The Patriots have been busy inside Gillette Stadium, formulating a response to the Ted Wells report on Deflategate. 
 
 The Patriots escalated their high-stakes counterattack against the NFL and the Wells investigation of Tom Brady’s deflated footballs Thursday by launching a website to publish an exhaustive rebuttal portraying the inquiry’s findings as a Kafkaesque injustice. 
 
 The 20,000-word rebuttal includes a Nobel laureate’s rejection of the Wells Report’s scientific evidence and a stunning claim that team attendant Jim McNally referred to himself as “the deflator’’ because he was losing weight — not because he was removing air pressure from Brady’s footballs. 
 
 The website went up shortly before the NFL players’ union officially appealed Brady’s four-game suspension for allegedly having “at least a general awareness’’ of the scandal and failing to fully cooperate with investigators. 
 
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 “The conclusions of the Wells Report are, at best, incomplete, incorrect, and lack context,’’ stated the rebuttal’s author, Daniel L. Goldberg, a Patriots lawyer. 
 
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 Two days after chief investigator Ted Wells took the unusual step of publicly defending his integrity, the Patriots accused him of ignoring inconsistencies “in logic and evidence’’ and of assigning nefarious motives to texted “attempts at humor and exaggeration.’’ The team contended that he had essentially manipulated the evidence to show that Brady preferred underinflated footballs and that McNally and equipment assistant John Jastremski probably cheated to satisfy Brady’s desires. 
 
 A spokeswoman for Wells said he had no comment on the rebuttal. 
 
 On their new website, wellsreportcontext.com, the Patriots acknowledged no wrongdoing by Brady, McNally, or Jastremski. Nor did they offer an explanation for why they indefinitely suspended McNally and Jastremski last week without pay, except to assert that Jastremski secretly gave McNally Patriots sneakers and gear without permission. 
 
 Goldberg’s rebuttal repeatedly characterized Wells’s interpretation of events and evidence as flawed or offered alternative explanations. One of Goldberg’s most jarring assertions was aimed at countering Wells’s interpretation of McNally describing himself as “the deflator.’’ 
 
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 To Wells, the statement was evidence of possible wrongdoing. To the Patriots, it was innocuous wordplay. 
 
 While Jastremski is thin and works out to bulk up, Goldberg stated, “Mr. McNally is a big fellow and had the opposite goal: to lose weight. ‘Deflate’ was a term they used to refer to losing weight.’’ 
 
 Goldberg cited two texts from McNally to Jastremski to support his conclusion. In one, McNally wrote, “deflate and give somebody that jacket.’’ 
 
 In the other, they were discussing women and a party (the Patriots redacted part of the exchange “out of respect to Mrs. Jastremski.’’). McNally, apparently referring to himself, texted Jastremski in part, “Jimmy needs some kicks . . . lets make a deal . . . come on help the deflator.’’ 
 
 Several minutes later, after receiving no reply, McNally wrote, “Chill buddy im just [messing] with you . . . im not going to espn . . . yet.’’ 
 
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 Wells described the exchange as compelling evidence that McNally was threatening to disclose the alleged football deflation scheme to the media. 
 
 To the contrary, Goldberg wrote, McNally was mocking Jastremski’s concern that his boss would discover he had secretly been giving McNally sneakers and other Patriots property. It was “Mr. McNally’s way of saying, in substance: ‘Hey, don’t worry about whether giving me those sneakers will get you in trouble — I’ll never tell,’ ’’ Goldberg asserted. 
 
 In his voluminous rebuttal, Goldberg stated unequivocally that no evidence has surfaced of Brady saying he prefers his footballs deflated below the league’s minimum pressure standard of 12.5 pounds per square inch. Witness testimony appears to confirm that every time the topic arose, Brady made clear he wanted the footballs inflated to the lowest permissible level. 
 
 Goldberg also provides an alternative explanation for Brady engaging in six phone calls for nearly 55 minutes with Jastremski over three days, beginning at 7:26 the morning after news of the purported scandal broke in the hours after the AFC Championship game. 
 
 Wells depicted the purpose of the calls as damage control. Not so, according to Goldberg, who asserted Brady reached out to Jastremski because he apparently anticipated a “media frenzy’’ about the deflated balls and was concerned for a co-worker who lacked experience dealing with the media. 
 
 “Mr. Brady’s reaching out to Mr. Jastremski to see how he was holding up in these circumstances is not only understandable, but commendable,’’ Goldberg wrote. 
 
 He said the phone calls were “totally consistent with complete innocence.’’ 
 
 Wells, in defending his report to the media Tuesday, described a text exchange between McNally and Jastremski that convinced him “in the bottom of my heart’’ that they were implicating Brady in the alleged deflation conspiracy. 
 
 McNally, unhappy that Brady had complained about his footballs being overinflated in a game against the New York Jets, texted to Jastremski: “Tom sucks . . . im going make that next ball a [expletive] balloon.’’ 
 
 Jastremski replied, “Talked to him last night. He actually brought you up and said you must have a lot of stress trying to get them done.’’ 
 
