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 AND 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE) > (REMARK AND Part of HIC-Up: http://xray.bmc.uu.se/hicup) > (REMARK AND Extracted from PDB file pdb1coy.ent) > (REMARK AND Formula C19 H28 O2) Formula : (AND C19 H28 O2) > (REMARK AND Nr of non-hydrogen atoms 21) > (REMARK AND Eigen-values covariance X/Y/Z 197.7 30.5 9.6) > (REMARK AND Residue type AND) > (REMARK AND Residue name 1624) > (REMARK AND Original residue name (for O) $508) > (REMARK AND RESOLUTION. 1.80 ANGSTROMS.) > (REMARK AND occurs in 4 other PDB entries) > (REMARK AND Also in 1.5-2.0A : 1J99) > (REMARK AND Resolution (A) : 1.99) > (REMARK AND Also in 2.0-2.5A : 3DHE 1E3R 1Q22) > (REMARK AND Resolution (A) : 2.30 2.50 2.50) > (REMARK AND) Using residue : (AND) Identifier : ( 1624) Segment ID : ( ) Using formula : ( C19 H28 O2) Element ? | C| Carbon | 6 19 Element ? | H| Hydrogen | 1 28 Element ? | O| Oxygen | 8 2 Atom # 1 = C1 @ 1.325 -0.869 -2.372 1.00 20.00 Atom # 2 = C2 @ 1.345 -0.340 -3.807 1.00 20.00 Atom # 3 = C3 @ -0.065 -0.391 -4.395 1.00 20.00 Atom # 4 = O3 @ -0.026 0.021 -5.763 1.00 20.00 Atom # 5 = C4 @ -0.981 0.547 -3.605 1.00 20.00 Atom # 6 = C5 @ -0.911 0.161 -2.137 1.00 20.00 Atom # 7 = C6 @ -2.026 -0.039 -1.499 1.00 20.00 Atom # 8 = C7 @ -2.081 -0.431 -0.051 1.00 20.00 Atom # 9 = C8 @ -0.821 0.076 0.657 1.00 20.00 Atom # 10 = C9 @ 0.402 -0.481 -0.081 1.00 20.00 Atom # 11 = C10 @ 0.426 0.032 -1.511 1.00 20.00 Atom # 12 = C11 @ 1.706 -0.112 0.620 1.00 20.00 Atom # 13 = C12 @ 1.699 -0.541 2.096 1.00 20.00 Atom # 14 = C13 @ 0.503 0.124 2.749 1.00 20.00 Atom # 15 = C14 @ -0.768 -0.467 2.086 1.00 20.00 Atom # 16 = C15 @ -1.873 0.032 3.026 1.00 20.00 Atom # 17 = C16 @ -1.229 -0.149 4.428 1.00 20.00 Atom # 18 = C17 @ 0.292 -0.147 4.210 1.00 20.00 Atom # 19 = O17 @ 1.146 -0.331 5.043 1.00 20.00 Atom # 20 = C18 @ 0.557 1.633 2.508 1.00 20.00 Atom # 21 = C19 @ 1.039 1.434 -1.491 1.00 20.00 > (REMARK AND ENDHET) Nr of atoms read : ( 21) Nr of extra examples : ( 0) Expected formula : ( C19 H28 O2) Observed formula : (C19 O2) Element | H| Expected 28 | Observed 0 Element | C| Expected 19 | Observed 19 Element | O| Expected 2 | Observed 2 Expected and observed formulae agree (ignoring any hydrogens) ! Looking for bonded atoms ... Bond C1 - C2 = 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 C1 - C10 = 1.537 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) 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 - O3 = 1.429 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.43 (devn. 0.00) For: C-O single Bond C3 - C4 = 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 C4 - C5 = 1.520 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C5 - C6 = 1.300 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.34 (devn. 0.04) For: C-C double or partial triple; range 1.309-1.337 Bond C5 - C10 = 1.482 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.44 (devn. 0.04) For: C-C single shortened; range 1.421-1.46 Bond C6 - C7 = 1.501 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.03) For: C-C single; range 1.49-1.54 Bond C7 - C8 = 1.532 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 = 1.533 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 - 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 C9 - C10 = 1.519 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C9 - C11 = 1.526 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 - C19 = 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 C11 - C12 = 1.537 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C12 - C13 = 1.516 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C13 - C14 = 1.551 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 