(CNN) One morning in 1998, US District Court Judge Walter Smith called a deputy clerk into his chambers in the Waco, Texas, courthouse and closed the door behind her.

"He basically came over to me and put his arms around me and kissed me, and I just froze. I couldn't move," the woman said in a deposition. "And he said, 'Let me make love to you.' And I just freaked out. ... And then he pulled me to him again, and he kissed me again and stuck his tongue down my throat, and he pressed himself against me. ... And then he started to try touch my breasts, and I kind of pushed away and said ... 'I need to go.'"

The next day, Smith sent her a dozen yellow roses.

In recent months, powerful men in Hollywood, the media, Congress and other spheres have been accused of sexual harassment. A common theme has been men abusing their positions in settings where women feel they have no recourse.

The abuse women have suffered in the nation's courthouses has been a largely untold story. And its system for complaints -- where judges police fellow judges -- is a world so closely controlled and cloaked in secrecy that it defies public scrutiny.

Rarely do sexual misconduct allegations against federal judges become public, even belatedly, as in the Waco episode or as they did in late 2017, with myriad complaints against California-based US Appeals Court Judge Alex Kozinski that drew national attention in the current #MeToo moment, forcing his resignation

The federal judiciary occupies a distinct place in American life that makes what happens there potentially more striking than in other spheres. The nearly 900 federal judges who sit on trial and appellate courts are appointed for life. They have the authority to interpret the law on sex-based offenses. Their attitudes about harassment could reverberate in legal disputes that arise in other realms.

But the judiciary itself is hiding the depth of the problem of misconduct by judges.

CNN compiled and reviewed nearly 5,000 judicial orders related to misconduct complaints and available online over the past 10 years. The documents, covering an array of misbehavior beyond sexual misconduct, are remarkably short on details.

The CNN analysis found that:

Very few cases against judges are deeply investigated, and very few judges are disciplined in any way. In many years, not a single judge is sanctioned.

None of the actual complaints (more than 1,000 are filed annually) are made public. In the public judicial orders, claims are sparingly summarized, and accused judges' names rarely appear. Some orders refer to "corrective action" by a judge without saying what happened.

Judicial orders are dumped onto circuit court websites as a series of numbered files with no indication of the allegations, person complaining or outcome. The practice makes it even more difficult to identify the most serious misconduct cases hidden among the opaque lists of documents because each order must be opened and individually read to gain even minimal information about the nature of the complaint.

In the 12-month period that ended September 30, 2016, there were 1,303 complaints filed. Of those, only four were referred to a special committee for the most serious level of investigation, according to the Administrative Office of the US Courts. In 2015, of the 1,214 complaints, four went to a special committee.

Going back to 2006, fewer than 10 cases annually were deeply investigated and even fewer resulted in disciplinary action. In six of the past 11 years, not a single judge was reprimanded, suspended or otherwise sanctioned for misconduct.

In some cases, judges simply retire -- and receive their full pension.

And then he pulled me to him again, and he kissed me again and stuck his tongue down my throat, and he pressed himself against me. Woman in deposition describing assault by Judge Walter Smith

After Smith cornered the clerk in Waco, she told supervisors and word eventually made it to a regional boss who was, in the woman's telling, upset about the incident and wanted to stop her from outright quitting. That supervisor reached out to District Court Chief Judge Harry Lee Hudspeth. According to the woman, Hudspeth called her and said, "What do you want me to do about it? What exactly do you want me to do about this?"

Hudspeth told CNN he did not believe his reaction had been so "harsh" but would have told the woman he had no responsibility in the matter. Smith declined to comment. The woman left her job soon after the incident.

US District Judge Walter Smith outside the federal courthouse in 1994 in San Antonio.

Sixteen years later, the case resurfaced when a lawyer who clashed with Smith in a separate matter unrelated to sexual misconduct was tipped off by a court employee about the 1998 episode. After he filed a complaint against Smith, a judicial council investigated the woman's story. It verified the harassment, ordered "sensitivity training" and temporarily blocked new cases from being assigned to Smith. The lawyer was not satisfied with either the scope of the investigation or the penalty, so he appealed and a second investigation was launched. Smith retired before it finished and eluded further discipline.