 Wells described the exchange as direct evidence that “two participants in the scheme’’ were helping Brady. 
 
 Wrong, according to Goldberg, who asserted the “Tom’’ in question was not Brady but a friend of Jastremski’s. He said the conversation involved “McNally’s stress relating to reselling family tickets’’ to Patriots games. 
 
 Goldberg said the Patriots made Jastremski’s friend, Tom, available for a phone interview with Wells’s team. But “the investigators, rather than take further steps to check out this information, simply chose to disbelieve input that did not square with their conclusions,’’ Goldberg wrote. 
 
 He also took issue with Wells’s complaint that the Patriots refused to make McNally available for a final interview with investigators. Wells said the interview was crucial because he had discovered McNally’s “deflator’’ texts after his first conversation with McNally and needed to confront him about them. 
 
 Wells has cited the refusal to make McNally available again as evidence of the Patriots’ failure to cooperate. 
 
 Goldberg countered that Wells received the “deflator’’ texts before his first interview with McNally but overlooked them. When Wells sought the second interview, Goldberg said, the Patriots offered alternatives to an in-person interview to provide the information Wells needed. 
 
 “There was no follow-up from investigators,’’ Goldberg wrote. “It now appears that the Patriots are being severely punished because the Wells investigative team apparently overlooked materials they had in their possession long before their interview with Mr. McNally.’’ 
 
 Goldberg suggested Wells also ignored scientific evidence that atmospheric pressure may have accounted for Brady’s underinflated footballs when the Patriots played the Indianapolis Colts Jan. 18 in the AFC Championship game. 
 
 As part of a detailed analysis that raised questions not only about which gauges the officials used to measure the Patriots footballs but the league’s apparent lax attention to the inflation levels of the Colts’ balls, Goldberg cited the conclusions of Roderick MacKinnon, a 2003 Nobel Prize recipient in chemistry, that Wells’s scientific findings were “incorrect.’’ 
 
 The new Patriots website initially stated MacKinnon offered them his expertise and had no personal relationship with the team. 
 
 Several hours later, after reports of a possible conflict of interest arose, the Patriots updated the site to say they are a passive investor in MacKinnon’s biotechnology company, Flex Pharma. 
 
 The team was fined $1 million and docked two draft picks — a first-rounder in 2016 and fourth-rounder in 2017. 
 
 Bob Hohler can be reached at robert.hohler@globe.com ||||| Tom Brady not only violated his sport’s integrity by participating in a scheme to tamper with the inflation levels of footballs but actively tried to cover up the conspiracy, National Football League commissioner Roger Goodell ruled Tuesday, upholding the Patriot quarterback’s four-game suspension. 
 
 In a stunning statement, Goodell alleged that Brady’s “very troubling’’ coverup effort involved instructing his assistant to destroy his cellphone less than 24 hours before he was interviewed by Ted Wells, the NFL’s special investigator in Deflategate. 
 
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 The scandal rose from the charge that Patriots equipment attendants improperly deflated footballs below the league standard before Brady led the team to a 45-7 victory over the Indianapolis Colts on Jan. 18 in the American Football Conference Championship game. 
 
 Goodell said Brady knew Wells sought evidence from his phone, which contained nearly 10,000 text messages in the previous four months, including the period of the alleged tampering. 
 
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 The case has attracted national attention because of Brady’s stature as a four-time Super Bowl champion and widespread suspicions that the Patriots have improperly cut corners while attaining their championships. 
 
 “Rather than simply failing to cooperate, Mr. Brady made a deliberate effort to ensure that investigators would never have access to information that he had been asked to produce,’’ Goodell wrote in a 20-page decision denying Brady’s appeal of his suspension. 
 
 Brady’s action “leads me to conclude that he was attempting to conceal evidence of his personal involvement in the tampering scheme,’’ Goodell ruled. 
 
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 Brady has denied any wrongdoing, and the NFL Players Association vowed Tuesday to appeal “this outrageous decision’’ in federal court. A judge could delay Brady’s suspension until a court resolves the issue. 
 
 The players union downplayed the significance of Brady’s destroyed phone and asserted that he provided league officials all of the information they sought. 
 
 “The fact that the NFL would resort to basing a suspension on a smoke screen of irrelevant text messages instead of admitting that they have all of the phone records they asked for is a new low, even for them, but it does nothing to correct their errors,’’ the union asserted in a prepared statement. 
 
 Brady’s agent, Don Yee, also attacked the ruling. 
 
 “The commissioner’s decision is deeply disappointing but not surprising because the appeal process was thoroughly lacking in procedural fairness,’’ Yee said. 
 
 Calling the process “a sham,’’ Yee said, “The decision is wrong and has no basis, and it diminishes the integrity of the game.’’ 
 
 The NFL, anticipating Brady’s appeal, immediately went to the US District Court in New York and filed a statement citing the commissioner’s power under the collective bargaining agreement to punish players for conduct detrimental to the sport. 
 