C13 - C17 = 1.501 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.03) For: C-C single; range 1.49-1.54 Bond C13 - C18 = 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 C14 - C15 = 1.534 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 = 1.553 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 C16 - C17 = 1.537 A (cutoff : 1.710) Nr of entries in library : ( 5) Closest to 1.53 (devn. 0.01) For: C-C single; range 1.49-1.54 Bond C17 - O17 = 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 : ( 24) 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: 2 ~Hs: 2 Carbon C2 Nbrs: 2 ~Hs: 2 Carbon C3 Nbrs: 3 ~Hs: 1 Oxygen O3 Nbrs: 1 ~Hs: 1 Carbon C4 Nbrs: 2 ~Hs: 2 Carbon C5 Nbrs: 3 ~Hs: 0 Carbon C6 Nbrs: 2 ~Hs: 1 Carbon C7 Nbrs: 2 ~Hs: 2 Carbon C8 Nbrs: 3 ~Hs: 1 Carbon C9 Nbrs: 3 ~Hs: 1 Carbon C10 Nbrs: 4 ~Hs: 0 Carbon C11 Nbrs: 2 ~Hs: 2 Carbon C12 Nbrs: 2 ~Hs: 2 Carbon C13 Nbrs: 4 ~Hs: 0 Carbon C14 Nbrs: 3 ~Hs: 1 Carbon C15 Nbrs: 2 ~Hs: 2 Carbon C16 Nbrs: 2 ~Hs: 2 Carbon C17 Nbrs: 3 ~Hs: 0 Oxygen O17 Nbrs: 1 ~Hs: 0 Carbon C18 Nbrs: 1 ~Hs: 3 Carbon C19 Nbrs: 1 ~Hs: 3 Est. total nr of hydrogens : ( 28) Looking for angles ... AtmJ AtmI AtmK Angle ---- ---- ---- ----- C2 C1 C10 109.30 C1 C2 C3 109.71 C2 C3 O3 109.48 C2 C3 C4 109.45 O3 C3 C4 109.49 C3 C4 C5 108.38 C4 C5 C6 118.27 C4 C5 C10 118.15 C6 C5 C10 123.58 C5 C6 C7 123.02 C6 C7 C8 109.23 C7 C8 C9 108.27 C7 C8 C14 110.05 C9 C8 C14 107.04 C8 C9 C10 110.06 C8 C9 C11 111.88 C10 C9 C11 109.71 C1 C10 C5 110.01 C1 C10 C9 109.79 C1 C10 C19 108.07 C5 C10 C9 114.37 C5 C10 C19 106.69 C9 C10 C19 107.66 C9 C11 C12 111.70 C11 C12 C13 107.14 C12 C13 C14 107.17 C12 C13 C17 116.80 C12 C13 C18 109.70 C14 C13 C17 103.43 C14 C13 C18 109.74 C17 C13 C18 109.67 C8 C14 C13 107.01 C8 C14 C15 115.59 C13 C14 C15 101.80 C14 C15 C16 102.50 C15 C16 C17 106.39 C13 C17 C16 106.11 C13 C17 O17 126.86 C16 C17 O17 127.03 Looking for dihedrals (and planes) ... AtmK AtmI AtmJ AtmL Dihedral ---- ---- ---- ---- ------- C10 C1 C2 C3 -62.08 C2 C1 C10 C5 53.48 C2 C1 C10 C9 -179.80 Flat ? C2 C1 C10 C19 -62.64 C1 C2 C3 O3 -176.22 Flat ? C1 C2 C3 C4 63.76 C2 C3 C4 C5 -55.20 O3 C3 C4 C5 -175.21 Flat ? C3 C4 C5 C6 -128.73 C3 C4 C5 C10 51.22 C4 C5 C6 C7 179.66 Flat ? C10 C5 C6 C7 -0.29 Flat ? C4 C5 C10 C1 -50.51 C4 C5 C10 C9 -174.61 Flat ? C4 C5 C10 C19 66.47 C6 C5 C10 C1 129.43 C6 C5 C10 C9 5.34 Flat ? C6 C5 C10 C19 -113.58 C5 C6 C7 C8 26.41 C6 C7 C8 C9 -55.96 C6 C7 C8 C14 -172.64 Flat ? C7 C8 C9 C10 62.07 C7 C8 C9 C11 -175.68 Flat ? C14 C8 C9 C10 -179.32 Flat ? C14 C8 C9 C11 -57.08 C7 C8 C14 C13 -178.18 Flat ? C7 C8 C14 C15 -65.62 C9 C8 C14 C13 64.38 C9 C8 C14 C15 176.94 Flat ? C8 C9 C10 C1 -160.52 C8 C9 C10 C5 -36.31 C8 C9 C10 C19 82.06 C11 C9 C10 C1 75.96 C11 C9 C10 C5 -159.83 C11 C9 C10 C19 -41.46 C8 C9 C11 C12 54.37 C10 C9 C11 C12 176.81 Flat ? C9 C11 C12 C13 -57.34 C11 C12 C13 C14 64.89 C11 C12 C13 C17 -179.75 Flat ? C11 C12 C13 C18 -54.20 C12 C13 C14 C8 -70.45 C12 C13 C14 C15 167.85 Flat ? C17 C13 C14 C8 165.56 Flat ? C17 C13 C14 C15 43.87 C18 C13 C14 C8 48.61 C18 C13 C14 C15 -73.09 C12 C13 C17 C16 -146.64 C12 C13 C17 O17 33.11 C14 C13 C17 C16 -29.21 C14 C13 C17 O17 150.54 C18 C13 C17 C16 87.80 C18 C13 C17 O17 -92.46 C8 C14 C15 C16 -156.16 C13 C14 C15 C16 -40.60 C14 C15 C16 C17 23.25 C15 C16 C17 C13 3.81 Flat ? C15 C16 C17 O17 -175.93 Flat ? Looking for impropers (and planes) ... Atm* Nbr1 Nbr2 Nbr3 Improper ---- ---- ---- ---- -------- C3 C2 O3 C4 35.75 C5 C4 C6 C10 -0.03 C8 C7 C9 C14 36.61 C9 C8 C10 C11 -33.35 --- Atom with 4 or more non-H neighbours --- C10 C1 C5 C9 -31.62 C10 C5 C9 C19 37.93 C10 C9 C19 C1 -36.34 C10 C19 C1 C5 36.42 --- Atom with 4 or more non-H neighbours --- C13 C12 C14 C17 -34.29 C13 C14 