Overall, the data compiled by CNN and separately collected from court officials could suggest that if people have valid complaints about judges, they are not using the system or not getting through it.

"It's very difficult for someone from outside to know what's happening, and it's not always easy for insiders to know what was happening," US Court of Appeals Judge Theodore McKee of the Philadelphia-based 3rd Circuit told CNN. "The public does have an interest in knowing when there are complaints that are meritorious."

"Events in recent months have illuminated the depth of the problem of sexual harassment in the workplace," Roberts wrote , "and events in the past few weeks have made clear that the judicial branch is not immune."

The head of the Judicial Conference's Committee on Judicial Conduct and Disability, US Appeals Court Judge Anthony Scirica, declined repeated requests for an interview. James Duff, director of the Administrative Office of the US Courts, also declined.

CNN sent a written request to Roberts asking if he would address questions about the overall system for resolving complaints and whether he had been aware of problems before the Kozinski matter became public. Roberts declined the request.

'Worshipful silence'

The federal judiciary is an independent branch of government, and judges have long asserted that they can keep their own house in order. Judges have vigorously fought efforts from Congress to install an inspector general to oversee potential judicial wrongdoing, based on the constitutional separation of powers and the view that they can root out wrongdoers on their own.

Courthouses are unique ecosystems that can add to the potential for secrecy and unaddressed misconduct. In their insular world, law clerks and staff may be intimidated by a judge or otherwise worried about harming their careers by speaking out.

"The relationships between law clerks and their judges are mostly built on worshipful silence," Dahlia Lithwick, a former 9th Circuit law clerk, wrote in Slate . "There is no other work relationship left in America that is comparable. Which is, as it happens, part of the problem."

Lithwick was referring to law clerks who generally serve for one year and tend to be among the highly educated elite of a courthouse. But the buildings are filled with far more employees of lower rank, such as the deputy court clerk in Waco, who might be even less willing to speak up about harassment.

A judge can be forcibly removed from office only through impeachment and conviction. But that process, which is controlled by the House and Senate and is the same one used for removing a president, has occurred only three times in the last 30 years , for issues related to bribery and perjury.

"A system that relies for investigation solely upon judges themselves risks a kind of undue 'guild favoritism' through inappropriate sympathy with the judge's point of view or de-emphasis of the misconduct problem," the committee wrote

How CNN crunched the data by Aaron Kessler CNN compiled and reviewed nearly 5,000 discipline orders posted on US appeals court websites, from roughly 2006-2017. There are 13 circuit courts of appeals, and the circuits vary on how many years' worth of orders they post and the accessibility of the documents. Some sites include records back only until September 2015, when federal law required the on-line posting. The documents rarely include the name of the judge who was the subject of the complaint or the specifics of the grievance asserted. The vast majority of the orders issued were only one or two pages and comprised of boilerplate procedural language. Of the 4,823 orders reviewed, more than a third of them -- 1,719 -- were only a single page in length. Another 1,552 were only two pages long. So more than two-thirds of all orders arising from misconduct complaints -- 68% -- clocked in at just two pages or less. Of the rest, 26% were between 3-5 pages, and another 6% between 6-9 pages. Less than 1% of the documents examined from the roughly 10 years (39 total) contained orders that were 10 pages or more in length. If there were patterns to detect, for example in judges who were repeat offenders, the system does not make it easy. Many of the documents are posted as non-searchable, scanned documents -- meaning that they cannot be searched for names, keywords or any content at all that a public citizen may seek to find. To try to assess the complaints and look for patterns, CNN used software designed to recognize the text images and converted the documents to searchable versions for analysis. One indicator of a more serious complaint is referral to a "special committee." These investigative committees can interview witnesses, review documents and take other steps to get to the bottom of the facts of a complaint. Of the nearly 5,000 documents examined, less than 1% noted the appointment of a special committee. Because the nature of the potential offense is rarely spelled out, it is impossible for the public to know if allegations of sexual misconduct occur with any frequency. After former law clerks publicly asserted that US Appeals Court Judge Alex Kozinski had sexually harassed them, CNN searched the orders for any references to "law clerk" and found that most of those instances involved complaints that a judge had let a law clerk handle his or her duties.

