2006 YAMAHA YZF-R1 check engine

TABLE OF CONTENTSSAFETY INFORMATION ..................1-1
DESCRIPTION ..................................2-1
Left view ..........................................2-1
Right view ........................................2-2
Controls and instruments.................2-3
INSTRUMENT AND CONTROL
FUNCTIONS.......................................3-1
Immobilizer system .........................3-1
Main switch/steering lock ................3-2
Indicator and warning lights ............3-3
Multi-function meter unit .................3-8
Anti-theft alarm (optional) .............3-13
Handlebar switches ......................3-14
Clutch lever ...................................3-15
Shift pedal .....................................3-15
Brake lever ...................................3-16
Brake pedal ..................................3-16
Fuel tank cap ................................3-17
Fuel ...............................................3-17
Fuel tank breather/overflow
hose ..........................................3-18
Catalytic converter ........................3-19
Seats ............................................3-19
Helmet holders .............................3-20
Adjusting the front fork ..................3-21
Adjusting the shock absorber
assembly ...................................3-23
Adjusting the seat height ..............3-26
Luggage strap holders ..................3-27EXUP system ............................... 3-27
Sidestand ..................................... 3-27
Ignition circuit cut-off system ........ 3-28
PRE-OPERATION CHECKS............. 4-1
Pre-operation check list .................. 4-2
OPERATION AND IMPORTANT
RIDING POINTS................................. 5-1
Starting the engine ......................... 5-1
Shifting ........................................... 5-2
Tips for reducing fuel
consumption ............................... 5-3
Engine break-in .............................. 5-3
Parking ........................................... 5-4
PERIODIC MAINTENANCE AND
MINOR REPAIR................................. 6-1
Owner’s tool kit ............................... 6-1
Periodic maintenance and
lubrication chart .......................... 6-2
Removing and installing panels ..... 6-6
Checking the spark plugs ............... 6-7
Engine oil and oil filter cartridge ..... 6-8
Coolant ......................................... 6-12
Replacing the air filter element ..... 6-14
Adjusting the engine idling
speed ........................................ 6-16
Checking the throttle cable
free play .................................... 6-16
Valve clearance ............................ 6-17Tires ............................................. 6-17
Forged wheels ............................. 6-20
Adjusting the clutch lever
free play .................................... 6-20
Adjusting the rear brake light
switch ....................................... 6-21
Checking the front and rear
brake pads ................................ 6-21
Checking the brake fluid level ...... 6-22
Changing the brake fluid .............. 6-23
Drive chain slack .......................... 6-23
Cleaning and lubricating the
drive chain ................................ 6-24
Checking and lubricating the
cables ....................................... 6-25
Checking and lubricating the
throttle grip and cable ............... 6-25
Checking and lubricating the
brake and clutch levers ............ 6-26
Checking and lubricating the
sidestand .................................. 6-26
Lubricating the swingarm
pivots ........................................ 6-27
Checking the front fork ................. 6-27
Checking the steering .................. 6-28
Checking the wheel bearings ....... 6-28
Battery ......................................... 6-29
Replacing the fuses ..................... 6-30
Replacing a headlight bulb .......... 6-32
Tail/brake light ............................. 6-35U4B1E0E0.book Page 1 Wednesday, October 12, 2005 2:32 PM

DESCRIPTION
2-2
2
EAU10420
Right view1. Luggage strap holder (page 3-27)
2. Helmet holder (page 3-20)
3. Passenger seat lock (page 3-19)
4. Rear brake fluid reservoir (page 6-22)
5. Engine oil filler cap (page 6-8)
6. Air filter element (page 6-14)
7. Front fork compression damping force adjusting bolt (page 3-21)
8. Engine oil level check window (page 6-8)9. Seat height adjusting bolt (page 3-26)
10.Shock absorber assembly rebound damping force adjusting screw
(page 3-23)
11.Coolant reservoir (page 6-12)
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INSTRUMENT AND CONTROL FUNCTIONS
3-4
3
EAU11060
Neutral indicator light “”
This indicator light comes on when the
transmission is in the neutral position.
EAU11080
High beam indicator light “”
This indicator light comes on when the
high beam of the headlight is switched
on.
EAU11250
Oil level warning light “”
This warning light comes on when the
engine oil level is low.
The electrical circuit of the warning light
can be checked by turning the key to
“ON”.
If the warning light does not come on
for a few seconds, then go off, have a
Yamaha dealer check the electrical cir-
cuit.NOTE:

Even if the oil level is sufficient, the
warning light may flicker when
riding on a slope or during sudden
acceleration or deceleration, but
this is not a malfunction.


