Had my honda gx 110 apart and now I wonder with the marks on camshaft and crankshaft lining up, the crankshaft can be 180 degrees out?

You have 2/4/6 timing marks 180 degress out on exhaust or intake cam .

Did your special tool ?
Rotate the crankshaft using the J 42098 until the #1 cylinder is at 60 degrees before top dead center (BTDC).
Install theJ 42069 Crankshaft Locking Tool.
Rotate the crankshaft in the engine rotational direction (clockwise) using the J 42098 until the #1 cylinder is at top dead center (TDC) and tighten the lever arm to the water pump pulley flange.
Important: Ensure that the alignment of the crankshaft is not 180 degrees off. The alignment mark must align with the corresponding notches on the rear timing belt cover.
Install the 1-2 and 3-4 camshaft locks, the J42069-1 Timing Belt Alignment Kit and the J42069-2.
Important: Do not rotate the crankshaft if the camshafts are not locked in place with the 1-2 and 3-4 camshaft locks (J42069-1 and J42069-2).
Important: Do not rotate the camshafts unless the crankshaft is at 60 degrees BTDC or the valves may contact the crankshaft.
Loosen the tensioner pulley.
Remove the timing belt.

You say that you checked the timing marks (Camshaft vs. crankshaft) for proper alignment, but it's possible that the camshaft and crankshaft are out of sequence since the crankshaft turns two 360-degree rotations for every one of the camshaft. It's possible that the crankshaft needs to be rotated another 360 degrees and lined up with the timing mark on the camshaft (remove the timing belt in order to do this). Good luck.

Timing belt set-up for a 2000 Seat Inca 1.9 SDi

1. Align the crankshaft timing marks on the flywheel / gearbox


2. Remove the valve cover
3. Lock the camshaft


4. Fit the injection pump locking pin



5. Loosen the camshaft gearwheel bolt, 180 degrees. Use a wrench to counter-hold
6. Loosen the camshaft gearwheel while holding it in place



7. Fit the timing belt in the sequence as shown in the below figure: a - b - c - d - e - f - g



8. Fit the timing belt and camshaft gearwheel together
9. Turn the tensioner clockwise to align both marks



10. Tighten the large bolt on the tensioner to a torque of 20 Nm
11. Check for correct fit
12. Lock the camshaft. Tighten the camshaft gearwheel bolts: 45 Nm. Use a wrench to counter-hold
13. Remove helping tools
14. Turn the engine two rotations by hand
15. Repeat the procedure if required
16. Fit the vacuum pump
17. Refit the crankshaft pulley. Tighten torque: 20 Nm + 20 degrees
18. Fit the timing belt cover
19. Refit the valve cover
20. Fit the ancillary drive belt
21. Refit the inlet air manifold hoses
22. Check the injection timing

Torque settings:
Camshaft gearwheel: 45 Nm
Tensioner pulley: 20 Nm
Crankshaft pulley: 20 Nm + 20 degrees

Do you mean 1.7L? I do not see a 1.6L in the manual. Instructions from autozone.com are pasted below.

lash:

Intake, 0.007-0.009 in (0.18-0.22mm).

Exhaust, 0.009-0.011 in. (0.23-0.27mm)

Civic
1.7L Engine
NOTE Adjust valves only when the cylinder head temperature is less than 100 degrees F.

