ok, here are all buttons explained:
Left thumbstick - emulate A, S, D and Shift+W - moving around and running forward
Right thumbstick - emulate mouse - moves the player head/move objects that are grabbed/move cursor around
D-pad - emulate W, A and D, arrow down emulate Right mouse button - examine game objects/cancels selections/throws grabbed objects (there is not enough buttons on pad)
Button 1 - emulate N - notes
Button 2 - emulate X - holster current tool
Button 3 - emulate G - turns glowstick on/off
Button 4 - emulate F - turns flashlight on/off
Button 5 - L2 - emulate space - jump
Button 6 - R2 - emulate left mouse button - interact with objects in the game/selects options in menus/throw or swing tool
Button 7 - L1 - emulate Q - lean left
Button 8 - R1 - emulate E - lean right
Button 9 - select - emulate TAB - opens up the inventory
Button 10 - start - emulate ESC - opens the main menu/pause
Button 11 - left thumbstick button - emulate CTRL - toggle to crouch (press again to stand)
Button 12 - right thumbstick button - emulate R - toggle normal/interact mode
and that's all
there is no SHIFT emulate because all you can do with it is running forward, so it's already in left thumbstick, no need to push two buttons... if you want to sneak, use d-pad. in my opinion it's much more comfortable, and in total darkness you don't have to look for some buttons around whole keyboard... i'm attaching also updated version.