C17 C18 35.83 C13 C17 C18 C12 -29.95 C13 C18 C12 C14 36.83 C14 C8 C13 C15 -36.33 C17 C13 C16 O17 -0.12 Number of possible flat planes : ( 20) Looking for more planes ... Number of possible flat planes : ( 28) Expanding planes ... WARNING - Reset negative RMSD in LSQGJK : ( -4.521E-09) WARNING - Reset negative RMSD in LSQGJK : ( -9.681E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.798E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.521E-09) WARNING - Reset negative RMSD in LSQGJK : ( -7.458E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.973E-07) WARNING - Reset negative RMSD in LSQGJK : ( -2.125E-08) WARNING - Reset negative RMSD in LSQGJK : ( -2.057E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.566E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.053E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.187E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.090E-07) WARNING - Reset negative RMSD in LSQGJK : ( -1.049E-07) WARNING - Reset negative RMSD in LSQGJK : ( -3.724E-08) WARNING - Reset negative RMSD in LSQGJK : ( -4.521E-09) WARNING - Reset negative RMSD in LSQGJK : ( -4.209E-07) WARNING - Reset negative RMSD in LSQGJK : ( -4.521E-09) WARNING - Reset negative RMSD in LSQGJK : ( -2.125E-08) WARNING - Reset negative RMSD in LSQGJK : ( -1.880E-07) Removing non-unique planes ... Plane nr : ( 9) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.027) Atom Dist (A) C7 0.027 C8 -0.025 C9 -0.029 C11 0.027 Plane nr : ( 11) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.041) Atom Dist (A) C7 0.047 C8 0.044 C14 -0.047 C13 0.002 C6 -0.046 Plane nr : ( 12) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.020) Atom Dist (A) C9 0.009 C8 -0.031 C14 -0.015 C15 0.024 C10 0.013 Plane nr : ( 15) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.528E-07) RMSD to least-squares plane (A): ( 0.078) Atom Dist (A) C12 0.079 C13 -0.087 C14 -0.068 C15 0.076 Plane nr : ( 16) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.092) Atom Dist (A) C17 0.092 C13 -0.086 C14 -0.098 C8 0.092 Plane nr : ( 19) Nr of atoms : ( 6) RMSD to least-squares plane (A): ( 0.031) Atom Dist (A) C5 0.008 C4 -0.024 C6 -0.006 C10 0.053 C7 0.016 C9 -0.047 Plane nr : ( 21) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.069E-07) RMSD to least-squares plane (A): ( 0.001) Atom Dist (A) C1 -0.001 C2 0.001 C10 -0.001 C9 0.001 Plane nr : ( 22) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -2.495E-07) RMSD to least-squares plane (A): ( 0.023) Atom Dist (A) C2 0.022 C1 -0.022 C3 0.024 O3 -0.024 Plane nr : ( 23) Nr of atoms : ( 4) WARNING - Reset negative RMSD in LSQGJK : ( -1.912E-07) RMSD to least-squares plane (A): ( 0.029) Atom Dist (A) C4 -0.027 C3 -0.031 C5 0.028 O3 0.030 Plane nr : ( 26) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.020) Atom Dist (A) C11 -0.021 C9 -0.019 C12 0.020 C10 0.020 Plane nr : ( 27) Nr of atoms : ( 4) RMSD to least-squares plane (A): ( 0.002) Atom Dist (A) C12 -0.001 C11 0.001 C13 -0.002 C17 0.002 Plane nr : ( 28) Nr of atoms : ( 5) RMSD to least-squares plane (A): ( 0.026) Atom Dist (A) C16 -0.036 C15 0.034 C17 -0.006 C13 -0.018 O17 0.026 ------------------- ----- SUMMARY ----- ------------------- Residue type : (AND) Identifier : ( 1624) Segment ID : ( ) Nr of atoms : ( 21) List of elements (from file) : ( C19 H28 O2) Deduced formula : (C19 O2) 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 : ( 24) ... bonds without ideal value : ( 0) ... bonds near ideal value : ( 24) ... bonds far from ideal value : ( 0) -"- % : ( 0.000) Nr of angles found : ( 39) Nr of dihedrals found : ( 58) Nr of atoms with impropers : ( 8) ... imprs far from ideal value : ( 0) -"- % : ( 0.000) Nr of flat planes : ( 12)