And now, the company will be fined for installing the logo on the roof without a permit.
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On Friday, a notice of violation was issued to the property owner of the X headquarters at 1355 Market, according to the Department of Building Inspection in San Francisco.
The DBI says fees will be for removal of the structure, building permits and to cover the costs of DBI and planning department's investigation.
Patrick Hannan, communications director with the DBI, said a building permit is required to remove the structure but, due to safety concerns, the permit can be secured after the structure is taken down.
Hannan said they received 24 complaints about the 'X' logo structure over the weekend including concerns about its safety and illumination.
VIDEO: SKY7 shows 'X' sign taken down from Twitter HQ in SF
SKY7 shows 'X' sign taken down from Twitter HQ in SF
ABC7 went to the building Monday morning and the sign was no longer up. Crews also worked on the vertical sign along the side of the building.
The sign was installed Friday, and lasted three days. The City of San Francisco said that they were opening an investigation and complaint into permit requirements for the sign.
VIDEO: Bright 'X' sign at Twitter HQ shines into apartments, angers residents
Bright 'X' sign at Twitter HQ shines into apartments, angers residents
Residents in the area were not pleased, as the sign pulsated light, illuminating the surrounding buildings.
"I see nothing now. Looks like they're dismantling the 'X'," said Kim Walton on Monday. She works two blocks away at Market Street and Van Ness. Walton said she's relieved the X has come down. Walton was peeved when she saw what CEO Elon Musk was doing.
"Does he have permits to do these things. What kind of permission does he have to do these things," asked Walton.
"I heard the "X" was coming down. I had to see it for myself," said Franky Francisco.
Francisco said he's been following the developments surrounding Twitter/X closely.
"I like the attention it got San Francisco. I like the conversation it started. But more importantly, I'm happy for these residents. I saw those night videos and they were pretty extreme," said Francisco.
While some people were fascinated and others were frustrated by the gigantic X, Supervisor Matt Dorsey issued this statement on Monday.
"I would like to extend an olive branch to X, as I think there's a lot of people in city government who would welcome the opportunity to work with a large employer such as them."
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Friday night the company unveiled their new X logo on top of the building by turning the lights of that X on. In the process, those lights beamed right into nearby apartments angering some living near Twitter, or X headquarters.
Videos posted to social media show the pulsating X light which has become the talk of San Francisco's Mid-Market neighborhood.
"It is pretty annoying from my perspective," said Jessica Xu who lives across the street.
The X, which sits atop Twitter headquarters, signifies Twitters rebrand and name change to X. The light was said to be off Saturday night, but was on Friday night and some residents from the buildings across the street were not so happy about it.
VIDEO: 'X' logo installed atop Twitter building, spurring San Francisco to investigate permit violation
'X' logo installed atop Twitter building, spurring San Francisco to investigate permit violation
"I think it's way too bright! It was flashing directly into my apartment and just lit up my entire place," said Xu.
"Too bright yeah. I would say too bright," said Viet Huynh who lives across the street.
"From below, we were walking our dog and saw it and were like, oh wow what a spectacle and then we get upstairs and we see like the ramifications of it and it is so bright and ridiculous," said Jennifer Freeman.
Twitter, or X's Elon Musk posted video showing the X all lit up.
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City officials say they've opened an investigation into the sign saying, "A building permit is required to make sure the sign is structurally sound and installed safely. Planning review and approval is also necessary for the installation of this sign. The City is opening a complaint and initiating an investigation."
MORE: 'The everything app': What Musk's rebranding of Twitter to X could mean for future of his companies
Sunday, the Twitter letters were completely removed from the sign, leaving just the X.
Tech analyst Rob Enderle of the Enderle Group says the change doesn't do any good for the social media platform.
"This is probably one of the worst times to do a brand change, a name change because they were having trouble retaining customers, and whenever you change the identity of a company you're going to lose a certain amount of customers as a result of the name change," said Enderle.
But Musk and X have their strong supporters even with this bright light.
"He's playing chess with City Hall. I love what he's doing. I think it's great, like I said he's a showman, he's going to turn the light down at night, it's going to be very subtle but everybody is talking San Francisco now. I love that!" said Dee Dee Damn.
MORE: Elon Musk says Twitter has 'negative cash flow' and 'heavy debt'
And while some say yes the light was bright Friday, they just dealt with it.
"I got curtains, I got blackout curtains," said CJ Randolph.
For those that don't have the blackout curtains -
"We were in the living room and we could see it flashing from the bedroom and I was like, what is that and I was like, oh no it's that big X we saw outside," said Freeman.
Yes, the gig X, the one that everyone seemed to be taking pictures of on Sunday, wondered what will come next.
Elon musk paid $44 billion to take over the company formerly known as Twitter. And he has quickly made some dramatic changes to one of the most influential platforms in the world.
Tech analyst Ian Sherr has followed developments concerning Twitter/X and Elon Musk since the beginning.
"It's very clear that he sees value in sticking around. The question will be is City of San Francisco willing to put up with huge bright lights, massive movement, and permit stuff. Typically, cities like people to follow the rules. And Elon is not a rule follower," said Sherr.