University of Denver law professor Nancy Leong, who teaches constitutional law and has focused on how sex discrimination claims are handled, also cites the insularity as a problem. She said some judges might balk at taking action against a colleague knowing that they would be hearing cases together in the future. "It's all a little bit too close-knit," she said.

"The judiciary is most responsive, and perhaps only responsive, when there's some kind of media attention," Leong said.

Administrative officials of the US judiciary minimize the importance of a publicly accessible, easily deciphered disciplinary system. They say the complaints are overwhelmingly frivolous, the product of litigants unhappy with a case decision rather than an individual judge's behavior.

Judiciary officials who spoke to CNN only on condition of anonymity say that when a real offense arises, the confidential process encourages judges to resign quietly, or perhaps seek alcoholism treatment or counseling, rather than to escalate the situation.

The Breyer committee found that complaints were not handled properly "about 2% to 3%" of the time. But for the 17 cases the committee deemed "high visibility," those receiving public attention, it found that close to 30% were mishandled -- a rate, the committee said, that is "far too high." The main problem detected, in high-visibility and other complaints, was chief judges' failure to conduct "adequate" inquires before dismissing a complaint or to submit "clear factual discrepancies" to investigators to pursue.

That two-year study was requested in 2004 by then-Chief Justice William Rehnquist, who was trying to head off congressional intervention in judicial discipline.

Now, more than a decade later, Roberts has established a working group to examine the judiciary's procedures for protecting court employees from misconduct. It is supposed to report back to the chief justice in May.

Breyer declined a request for an interview about the state of the disciplinary system since the 2006 report.

Sen. Mazie Hirono, concerned about the potential for sexual abuse among judges, has begun asking judicial nominees, who are subject to the Senate confirmation process, whether they ever made unwanted requests for sexual favors or committed verbal or physical harassment. The Hawaii Democrat is also asking whether they faced discipline or entered into a settlement related to such conduct.

"I was really afraid that this would be swept under the rug," Hirono told CNN, referring to sexual harassment concerns. "It shows that we are serious about asking these questions, particularly for nominees for lifetime appointments."

What's public -- and what's not

The complaint process dates to the Judicial Conduct and Disability Act of 1980. "A central purpose of the 1980 Act is to provide transparency," Judge Scirica, chairman of the Judicial Conference's conduct committee, wrote in a 2015 law review article, "so every order resolving a complaint must be made public, and reprimands may be made public as well."

But making information public and making it meaningful are not the same.

Many of the documents are provided to the public as non-searchable, scanned documents -- meaning that they cannot be searched for names, keywords or any content at all that a public citizen may seek to find. It is difficult to detect patterns among judges in various circuits or how they compare to other circuits.

It's very difficult for someone from outside to know what's happening, and it's not always easy for insiders to know what was happening. US Court of Appeals Judge Theodore McKee

CNN used software designed to recognize the text images and converted the documents to searchable versions for analysis.

It is exceedingly rare that judicial officials discipline a judge who was the subject of a complaint, according to the CNN review. Many of the instances that involved reported sexual misconduct had come to light from earlier media reports or another outside party.

The federal judiciary's general statistics that are made public reinforce that view of scant remedial action. In its public reports going back to 2006, in fact, no censures, reprimands, suspensions or other "remedial action" occurred in most years (2015, 2014, 2013, 2012, 2010, 2006). In the rest, there were no more than three instances of suspension, reprimand or other remedial action in any given year.

The judiciary's rules dramatically restrict when the name of the judge can be made public.

University of Pittsburgh law professor Arthur Hellman, who has long studied the third branch, said it is difficult to assess whether the judiciary has a sexual harassment problem. "Not from anything that's public," he said. "How can you know what isn't there?"

What happens to complaints

The process begins when a complaint is filed in one of the 13 federal circuit courts. Circuit chief judges dismiss the overwhelming majority out of hand because they target a court ruling, rather than a judge's conduct.

Of the rest, the most common complaint is personal bias against a litigant or attorney (320 complaints in 2016). Other major categories cover conflicts of interest (144 complaints in 2016) or racial, religious or ethnic bias (128 complaints in 2016), according to figures provided by the courts' administrative office.

The courts do not separate out complaints that relate to a judge's conduct toward an employee. They may be included in a catch-all category for "other misconduct," for which 354 complaints were filed in 2016.

