I've got a new hard disk. On the label there is a description of the jumper settings:
One of them is:
Jumpered pins 5 and 6 enables 1.5GB PHY
What does PHY stand for?
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PHY stands for "physical layer". By jumpering pins 5 & 6 will cause the drive to go into a legacy 1.5 Gbit/s mode, rather than its default 3.0 Gbit/s mode. Check out the Wikipedia article on SATA for a bit more info.
By jumping the two pins, 5 and 6, you limit the transfer rate to 1.5 GB/s.
PHY is simply the physical layer in question, between the drive and cables/transfer.
Take a look at Wikipedia's page on SATA throughput.
I bought the same disk 2 days ago. What everyone else says is right, jumpering those pins will limit the transfer rates to 1.5Gb/s rather that the 3Gb/s it is capable of.
Pins 1 & 2 enable Spread Spectrum Clocking which reduces the drives electronic noise, at the cost of some performance.
Pins 3 & 4 enable Power-Up In Standby (low power mode). Your motherboard needs to support this. I couldn't find any way in Vista to get my external drive out of standby.