Judge Gaughan said he will instruct the jury to stop deliberating for the day and sequester them for the evening. He noted the jurors have been at court since 7 a.m.
Attorneys and Van Dyke were called back into the courtroom just after 5 p.m. because the jurors had a question. Van Dyke is required to appear per his bond conditions. When he was not there immediately, the judge asked him to explain.
Van Dyke said his daughter allegedly received a threat and he had to move her. He apologized for not informing the court about the threat.
LIVE BLOG: Jason Van Dyke trial on Laquan McDonald murder charges
The judge said he wants independent corroboration of the threat and will revoke Van Dyke's bail if he doesn't get it. He reminded Van Dyke about his strict bail conditions.
The jury requested to see the transcript of Van Dyke's partner's testimony and two jurors requested a cigarette break. The judge then said he'd instruct them to stop deliberations for the day and sequester them overnight. While sequestered, the jury will not be allowed to see or read any media reports, and will be kept in a private location away from their homes and workplaces.
"I don't want to speculate why the jury wants that transcript, but clearly Officer Walsh's testimony is important to both sides," said ABC7 Legal Analyst Bob Milan.
Alternate jurors 255 and 256 were released and spoke with ABC7 Eyewitness News afterwards. Both of them said they were leaning toward a guilty verdict.
"I would say guilty," one alternate said when asked which way they were leaning. "He should have waited longer. I mean, he knew the Taser was coming. That's what did it for me."
"I would have leaned toward a guilty verdict," the other alternate said. "I think the fact that other officers had encountered him, Laquan McDonald, that night, and they didn't feel the need to use deadly force.
In closing arguments presented Thursday morning, the state revealed for the first time that the jury can consider the lesser charge of second-degree murder.
Prosecutor Jody Gleason told the jury, Laquan McDonald's body was riddled with 16 bullets, pulling out an anatomy drawing of all of his wounds and then showing the graphic autopsy photos.
WATCH: Prosecution makes closing arguments, rebuttal closing arguments
Gleason said Van Dyke made up his story to justify the shooting and exaggerated the threat McDonald posed to officers, pointing to the dash camera video showing the 17-year-old appearing to walk away from officers as shots were fired.
Milan, who is also a former prosecutor, said the prosecution honed in on several key aspects of their case during both closing and rebuttal; first that Van Dyke displayed indifference to human life in his actions, and that his contention he feared for his life is contradicted by statements he made inside his squad car wondering why no one had already shot McDonald, and saying they would have to shoot him.
Milan said a key part of the prosecution's case is that Van Dyke's fellow officers at the scene saw and heard the same things as Van Dyke, but none of them opened fire on McDonald.
The defense argued that this case is a tragedy, but not a murder. Defense attorneys reiterated once that McDonald was ordered more than 30 times to drop the knife and had he, he likely would have survived the encounter.
"It would have been prevented with one simple step. At any point if he would have dropped that knife, he would have been here today," said lead defense attorney Dan Herbert.
WATCH: Defense makes closing arguments
The defense continued to maintain that McDonald was ultimately responsible for his own death and that Officer Van Dyke reasonably feared for his life.
Dan Herbert talked about the perspective of Officer Van Dyke, not captured on video and he talked about the threat level McDonald posed as he punctured a police tire and ignored commands to drop the knife. He disputed the state's assertion that McDonald was walking away from Van Dyke.
TIMELINE: Laquan McDonald Shooting, Jason Van Dyke Case
Following closing arguments, the judge presented the jury with their instructions. They began deliberations at about 1 p.m.
Van Dyke is charged with first degree murder, official misconduct and aggravated battery. He was among the officers to respond to 41st and Pulaski on Oct. 20, 2014, after residents called 911 saying 17-year-old Laquan McDonald was breaking into cars and walking around with a knife. Van Dyke shot McDonald 16 times.
In his initial reports from CPD, Van Dyke said McDonald lunged at him with a knife. After a year of FOIA request and court battles, the city released dashcam video from that night that contradicted that narrative. In the video, McDonald is seen walking away from officers. He had a pocket knife.
Video of the shooting was made public on Nov. 24, 2015. Van Dyke was charged by then-Cook County State's Attorney Anita Alvarez the same day.
The video released sparked weeks of protests, including massive demonstrations in downtown Chicago on Black Friday.