This model is also equipped with a
self-diagnosis device for the oil
level detection circuit. If the oil lev-
el detection circuit is defective, the
following cycle will be repeated un-
til the malfunction is corrected: The
oil level warning light will flash ten
times, then go off for 2.5 seconds.
If this occurs, have a Yamahadealer check the vehicle.
EAU11361
Fuel level warning light “”
This warning light comes on when the
fuel level drops below approximately
3.4 L (0.90 US gal) (0.75 Imp.gal).
When this occurs, refuel as soon as
possible.
The electrical circuit of the warning light
can be checked by turning the key to
“ON”.
If the warning light does not come on
for a few seconds, and then go off,
have a Yamaha dealer check the elec-
trical circuit.
NOTE:This model is also equipped with a self-
diagnosis device for the fuel level de-
tection circuit. If the fuel level detection
circuit is defective, the following cycle
will be repeated until the malfunction is
corrected: The fuel level warning light
will flash eight times, and then go off for
3.0 seconds. If this occurs, have aYamaha dealer check the vehicle.
EAU11422
Coolant temperature warning light
“”
This warning light comes on when the
engine overheats. When this occurs,
stop the engine immediately and allow
the engine to cool.
The electrical circuit of the warning light
can be checked by turning the key to
“ON”.
If the warning light does not come on
for a few seconds, then go off, have a
Yamaha dealer check the electrical cir-
cuit.
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INSTRUMENT AND CONTROL FUNCTIONS
3-7
3
EAU11530
Engine trouble warning light “”
This warning light comes on or flashes
when an electrical circuit monitoring the
engine is defective. When this occurs,
have a Yamaha dealer check the self-
diagnosis system. (See page 3-8 for an
explanation of the self-diagnosis de-
vice.)
The electrical circuit of the warning light
can be checked by turning the key to
“ON”. If the warning light does not come
on for a few seconds, then go off, have
a Yamaha dealer check the electrical
circuit.
EAU11571
Shift timing indicator light
This indicator light can be set to come
on and go off at the desired engine
speeds and is used to inform the rider
when it is time to shift to the next higher
gear.
The electrical circuit of the indicator
light can be checked by turning the key
to “ON”.
If the indicator light does not come on
for a few seconds, then go off, have a
Yamaha dealer check the electrical cir-cuit. (See page 3-8 for a detailed expla-
nation of the function of this indicator
light and on how to set it.)
EAU38610
Immobilizer system indicator light
The electrical circuit of the indicator
light can be checked by turning the key
to “ON”.
If the indicator light does not come on
for a few seconds, then go off, have a
Yamaha dealer check the electrical cir-
cuit.
When the key is turned to “OFF” and 30
seconds have passed, the indicator
light will start flashing indicating the im-
mobilizer system is enabled. After 24
hours have passed, the indicator light
will stop flashing, however the immobi-
lizer system is still enabled.NOTE:This model is also equipped with a self-
diagnosis device for the immobilizer
system. If the immobilizer system is de-
fective, the indicator light will start flash-
ing a pattern and the
odometer/tripmeter will display a 2-digit
code when the key is turned to “ON”.
When this occurs, have a Yamahadealer check the self-diagnosis system.
However, if the indicator light slowly
flashes five times, and then quickly
flashes two times repeatedly, error
code 52 will be displayed. This error
could be caused by signal interference.
If this occurs, try the following.
1. Use the code re-registering key to
start the engine.NOTE:Make sure there are no other immobi-
lizer keys close to the main switch, and
do not keep more than one immobilizer
key on the same key ring! Immobilizer
system keys may cause signal interfer-
ence, which may prevent the enginefrom starting.
2. If the engine starts, turn it off, and
try starting the engine with the
standard keys.
3. If one or both of the standard keys
do not start the engine, take the
vehicle, the code re-registering
key and both standard keys to a
Yamaha dealer and have the stan-
dard keys re-registered.
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INSTRUMENT AND CONTROL FUNCTIONS
3-11
3