If the facts of a complaint are "reasonably in dispute" after an initial inquiry, the chief judge is required to send the complaint to a special committee to investigate. That action is rarely taken. Of the nearly 5,000 complaints filed between the 2006 and 2016 fiscal years, 33 went to a special committee, CNN found.

In those situations when a complaint was investigated deeply, a party may appeal to the Judicial Conference Conduct Committee. Since 1993, that committee has issued reports in only 15 cases

CNN found that in several high-profile cases, judges simply resigned while a complaint was pending. The judiciary's published statistics do not specifically tally such situations, although they do note when a complaint was ended because of an "intervening event," which could cover a resignation. "Intervening events" occurred 16 times in 2016.

In glare of media spotlight

Much of the known judicial action related to sexual misconduct was taken because of forces outside the established system, such as media coverage or complainants using other law enforcement channels.

In Denver, the 10th Circuit judicial council followed local media when it began looking into alleged misconduct involving prostitutes by District Court Judge Edward Nottingham. According to the judicial council's October 2008 order, the council was following up on numerous allegations, including whether Nottingham "spent more than $3,000 at a topless nightclub in one evening [and] that he could not remember how he had spent that money because he had a lot to drink."

As an investigation was underway, another misconduct complaint came in from a woman who said she had been a prostitute and that Nottingham had been one of her clients.

Events in recent months have illuminated the depth of the problem of sexual harassment in the workplace, and events in the past few weeks have made clear that the judicial branch is not immune. Chief Justice John Roberts, December 31

The woman, according to the judicial council report , further alleged that "Nottingham asked her to lie to federal investigators about the nature of their relationship and not disclose that she was a prostitute whom he paid in exchange for sex."

As the investigation was being completed, Nottingham resigned. The 10th Circuit judicial council, which repeated the salacious allegations in its report, dismissed the complaint the next day but said his resignation was "in the interest of justice and the judiciary."

Nottingham did not respond to multiple CNN requests to his law office for comment.

Kozinski was twice brought into the spotlight by the press. The Los Angeles Times in 2008 reported that as he was presiding over an obscenity trial in Los Angeles, Kozinski was maintaining "a publicly accessible website featuring sexually explicit photos and videos."

After he publicly apologized and took the server offline, a judicial council admonished Kozinski but concluded that he deserved no further discipline. According to the judges' June 2009 report in the matter, Kozinski "testified that he does not visit and has no interest in pornographic websites" and that he "certainly did not send" sexually explicit files to anyone.

9th US Circuit Appeals Court Judge Alex Kozinski looks on during a House Judiciary Committee hearing on March 16, 2017, in Washington.

Despite what some former clerks declared was an "open secret" of continuing misbehavior by Kozinski, it was not until a Washington Post story in December 2017 that a new investigation of the Pasadena-based judge was triggered. That story highlighted an account from a woman who said Kozinski asked her to look at pornographic images on his office computer. Several other women subsequently came forward with allegations about misconduct.

Kozinski resigned shortly thereafter, saying that he "may not have been mindful enough of the special challenges and pressures that women face in the workplace."

Nottingham, Kozinski or any other life-tenured judge who resigns in the middle of a complaint and is of retirement age is entitled to full pension of roughly $200,000 annually (the amount differs for district court and appeals court judges based on their annual salary).

Leave the bench, and all investigations stop

Disciplinary proceedings are typically halted once the subject of a complaint leaves the bench. That means that the source of potential bad behavior would no longer be hearing cases or overseeing employees. But it also means that the extent of any misconduct -- and whether other people may have been involved -- goes uncovered by the judiciary. Prosecutors may follow up, or civil lawsuits against a judge could be filed. Conversely, without any further action, nothing would prevent the subject of a complaint from moving on to another job in the law.

Even when cases are resolved, judges are not always willing to release reports of what they found.

In 2013, the judicial council of the 9th Circuit -- headed by then-Chief Judge Kozinski -- pursued the case of Montana US District Court Judge Richard Cebull, who had forwarded a racist joke about President Barack Obama to six acquaintances, according to a story in the Great Falls Tribune and, later, according to US judicial authorities.