ACTIVISTS, CITY PREPARE FOR OUTCOME OF VAN DYKE TRIAL
Activists are preparing for the outcome of the case. Outside the courthouse Thursday morning, protesters took a knee for 16 minutes - one minute for each shot Van Dyke fired.
Community activists are calling for mass protests for anything less than a murder conviction.
Thursday night on the South Side, two meetings were called to prepare for the verdict.
"As a city, we just can't take any more of this," said Jared Steverson.
Police have deployed 4,000 additional officers across the city in anticipation of the verdict. The department has officers working 12-hour shifts and cancelled days off.
"We don't care how many officers are being deployed on the streets. We don't care about any of that. We are going to do what we have to do to make sure we get justice for Laquan McDonald," said William Calloway, community activist, at a South Shore meeting.
At a meeting in South Shore near where Harith Augustus was fatally shot by police earlier this summer, community activists including Calloway, Jedidiah Brown, Aleta Clark and Demeterius Nash, called for mass protests and demonstrations if Van Dyke is acquitted.
"Justice is nothing less than a murder conviction," Brown said.
If the verdict is not guilty or if there is a hung jury, the activists are asking Chicagoans to take their frustrations to City Hall instead of taking them out on the neighborhoods.
"As a leader I am not asking to tear, that we tear down our communities. But Chicago and all across America needs to know that this is not acceptable," said Clark.
"At the end of the day, Chicago will hear our voices, they will hear our pain," Steverson said.
Community leaders have continuously called for peaceful protests, but they said if necessary some of them are prepared to be arrested and jailed.
Father Michael Pfleger called for an economic boycott and peaceful protests.
"Nobody go to work. Nobody go to school. Nobody go shopping. Have an economic boycott that day in Chicago," Fr. Pfleger said.
State Senator Elgie Sims, Jr., (D-Chicago) said he echoed the McDonald family's request for peace in the wake of the verdict.
"Tensions are high as we await this much anticipated verdict, but I echo Mr. McDonald's family in asking for peace and constructive responses no matter what the verdict is," he said in a statement.
The Illinois Legislative Black Caucus also called for peaceful protest, and said the verdict should bring a moment of solidarity to the city.
"As we await a decision from the jury, I would like to make it clear how important this trial is to our communities throughout the state of Illinois. The last time a Chicago officer was convicted of murder was nearly 50 years ago, and there are many who feel justice has not been served time and time again in Chicago and across the country," said State Senator Kimberly Lightford, caucus chair, in a statement.
"I urge the public to react with solidarity regardless of the verdict. We need to come together and let our voices be heard for all of the times Black people missed out on their due justice. If you want to yell, yell. If you want to gather, gather. Let's show how we feel in a peaceful and impactful manner," the statement continued.
Chicago police said they have a 150 page contingency plan to handle reaction to the verdict regardless of the outcome.
SCHOOLS PREPARE FOR VERDICT AFTERMATH WITH EYE TOWARDS LEARNING AND SAFETY
Public and private schools in the city are preparing their students for the aftermath.
"We talked to our security staff and have increased security. We have met with the commander of the 8th District to find out what resources are available and what we need to do on our end," said Fr. Paul Galetto, head of St. Rita of Cascia High School.
DePaul College Prep sent a letter home to parents, safety their top priority.
"If the city does move into a period of unrest, that they would have a plan of where they would be and where they would be the safest," said Dr. Megan Stanton-Anderson, principal.
But Stanton-Anderson said safety is just one aspect. The school chose to discuss the case and its implications to the city in special student sessions, as well as woven into Tim O'Reilly's U.S. history class.
"When you get these divisive issues that occur like this case, I think it is really important for kids to be well-informed about the case instead of having emotions and prejudice driving the conversation," O'Reilly said.
Students hope understanding each other's views will help bring peace to the city.
"Whether he gets off or not, use it as a teachable moment," said sophomore Aaron Holton.
"I hope resolutions can be made in a peaceful manner so that these sort of things never happen again," said junior Jack Mueller.
"The school doing this has given the voice we need to speak our mind, sit across from other classmates and say, 'I feel your hurt, let's try to work together," said senior Ricky Rivera, Jr.
Chicago Public Schools is also preparing. South Loop Elementary School told parents it plans to go into lockdown mode if there are protests. CPS has sent out a series of guidelines for the schools. They include support for student-led walkouts and protests.
CPS said students will not be disciplined for the first 30 minutes of a walkout.