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St. George • In a rare move for the sect, the man running the day-to-day operations of the Fundamentalist Church of Jesus Christ of Latter-Day Saints has agreed to let his estranged wife have some custody over their two teenage children.

The agreement between Lyle and Charlene Wall Jeffs was approved by a judge at a hearing Wednesday. It gives the parents joint custody, but specifies that the children will live with their mother.

The children, a 17-year-old boy and a 14-year-old girl, will visit Lyle Jeffs every other weekend and for a stretch during the summer, according to the agreement, a copy of which was obtained by The Salt Lake Tribune.

While Lyle Jeffs agreed to most of the terms, he apparently didn't like all of them. Below his signature, there is a handwritten note saying: "RESPONDENT SIGNS UNDER PROTEST OF MOTHER BEING CUSTODIAL PARENT."

Lyle Jeffs is the brother of imprisoned FLDS President Warren Jeffs. His former followers say Lyle Jeffs, 55, runs the church in his brother's absence.

The FLDS, under the Jeffses leadership, have taught that non-believers and people who break with the church are unrighteous and should not be associated with. Parents who leave the church often have to go through lengthy court battles against spouses — legal or spiritual — just to visit their children.

Ron Rohbock, a former follower of the Jeffses, has six juvenile daughters he hasn't seen in years. He worries about them, and hopes that today's agreement signals the start of the FLDS reuniting children and parents. "This is a great beginning, but it's just a beginning," he said.

This is thought to be the first such custody case involving Lyle Jeffs' children. He seldom appears in public, and a custody battle would have focused on both his conduct and that of the FLDS.

The agreement and order signed Wednesday by 5th District Juvenile Court Judge Michael Leavitt also specifies:

• Lyle Jeffs must provide $1,000 a month in child support. It declines to $600 when the boy turns 18.

• Lyle Jeffs is responsible for paying for the children's health care and education.

• He must provide a vehicle and expenses for the boy to drive him and his sister back and forth between the parents' homes.

• Lyle Jeffs must pay his wife two-thirds of her housing costs, not to exceed $2,000 a month.

If the children misbehave and conventional parenting doesn't solve the problem, the order says, their next visit with their father can be canceled. Lyle Jeffs then will have to pay the cost of professional intervention for the children.

Neither Lyle Jeffs nor his attorney were present for a custody hearing Wednesday in St. George. An attorney representing him in another matter did not return messages seeking comment last week. Charlene Jeffs and her attorneys declined comment Wednesday.

Charlene Jeffs filed a petition April 10 asking the teens be removed from the compound in Hildale that is the home of Lyle Jeffs.

In her petition, Charlene Jeffs described what she deemed two "illegal practices," including one adopted in recent years referred to as the "seed bearer" doctrine in which men no longer are allowed to have children with their wives. Instead, a group of men have been chosen as seed bearers.

"It is the husband's responsibility to hold the hands of their wives while the seed bearer 'spreads his seed,'" Charlene Jeffs wrote. "In layman terms, the husband is required to sit in the room while the chosen seed bearer, or a couple of them, rape his wife or wives."

Charlene Jeffs, 58, also described the "Law of Sarah," in which FLDS women perform sex acts on one another to prepare for an encounter with a man in the FLDS leadership, referred to as the Priesthood. In her petition, Charlene Jeffs worried her daughter will be made to participate in the practice.

Charlene Jeffs said she has been "excluded" from the teens' lives for about three years and was ordered to leave her husband's compound Sept. 27, 2014, for being "unrighteous." She has not been allowed to see the teens since then.

Lyle and Charlene Jeffs have been married since August 1983 and have 10 children together, the petition says. The two teenagers discussed in court documents appear to be the youngest.

Charlene Jeffs has filed for divorce in a separate proceeding in state court in Tooele.

Other members of Lyle Jeffs' family who have left the FLDS have said Charlene Jeffs was the first of nine wives. One of the spiritual wives is Pauline Barlow, was named as a respondent in the custody petition. She is not mentioned in the order and agreement finalized Wednesday.

Leavitt closed Wednesday morning's hearing to the public and reporters. In explaining why he was closing the courtroom, Leavitt cited the agreement and said disclosing it could be detrimental to the children — a qualification for closing a juvenile court hearing in Utah. A Tribune reporter objected, but Leavitt sided with the guardian ad litem and Charlene Jeffs' attorney, who wanted the hearing closed.

Curtis Cooke, a town marshal from Hildale and adjacent Colorado City, Ariz., also was ordered to leave the courtroom because he was not a party in the case.

Warren Jeffs, 59, is serving a sentence of life plus 20 years in Texas for 2011 convictions related to taking two girls as child brides. He is still considered the president and prophet of the church and communicates orders through his family.

Twitter: @natecarlisle