1. Before servicing the vehicle, refer to the precautions in the beginning of this section. Disconnect the negative battery cable.
2. Note the radio security code and the radio presets.
3. Remove the ignition coil cover. Remove the ignition coils. Remove the throttle cable clamps and harness holder from the cylinder head cover.
4. Remove the cylinder head cover retaining bolts. Remove the cylinder head cover from the engine.
5. Remove the grommet from the upper cover and disconnect the camshaft position (CMO) sensor connector. Remove the upper cover.
6. Set the number one piston at TDC. The UP mark on the camshaft pulley should be at the top, and the TDC marks on the pulley should line up with the top edge of the cylinder head.
7. Using the proper gauge feeler gauge, adjust the valves on cylinder number one.
8. Rotate the crankshaft 180 degrees counterclockwise. The UP mark on the camshaft pulley should be toward the exhaust side of the cylinder head.
9. Using the proper gauge feeler gauge, adjust the valves on cylinder number three.
10. Rotate the crankshaft 180 degrees counterclockwise and bring the number four piston to TDC.
11. Using the proper gauge feeler gauge, adjust the valves on cylinder number four.
12. Rotate the crankshaft 180 degrees counterclockwise. The UP mark on the camshaft pulley should be toward the intake side of the cylinder head.
13. Using the proper gauge feeler gauge, adjust the valves on cylinder number two.
14. Install the cylinder head cover.
15. As required, reprogram the ECM/PCM engine idle characteristics. Be sure all electrical items are OFF.
16. Start the engine. Hold the idle speed at 3000 RPM-s in park or neutral until the radiator fan comes on or the temperature reached 194 degrees.
17. Let the engine idle for about five minutes with the throttle fully closed.
18. If the radiator fan comes on during the five minutes, do not count this toward the five minute programming time.
19. Set the clock.

it would help if you gave an engine size but I'll guess its a 3.1 with a timing chain. there is a mark on the lower gear (crankshaft) which should be at 12 o clock position. on the camshaft there may be 2 marks 180 degrees apart from each other. number 1 cylinder is on the passenger side front, remove the distributor cap and align the ignition rotor to face where #1 spot on the distributor cap is by rotating the camshaft. this should put 1 of the marks at 12 o clock and 1 of the marks at 6 o clock. thats where you want the gears to be.

TDC is top dead center/ remove spark plug on cylinder no. 1/ rotate the crankshaft pulley using a socket wrench and power handle and check if the piston on your cylinder no. 1 reach the top center that is TDC/ remove timing belt cover and locate a synchronized marking on your camshaft and crankshaft pulley/ remove old timing belt/ install a new one but make sure that the mark on your camshaft and crankshaft is perfectly synchronized before putting the cover/ manually rotate the crankshaft pulley again and see if it rotates 360 deg. freely then you can be sure you did the job correctly.

On the crankshaft gear there is a VERY small dimple that aligns with a mark on the motor. The mark on the motor (a small triangle) is at roughly 11 o'clock. After you line these timing marks up look at the camshaft gear and you will see that on one of the spokes there is a hole. You need to use a mirror to line this hole up with the dimple on the cover that is behind the camshaft gear. (It is at roughly 1 o'clock) If this hole is 180 degrees from where it should be you need to rotate the motor 1 more revolution at the crankshaft and it should now be lined up, or close. Once lined up I like to take a silver (metallic) Sharpie and make my own mark on the camshaft gear and on the backing plate that is behind it. You can make this mark where ever it is convenient for you. As long as you know where your marks line up, that is all that matters. This way I don't have to use the mirror as often.

Step 5 Once you have your timing marks aligned you need to locate the tensioner. The tensioner obviously keeps the appropriate amount of tension on the timing belt.

timing on all camshaft im familiar with have a dot stamped on the gear and one on the adjacent gear it meshes with, the trick is to get the two dots to line up with each other for proper timing.
the camshaft runs 2:1 to the crankshaft, so if it wont run, that means your 180 degrees off. line everything back up the dots that is, take the belt off and rotate the cam 360 until the dots are in line again and reinstall the belt.
should fix you up.
hope this helps, good luck

If you can't find specs on this in a rebuild manual, you will need a dial indicator. find tdc on crankshaft, with #1 piston at top of stroke. Find exact point where #1cyl intake lobe on cam is 180 degrees from full open position. It is likely that you will find that there are alignment markings that will line up with reference points on block & head after you do this. The cam reference may be off by a couple of degrees, depending upon if the cam is intended to be installed "straight up" or a few degrees advanced.

easyiest way to do that is to go to your local library and look up you torque specs and sequence for your car.