###################################################################### ########################################################################## ### ### ### Tinker --- Software Tools for Molecular Design ### ## ## ## Version 25.6 December 2025 ## ## ## ## Copyright (c) Jay William Ponder 1990-2025 ## ### All Rights Reserved ### ### ### ########################################################################## ###################################################################### Enter Cartesian Coordinate File Name : Number of Distance Geometry Structures Desired [1] : Impose Chirality Constraints on Tetrahedral Atoms [Y] : Use "Floating" Chirality for -XH2- and -XH3 Groups [N] : Impose Planarity and/or Chirality of Trigonal Atoms [Y] : Impose Torsional Planarity on Adjacent Trigonal Atoms [Y] : Do You Wish to Examine or Alter the Bounds Matrix [N] : Select the Enantiomer Closest to the Input Structure [N] : Refinement via Minimization or Annealing [M or A, =A] : Bounds Smoothing via Triangle and Inverse Triangle Inequality : Largest Upper Bound Distance : 65.6036 Generation via Distance Geometry of Structure 1 Trial Distance Beta Distribution : 0.58 +/- 0.15 Alpha-Beta 5.52 4.00 RMS Superposition for Original and Enantiomer : 128.8477 128.8541 Molecular Dynamics Simulated Annealing Refinement : Steps: 1000 Time/Step: 0.040 ps LogMass: 4.00 Temp: 200.0 to 200.0 Molecular Dynamics Simulated Annealing Refinement : Steps: 10000 Time/Step: 0.200 ps LogMass: 4.00 Temp: 200.0 to 0.0 Results of Distance Geometry Protocol : Final Error Function Value : 29.3815 Distance Restraint Error : 4.9898 Hard Sphere Contact Error : 7.5217 Local Geometry Error : 8.5172 Chirality-Planarity Error : 2.2713 Torsional Restraint Error : 6.0816 Fit to Bounds after Refinement : Num Upper Bound Violations : 2951 of 2233441 Num Lower Bound Violations : 4963 of 2233441 Max Upper Bound Violation : 1.0127 at 124 2028 Max Lower Bound Violation : 1.2075 at 385 452 RMS Deviation from Bounds : 0.0049 Num Upper Restraint Violations : 251 of 13587 Num Lower Restraint Violations : 34 of 13587 Max Upper Restraint Violation : 1.0127 at 124 2028 Max Lower Restraint Violation : 0.1164 at 1867 1967 RMS Restraint Dist Violation : 0.0290 Radius of Gyration after Refinement : 13.3354 Generation via Distance Geometry of Structure 2 Trial Distances Selected at Random from Uniform Distribution RMS Superposition for Original and Enantiomer : 128.7524 128.7425 Molecular Dynamics Simulated Annealing Refinement : Steps: 1000 Time/Step: 0.040 ps LogMass: 4.00 Temp: 200.0 to 200.0 Molecular Dynamics Simulated Annealing Refinement : Steps: 10000 Time/Step: 0.200 ps LogMass: 4.00 Temp: 200.0 to 0.0 Results of Distance Geometry Protocol : Final Error Function Value : 40.8987 Distance Restraint Error : 4.7908 Hard Sphere Contact Error : 9.3324 Local Geometry Error : 9.8827 Chirality-Planarity Error : 2.4360 Torsional Restraint Error : 14.4568 Fit to Bounds after Refinement : Num Upper Bound Violations : 2943 of 2233441 Num Lower Bound Violations : 5081 of 2233441 Max Upper Bound Violation : 0.9285 at 279 328 Max Lower Bound Violation : 1.3924 at 209 268 RMS Deviation from Bounds : 0.0053 Num Upper Restraint Violations : 259 of 13587 Num Lower Restraint Violations : 33 of 13587 Max Upper Restraint Violation : 0.9285 at 279 328 Max Lower Restraint Violation : 0.1230 at 1327 1431 RMS Restraint Dist Violation : 0.0292 Radius of Gyration after Refinement : 13.3003 Generation via Distance Geometry of Structure 3 Trial Distances Selected at Random from Uniform Distribution RMS Superposition for Original and Enantiomer : 129.5543 129.5626 Molecular Dynamics Simulated Annealing Refinement : Steps: 1000 Time/Step: 0.040 ps LogMass: 4.00 Temp: 200.0 to 200.0 Molecular Dynamics Simulated Annealing Refinement : Steps: 10000 Time/Step: 0.200 ps LogMass: 4.00 Temp: 200.0 to 0.0 Results of Distance Geometry Protocol : Final Error Function Value : 11.9604 Distance Restraint Error : 2.8508 Hard Sphere Contact Error : 3.3100 Local Geometry Error : 4.5207 Chirality-Planarity Error : 1.1262 Torsional Restraint Error : 0.1526 Fit to Bounds after Refinement : Num Upper Bound Violations : 2852 of 2233441 Num Lower Bound Violations : 4756 of 2233441 Max Upper Bound Violation : 0.8129 at 1631 1643 Max Lower Bound Violation : 0.6448 at 2058 2080 RMS Deviation from Bounds : 0.0033 Num Upper Restraint Violations : 205 of 13587 Num Lower Restraint Violations : 17 of 13587 Max Upper Restraint Violation : 0.8129 at 1643 1631 Max Lower Restraint Violation : 0.1141 at 2067 105 RMS Restraint Dist Violation : 0.0204 Radius of Gyration after Refinement : 13.5074