"They will continue to amicably work at their relationship to make this new phase work for the kids," a source tells PEOPLE

Since first announcing their split in June 2015, Jennifer Garner and Ben Affleck have remained close, sharing parenting duties and vacations — the actor even lives in the guest house of their L.A. property.

Now that their divorce is proceeding, the two “will continue to amicably work at their relationship to make this new phase work for the kids,” Violet, 11, Seraphina, 8, and Samuel, 5, a source close to the couple tells PEOPLE in this week’s issue.

So what finally drove them to file? Sources on both sides insist a divorce was always the plan and the decision to file was mutual. “It was just time,” says a source. “There was no catalyst.”

Celebrity Sightings In Los Angeles - April 16, 2017
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But other insiders say strain over Affleck’s problems early this year dashed any hopes of a reconciliation — and led Garner to be finally ready to move on. “It came down to his last-ditch attempt at saving things by going to rehab,” says a source close to the situation. “But it was just too little too late.”

For more behind Affleck and Garner’s decision to divorce, pick up this week’s issue of PEOPLE, on newsstands Friday.

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The two filed divorce papers one month after Affleck completed treatment for alcohol addiction. “Jen waited for the right time,” says a Garner source. “She wasn’t going to file for divorce while Ben was struggling. She is very proud of him for getting help.”

However, says the source close to the couple: “As in any marriage, there were numerous reasons why it didn’t work.”

For now, as the two work with divorce attorney Laura Wasser to divide their assets, Affleck will continue to live in the couple’s guest house. “When and if he moves out, it will be when he finds a place suitable for their situation,” says the source close to the couple. “They want to keep the kids close.”