When the air intake temperature
display is selected, “A” is displayedbefore the temperature.
Self-diagnosis devices
This model is equipped with a self-diag-
nosis device for various electrical cir-
cuits.
If any of those circuits are defective, the
engine trouble warning light will come
on, and then the right display will indi-
cate a two-digit error code (e.g., 11, 12,
13).
This model is also equipped with a self-
diagnosis device for the immobilizer
system.
If any of the immobilizer system circuits
are defective, the immobilizer system
indicator light will flash, and then the
right display will indicate a two-digit er-
ror code (e.g., 51, 52, 53).
NOTE:If the right display indicates error code
52, this could be caused by transpon-
der interference. If this error code ap-pears, try the following.1. Use the code re-registering key to
start the engine.
NOTE:Make sure there are no other immobi-
lizer keys close to the main switch, and
do not keep more than one immobilizer
key on the same key ring! Immobilizer
system keys may cause signal interfer-
ence, which may prevent the enginefrom starting.
2. If the engine starts, turn it off and
try starting the engine with the
standard keys.
3. If one or both of the standard keys
do not start the engine, take the
vehicle, the code re-registering
key and both standard keys to a
Yamaha dealer and have the stan-
dard keys re-registered.
If the right display indicates any error
codes, note the code number, and then
have a Yamaha dealer check the vehi-
cle.
CAUTION:
ECA11590
If the display indicates an error
code, the vehicle should be checked
as soon as possible in order to avoidengine damage.
Display brightness and shift timing
indicator light control mode
This mode cycles through five control
functions, allowing you to make the fol-
lowing settings in the order listed be-
low.1. Display brightness
2. Shift timing indicator light activation/deacti-
vation
3. Shift timing indicator light
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INSTRUMENT AND CONTROL FUNCTIONS
3-18
3
CAUTION:
ECA10070
Immediately wipe off spilled fuel
with a clean, dry, soft cloth, since
fuel may deteriorate painted surfac-es or plastic parts.
EAU13390
CAUTION:
ECA11400
Use only unleaded gasoline. The use
of leaded gasoline will cause severe
damage to internal engine parts,
such as the valves and piston rings,as well as to the exhaust system.
Your Yamaha engine has been de-
signed to use premium unleaded gaso-
line with a research octane number of
95 or higher. If knocking (or pinging) oc-curs, use a gasoline of a different
brand. Use of unleaded fuel will extend
spark plug life and reduce maintenance
costs.
EAU34072
Fuel tank breather/overflow
hose Before operating the motorcycle:

Check the fuel tank breather/over-
flow hose connection.


Check the fuel tank breather/over-
flow hose for cracks or damage,
and replace it if damaged.


Make sure that the end of the fuel
tank breather/overflow hose is not
blocked, and clean it if necessary.


Make sure that the end of the fuel
tank breather/overflow hose is po-
sitioned outside of the cowling.
Recommended fuel:
PREMIUM UNLEADED GASOLINE
ONLY
Fuel tank capacity:
18.0 L (4.76 US gal) (3.96 Imp.gal)
Fuel reserve amount (when the fuel
level warning light comes on):
3.4 L (0.90 US gal) (0.75 Imp.gal)
1. Fuel tank breather/overflow hose
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INSTRUMENT AND CONTROL FUNCTIONS
3-27
3
EAU15181
Luggage strap holders There are four luggage strap holders on
the bottom of the passenger seat. To
use the strap holders, remove the pas-
senger seat, unhook the straps from
the hooks, and then install the seat with
the straps hanging out from under the
passenger seat. (See page 3-19.)
EAU15281
EXUP system This model is equipped with Yamaha’s
EXUP (EXhaust Ultimate Power valve)
system. This system boosts engine
power by means of a valve that regu-
lates the diameter of the exhaust pipe.
The EXUP system valve is constantly
adjusted in accordance with the engine
speed by a computer-controlled servo-
motor.CAUTION:
ECA10191


The EXUP system has been set
and extensively tested at the
Yamaha factory. Changing
these settings without sufficient
technical knowledge may result
in poor performance of or dam-
age to the engine.


If the EXUP system cannot be
heard when the main switch is
turned on, have a Yamaha deal-er check it.
EAU15301
Sidestand The sidestand is located on the left side
of the frame. Raise the sidestand or
lower it with your foot while holding the
vehicle upright.NOTE:The built-in sidestand switch is part of
the ignition circuit cut-off system, which
cuts the ignition in certain situations.
(See further down for an explanation ofthe ignition circuit cut-off system.)
WARNING
EWA10240
The vehicle must not be ridden with
the sidestand down, or if the side-
stand cannot be properly moved up
(or does not stay up), otherwise the
sidestand could contact the ground
and distract the operator, resulting
in a possible loss of control.
Yamaha’s ignition circuit cut-off
system has been designed to assist
the operator in fulfilling the respon-
sibility of raising the sidestand be-
fore starting off. Therefore, check
this system regularly as described
1. Luggage strap holder
2. Hook
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INSTRUMENT AND CONTROL FUNCTIONS
3-28
3below and have a Yamaha dealer re-
pair it if it does not function proper-
ly.
EAU15311
Ignition circuit cut-off system The ignition circuit cut-off system (com-
prising the sidestand switch, clutch
switch and neutral switch) has the fol-
lowing functions.

It prevents starting when the trans-
mission is in gear and the side-
stand is up, but the clutch lever is
not pulled.


It prevents starting when the trans-
mission is in gear and the clutch le-
ver is pulled, but the sidestand is
still down.


It cuts the running engine when the
transmission is in gear and the sid-
estand is moved down.
Periodically check the operation of the
ignition circuit cut-off system according
to the following procedure.WARNING
EWA10250
If a malfunction is noted, have a
Yamaha dealer check the system be-fore riding.
U4B1E0E0.book Page 28 Wednesday, October 12, 2005 2:32 PM