The documents released Tuesday also gave details about the hushed phone calls that triggered the raid, by a 16-year-old girl at the West Texas ranch who said her 50-year-old husband beat and raped her. Days after raiding the compound, officials still aren't sure where the girl is.
Officials have completed removing all 416 children from the ranch and have won custody of all of them, Child Protective Services spokeswoman Marleigh Meisner told reporters in San Angelo, about 40 miles from the compound in Eldorado.
Court documents said a number of teen girls at the 1,700-acre compound were pregnant, and that all the children were removed on the grounds that they were in danger of "emotional, physical, and-or sexual abuse." Another 139 women left on their own.
"Investigators determined that there is a widespread pattern and practice of the (Yearn for Zion) Ranch in which young, minor female residents are conditioned to expect and accept sexual activity with adult men at the ranch upon being spiritually married to them," read the affidavit signed by Lynn McFadden, a Department of Family and Protective Services investigative supervisor.
McFadden said the girls were spiritually married to the men as soon as they reached puberty and were required to produce children.
An unknown number of men and women were being held at the ranch while authorities completed the search of the gleaming 80-foot-high temple, a cheese-making plant, a cement plant, a school, a doctor's office and housing units. Tela Mange, a spokeswoman for the Department of Public Safety, said Tuesday the adults were not being held, but if they left the compound, they could not return while the search continued.
Church lawyer Patrick Peranteau did not immediately return a phone message seeking comment Tuesday.
The compound was raided Thursday after the 16-year-old girl called a local family violence shelter March 29 and 30, using someone else's cell phone and speaking in hushed tones to avoid being overheard, McFadden's affidavit said.
The girl said she was not allowed to leave the compound unless she was ill. She told the shelter that her husband would "beat and hurt" her when he got angry, including hitting her in the chest and choking her while another woman in the house held her baby.
The girl also said her husband sexually assaulted her, and that she was several weeks pregnant. The girl told the shelter her husband went to "the outsiders' world" but didn't know where.
Authorities have issued an arrest warrant for church member Dale Barlow, who is believed to be in Arizona, but the girls' husband is not identified in the court documents released Tuesday.
In the March 30 call, the girl told the shelter she was being held against her will. If she left, church members told her, "outsiders will hurt her, force her to cut her hair, to wear makeup and (modern) clothes and to have sex with lots of men."
At the end of the call, she began to cry.
Meisner said the agency still didn't know whether the 16-year-old was among the children removed from the ranch. Child welfare officials have been interviewing the children in search of the girl and to investigate allegations of abuse.
Investigators said some of the children were unwilling or unable to provide the names of their biological parents or identified multiple mothers.
The boys were groomed to be ready to marry underage girls upon adulthood and engage in sexual activity, "resulting in them becoming sexual perpetrators," the affidavit said.
Children in the sect were deprived of food and forced to sit in closed closets as a form of discipline, the affidavit said.
Former members of the Fundamentalist Church of Jesus Christ of Latter-Day Saints predicted an uneasy adjustment to foster care. They are likely the grandchildren or great-grandchildren of those taken by Arizona authorities 54 years ago in a similar raid.
That raid a half-century ago and the one this week pulled children of polygamist families from the only community and culture they'd ever known - an event that decades later a former community member recalls as traumatizing.
"It was total misery for them," said Ben Bistline, now 72. He was 18 when authorities raided the remote community of Short Creek
now known as the twin towns of Colorado City, Ariz., and Hildale, Utah. Authorities took 200 children into custody as part of an effort to wipe out a "nest of polygamy."
Bistline, who is now a Mormon, was not rounded up in the 1953 raid, but the woman he married later in life was 15 when she and her seven siblings were shipped to Phoenix, pulled from the friends and family who constituted their whole world. Nearly two years passed before they were allowed to return, he said.
Most of the current sect members are descended from families from the Arizona-Utah community.
The 1953 Short Creek raid also changed the community, said Carolyn Jessop, the former wife of the man believed to be running the Eldorado compound.
The distinct pioneer-style dresses, worn over long underwear year-round and sewn by the women, became part of the dress code after the 1953 raid as each generation added more restrictions, said Jessop, who left the community five years ago.
Despite the new hardships for the children and women in Texas, Bistline said the raid is appropriate if children are being forced into marriages.
"This situation in Texas is a justifiable raid," he said.
But an FLDS member now living in the Texas Panhandle, Samuel Fischer, had a different view.
"It's religious persecution," said Fischer, who moved to a ranch near Lockney with his two wives and 12 of his children from Hildale, Utah, last year.
The Texas investigation is the state's first with FLDS, but prosecutors in Utah and Arizona have pursued several church members in recent years, including sect leader Warren Jeffs, who is serving two consecutive sentences of five years to life for being an accomplice to the rape of a 14-year-old wed to her cousin in Utah. He awaits trial on other charges in Arizona.
Authorities investigating the Eldorado compound have described FLDS members as cooperative, but the house-by-house search of the temple, factories and living quarters has triggered some trouble.
On Monday, 41-year-old Leroy Johnson Steed was arrested on charges of felony tampering with evidence - a day after 19-year-old Levi Barlow Jeffs was arrested on misdemeanor charges of interfering with the duties of a public servant, said DPS spokesman Tom Vinger.
Authorities say that Steed was being held in a jail near the compound, CBS News correspondent Hari Sreenivasan reports.
He declined to give details on the arrests or how Levi Barlow Jeffs might be related to the FLDS leader.
Attorneys for the church and church leaders have filed motions asking a judge to quash the search on constitutional grounds, saying state authorities didn't have enough evidence and that the warrants were too broad. A hearing on their motion was scheduled for Wednesday in San Angelo.