LED Binary Clock

I added the 2 time setting pushbuttons on the PCB, all the 13 resistors and the reset pushbutton. 
place your crystal, remember, the frequency is not critical, as long as you specify it on the arduino software, if you don’t know how to do this, stick with 16Mhz, also, if you´re using another frequency, remember that its recommended that it’s a multiple of 8, e.g. 16mhz or 8 Mhz because Atmega chips are 8Bit micros.

if you’re a beginner, it’s recommended to use an arduino, or at least an arduino ready, pre-bootloaded chip.
the advantages of using an Atmega48 instead of an atmega328/arduino is mainly the price;
an arduino costs about USD $30, an arduino pre boot loaded chip costs about USD $6, and an Atmega48 costs only about USD $1.5.

NOTE: to be able to program Atmega chips without boot loader, using ISP from the arduino IDE you need to make some modifications to  the IDE (I will not cover that in this guide).

if you use an Atmega48/88 without bootloader, you need to have some basic knowedlage on AVR fuses and how to work with the bare chip and program thru ISP.

remember to add  a 2 pin header for power and, mark which pin is Gnd and which one is 5V and add a 3 pin female header for connecting the (optional) pushbutton or LDR. one pin to Gnd, one to 5V and the other one to digital pin 18 (analog 4).