Chief Judge Richard Cebull makes a speech at the federal courthouse in Billings, Montana, on June 23, 2011.

The Cebull email said in part, "A little boy said to his mother, Mommy, how come I'm black and you're white? His mother replied, 'Don't even go there Barack! From what I can remember about that party, you're lucky you don't bark!'"

The judicial panel found that the email and numerous others discovered constituted misconduct. A later judicial order characterized some emails as concerning "women and/or sexual topics and were disparaging of women." Some jokes related to sexual orientation and religion.

As it finished its report, the 9th Circuit council said no new cases should be assigned to Cebull for six months and that he should be trained on judicial ethics and racial awareness. Amid a public uproar that followed the initial reports of the racist email, Cebull sent Obama a letter of apology. He resigned soon after the judicial council had resolved his case but before its report had been made public.

Once Cebull resigned, in 2013, the council said disciplinary procedures no longer applied and declined to issue its full report.

US Court of Appeals Judge McKee of the 3rd Circuit petitioned the Judicial Conference's Conduct Committee, arguing that the 9th Circuit was concealing the extent of Cebull's misbehavior and that the full report should be made public. The committee agreed, and the report is now online

When outsiders accelerate the process

It has, at times, also taken external legal pressure to fight an outcome seen as too lenient or to jump-start a dormant case.

Perhaps one of the most serious examples came in Galveston, Texas, after Judge Samuel Kent repeatedly attacked a woman in his chambers, including trying to force her to perform oral sex. When the woman filed a formal complaint in 2007 after years of abuse, a 5th Circuit judicial council reprimanded Kent, suspended his cases for four months and transferred him to a courthouse in Houston. The council's 2007 public order did not reveal the findings by the special investigative committee.

After that woman and another female courthouse employee told federal law enforcement authorities of Kent's sexual attacks, Kent in 2008 was charged with sexual abuse counts and obstruction of justice.

Just before the scheduled trial, Kent pleaded guilty to obstruction of justice and received three years in prison.

A system that relies for investigation solely upon judges themselves risks a kind of undue 'guild favoritism' through inappropriate sympathy with the judge's point of view or de-emphasis of the misconduct problem Breyer Committee report, 2006

And how did the case against Judge Smith in Waco begin and end?

The disciplinary complaint started with a disgruntled Texas lawyer.

More than a decade after the deputy court clerk told supervisors about the encounter with Smith, lawyer Ty Clevenger tried to bring it to light after being fined $25,000 by Smith in a separate case.

Clevenger, who said he heard from a courthouse employee about the 1998 incident in Smith's chambers, acknowledged to CNN his grievances with Smith and other judges against whom he has lodged complaints.

"I'm not going to claim that I'm unbiased," Clevenger said, adding that many lawyers would not dare challenge a judge for fear of some retaliation. "I had nothing to lose," he said.

After receiving Clevenger's complaint in 2014, which included a deposition from the woman involved, a 5th Circuit judicial council confirmed the harassment.

"Judge Smith made inappropriate and unwanted physical and non-physical sexual advances toward a court employee," the council wrote in December 2015, adding that, "Judge Smith does not understand the gravity of such inappropriate behavior."

Smith had tried to get the complaint dismissed, saying the claim was too old to be fully investigated, and questioned Clevenger's motives in bringing it. Rejecting Smith's defenses, the judicial council suspended him from hearing cases for one year and ordered him to attend "sensitivity training about appropriate professional interaction." Clevenger said he thought Smith deserved stronger punishment and appealed to the Judicial Conference conduct committee.

That top committee ordered the case reopened, noting that there were names of people who had allegedly witnessed Smith sexually harassing other women.

The second investigation was never fully concluded when Smith retired in September 2016, at age 75. Through his lawyer, Greg White, he declined a CNN request for comment.

Clevenger had also filed a complaint against Hudspeth , saying he failed to fulfill his responsibilities by not referring the deputy clerk's complaint to authorities. Hudspeth told CNN he believed it was the woman's responsibility to file a formal complaint. Fifth Circuit judicial officials said in 2016 that they were waiting to pursue that complaint against Hudspeth until after the situation with Smith was resolved.

But once Smith resigned, Hudspeth, too, had retired at age 80, so the complaint against him was dismissed.

No further inquiry was made.