CB4 CB6 OAB -179.96 Flat ? CB4 CB6 CB5 CB1 -0.29 Flat ? OAB CB6 CB5 CB1 179.72 Flat ? CB4 CB6 OAB CA1 89.38 CB5 CB6 OAB CA1 -90.63 CB6 CB5 CB1 CB2 0.54 Flat ? N C2 C1 CB2 64.95 CO2 C2 C1 CB2 -175.04 Flat ? C1 C2 N C -154.97 CO2 C2 N C 85.01 C1 C2 CO2 OC1 -120.02 C1 C2 CO2 OC2 60.00 N C2 CO2 OC1 -0.03 Flat ? N C2 CO2 OC2 179.99 Flat ? C2 N C O 0.00 Flat ? C2 N C CC1 -180.00 Flat ? N C CC1 CC2 179.99 Flat ? N C CC1 CC6 -60.02 N C CC1 CC7 60.02 O C CC1 CC2 -0.01 Flat ? O C CC1 CC6 119.98 O C CC1 CC7 -119.98 CB6 OAB CA1 CA2 -178.74 Flat ? CB6 OAB CA1 CA6 1.55 Flat ? OAB CA1 CA2 CA3 179.74 Flat ? OAB CA1 CA2 BRA2 0.31 Flat ? CA6 CA1 CA2 CA3 -0.55 Flat ? CA6 CA1 CA2 BRA2 -179.98 Flat ? OAB CA1 CA6 CA5 179.99 Flat ? CA2 CA1 CA6 CA5 0.28 Flat ? CA1 CA2 CA3 CA4 0.58 Flat ? BRA2 CA2 CA3 CA4 -180.00 Flat ? CA2 CA3 CA4 CA5 -0.33 Flat ? CA3 CA4 CA5 CA6 0.06 Flat ? CA4 CA5 CA6 CA1 -0.03 Flat ? CC5 CC4 CC3 CC6 -59.97 CC5 CC4 CC3 CC9 60.01 CC3 CC4 CC5 CC2 59.97 CC3 CC4 CC5 C10 -59.97 CC4 CC3 CC6 CC1 60.00 CC9 CC3 CC6 CC1 -59.96 CC4 CC3 CC9 CC8 -59.99 CC6 CC3 CC9 CC8 59.96 CC4 CC5 CC2 CC1 -59.97 C10 CC5 CC2 CC1 59.99 CC4 CC5 C10 CC8 59.95 CC2 CC5 C10 CC8 -60.01 CC5 CC2 CC1 C -179.99 Flat ? CC5 CC2 CC1 CC6 60.00 CC5 CC2 CC1 CC7 -60.00 CC3 CC6 CC1 C -179.99 Flat ? CC3 CC6 CC1 CC2 -60.02 CC3 CC6 CC1 CC7 59.96 C CC1 CC7 CC8 179.95 Flat ? CC2 CC1 CC7 CC8 59.99 CC6 CC1 CC7 CC8 -59.99 CC5 C10 CC8 CC9 -59.99 CC5 C10 CC8 CC7 60.03 C10 CC8 CC9 CC3 60.02 CC7 CC8 CC9 CC3 -60.01 C10 CC8 CC7 CC1 -60.04 CC9 CC8 CC7 CC1 60.02 Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- CB2 CB3 CB1 C1 -0.19 CB6 CB4 CB5 OAB 0.00 C2 C1 N CO2 -35.34 C N O CC1 0.00 CO2 C2 OC1 OC2 0.01 CA1 OAB CA2 CA6 0.17 CA2 CA1 CA3 BRA2 0.36 CC3 CC4 CC6 CC9 -35.27 CC5 CC4 CC2 C10 35.30 --- Atom with 4 or more non-H neighbours --- CC1 C CC2 CC6 -35.35 CC1 CC2 CC6 CC7 35.27 CC1 CC6 CC7 C -35.03 CC1 CC7 C CC2 35.41 CC8 C10 CC9 CC7 -35.26 Number of possible flat planes : ( 39) Looking for more planes ... Number of possible flat planes : ( 53) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -5.421E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.463E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.912E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.103E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.898E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.249E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.761E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.746E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.741E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.986E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.835E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.183E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.958E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.445E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.645E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.154E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.035E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.574E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.425E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.702E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.211E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.161E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.760E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.230E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.135E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.455E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.916E-09) WARNING - Reset negative RMSD in LSQGJK : ( -5.670E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.926E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.965E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.926E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.455E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.406E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.265E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.481E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.287E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.604E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.455E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.165E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.878E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.616E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.323E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.197E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.377E-07) WARNING - Reset negative RMSD in LSQGJK : ( -7.170E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.047E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.268E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.616E-08) WARNING - Reset negative RMSD in LSQGJK : ( -9.006E-10) WARNING - Reset negative RMSD in LSQGJK : ( -1.830E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.933E-08) WARNING - Reset negative RMSD in LSQGJK : ( -6.616E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.301E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.792E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.617E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.130E-08) WARNING - Reset negative RMSD in LSQGJK : ( -7.230E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.101E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.928E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.458E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.425E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.481E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.444E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.831E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.916E-09) WARNING - Reset negative RMSD in LSQGJK : ( -3.965E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.423E-07) WARNING - Reset negative RMSD in LSQGJK : ( -6.772E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.299E-08) WARNING - Reset negative RMSD in LSQGJK : ( -3.058E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.200E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.964E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.421E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.273E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.928E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.958E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.574E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.135E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.455E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.686E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.194E-07) WARNING - Reset negative RMSD in LSQGJK : ( -5.268E-08) WARNING - Reset negative RMSD in LSQGJK : ( -8.706E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.604E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.792E-08) WARNING - Reset negative RMSD in LSQGJK : ( -5.871E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.001E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.165E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.687E-08) Removing non-unique planes ... Plane nr : ( 37) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) CO2 0.000 C2 0.000 OC1 0.000 OC2 0.000 N 0.000 Plane nr : ( 43) Nr of atoms : ( 8) WARNING - Reset negative RMSD in LSQGJK : ( -2.719E-08) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) CB1 -0.003 CB2 0.001 CB5 0.002 CB3 -0.001 C1 0.001 CB6 0.000 CB4 0.000 OAB 0.000 Plane nr : ( 44) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -2.554E-08) RMSD to least-squares plane (A): ( 0.031) Atom Dist (A) C1 -0.031 CB2 0.031 C2 -0.031 CO2 0.031 Plane nr : ( 50) Nr of atoms : ( 9) WARNING - Reset negative RMSD in LSQGJK : ( -1.557E-08) RMSD to least-squares plane (A): ( 0.008) Atom Dist (A) CA6 -0.008 CA1 -0.005 CA5 -0.003 OAB -0.011 CA2 -0.003 CA4 0.005 CB6 0.017 CA3 0.008 BRA2 0.001 Plane nr : ( 51) Nr of atoms : ( 7) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) CC2 0.000 CC5 0.000 CC1 0.000 C 0.000 N 0.000 O 0.000 C2 0.000 Plane nr : ( 52) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -6.434E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) CC6 0.000 CC3 0.000 CC1 0.000 C 0.000 Plane nr : ( 53) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -4.532E-08) RMSD to least-squares plane (A): ( 0.000) Atom Dist (A) CC7 0.000 CC1 0.000 CC8 0.000 C 0.000 ------------------- ----- SUMMARY ----- ------------------- Residue type : (PH9) Identifier : ( 6142) Segment ID : ( ) Nr of atoms : ( 32) List of elements (from file) : ( C26 H28 BR N O4) Deduced formula : (C26 N1 O4 BR1) Guestimated total nr of Hs : ( 28) Nr of extra examples : ( 0) Nr of distances < 0.8 A : ( 0) Nr of bond angles < 80 degrees : ( 0) Nr of bonds found : ( 36) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 36) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 53) Nr of dihedrals found : ( 70) Nr of atoms with impropers : ( 11) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 7)