It is VERY common for teenagers to go through Rebellious phases.
However for many others a common rejection of the faith of their parents at this age becomes entrenched.
I would propose that there is no One Right way to handle this situation, however, it is essential that your handling of it is done in a way that will let your daughter see that it is a response of Love.
The Atheist position, is very different from the Formal Agnostic or Skeptical Agnostic Positions.
To the Atheist, the “Fact” that there is no god, and no possibility of a God or god, is a position of belief. That position will reject any but the most incontrovertible evidence to the contrary. “There cannot be a God”.
The Formal Agnositc believes that it is impossible to know for certain either way, and therefore it is illogical to hold a firm belief either way, or to follow any one defined religion.
The informal or Skeptical Agnostic believes that there is no way on earth to know whether or not there is a God, unless good evidence is presented to the contrary, and any such evidence or argument will be treated with a critical analysis and skeptical mind.
These are very different positions, and it may be helpful to use debating style questions to probe where your daughters current mindset actually lies.
From the Time of St. Thomas Aquinas these issues have been defined and developed. In the absence of other evidence, formal or skeptical Agnosticism is a far more rational belief to adhere to than to true Atheism… but an attitude of skeptical agnosticism, or even a hybrid of Skeptical Atheism is a position which leaves far more hope that you or someone else will be able to reach your daughter and share with her the Good News of Jesus Christ.
As a 16 year old she may not be overly receptive to hearing a lot on the topic from you, however it is always possible that you can help steer her towards some other people or person who can help her to reassess these issues.
Remember: Knowledge about God, and Jesus. the raw belief that he exists is not the same thing as Faith. Faith - a Grace of the Holy Spirit, is the direct result of hearing the Good News, in a meaningful way, and very often the result of some form of conversion encounter resulting from that witness.
There are a wide range of evangelical outreach programmes aimed at teenagers which can help them and be a vehicle for that witness and encounter. Groups like Life Teen, Youth 2000, World Youth Day, and many more. Ask around in your parish or wider locality so see what organisations are active in your area.
It is possible that you may be able to persuade your daughter to attend one of their outreach programs.
Other than that all you can do that is sure to help is to Pray for her - every day.
St. Augustine similarly rejected his mothers faith. He did not revert to Christianity until his 30’s, but his mother had prayed for his conversion every day of his life.
Not only did he become one of the “Fathers of the Church”, but his mother was also canonized due to her unwavering Faith and prayers for the conversion of her son.
What you cannot do is force a person to believe or have Faith. - Even God himself does not attempt to do this.