 ‘Notwithstanding my enormous respect for his accomplishments on the field . . . I find that . . . Mr. Brady engaged in conduct detrimental to the integrity of, and public confidence in, the game of professional football.’ Roger Goodell, NFL commissioner 
 
 The Patriots — who previously agreed to pay a $1 million fine and forfeit a first-round pick in the 2016 draft and a fourth-rounder in 2017 because of the scandal — expressed extreme disappointment in Goodell’s ruling Tuesday. 
 
 “We cannot comprehend the league’s position in this matter,’’ the Patriots statement said. “Most would agree that the penalties levied originally were excessive and unprecedented, especially in light of the fact that the league has no hard evidence of wrongdoing.’’ 
 
 The Patriots accused the NFL of “attempting to destroy the reputation of one of its greatest players and representatives.” 
 
 Goodell’s finding that Brady “willfully obstructed’’ the league’s investigation by having his cellphone destroyed raised the stakes in the controversy. When Troy Vincent, the NFL’s chief of football operations, issued Brady’s four-game suspension in May, he couched his findings to say it was “more probable than not’’ that Brady was “at least generally aware’’ that Patriots equipment attendants had improperly deflated his footballs. 
 
 Goodell dropped such qualifiers in accusing Brady of both participating in the tampering and trying to cover it up. 
 
 “Notwithstanding my enormous respect for his accomplishments on the field and for his contributions and role in the community, I find that, with respect to the game balls used in the AFC Championship game and subsequent investigation, Mr. Brady engaged in conduct detrimental to the integrity of, and public confidence in, the game of professional football,’’ Goodell concluded. 
 
 Wells had developed potentially damaging evidence of tampering from the cellphones of Patriots football ball attendants Jim McNally and John Jastremski, and he began asking for Brady’s phone records more than two weeks before he interviewed the quarterback March 6. Wells did so again during the session. 
 
 At no time during that period did Brady disclose that his cellphone had been destroyed, according to Goodell. He said records show Brady stopped using the phone no earlier than March 5 and no later than March 6, the day of the interview. 
 
 What’s more, Brady did not inform the NFL that he had the phone destroyed until June 18 and did not confirm it until his 10-hour appeal hearing June 23 at NFL headquarters in New York, Goodell stated. 
 
 Brady testified during the hearing that he routinely destroys his phones and SIM cards or directs his assistant to do so when he begins using a new one, as he did before the Wells interview. However, Goodell cited evidence that Brady did not destroy the cellphone he stopped using Nov. 6, 2014, before the one in question. 
 
 A forensic expert for the players union, Brad Maryman, submitted testimony at the hearing about Brady’s cellphone use. But Goodell described the analysis as extremely limited and of little value. 
 
 “All we know is that Mr. Brady exchanged nearly 10,000 text messages with many individuals over this period of approximately four months’’ ending March 6 on the phone he destroyed, Goodell stated. That equates to 80 texts per day. 
 
 Yee took issue with Goodell’s characterizations. 
 
 “We presented the commissioner with an unprecedented amount of electronic data, all of which is incontrovertible,’’ Yee said, although he did not specify the nature or content of the data. 
 
 “Tom was completely transparent,’’ Yee said. “All of the electronic information was ignored; we don’t know why. The extent to which Tom opened up his private life to the commissioner will become clear in the coming days.’’ 
 
 If McNally or Jastremski had any information that might clear Brady, Goodell never received it because Brady’s legal team declined the commissioner’s invitation to testify during or after Brady’s hearing. 
 
 The Patriots have indefinitely suspended both employees. 
 
 Goodell suggested it was odd that Brady would not want McNally or Jastremski to testify because “both presumably would have firsthand knowledge of the facts related to Mr. Brady’s denials.’’ 
 
 McNally also has never been interviewed by investigators about why he described himself as “the deflator,’’ among other damaging statements he made in text exchanges with Jastremski. The Patriots produced a rebuttal statement in May in which they asserted McNally’s moniker came from his losing weight. 
 
 Goodell said the evidence from Brady’s hearing included a 450-page transcript, more than 300 exhibits, and more than 30 summaries of interviews conducted by NFL security officials before Wells launched his investigation. 
 
 The union submitted studies, including one by the American Enterprise Institute, aimed at refuting the NFL’s conclusions about the inflation levels of Brady’s footballs in the AFC title game. The NFL said all 11 balls were found to be deflated below the league’s minimum standard of 12.5 pounds per square inch after they were approved by an official before the game. 
 
 Goodell ruled that the deflation could not be attributed to environmental, physical, or other natural factors, as Brady’s legal team and the Patriots have asserted. 
 
 “Instead, at least a substantial part of the decline was the result of tampering,’’ he said. 
 
 How does Tom Brady’s suspension affect the Patriots ||||| In a major blow to Tom Brady’s golden reputation, a National Football League investigator concluded Wednesday that the Patriots quarterback most likely participated, at least tacitly, in violating the sport’s integrity by using improperly deflated footballs as he guided the team toward a Super Bowl championship. 
 
 A 243-page report on the NFL’s inquiry identified two low-level Patriots employees as the alleged chief conspirators in the scandal and cited “substantial and credible evidence’’ that Brady was “at least generally aware of the inappropriate activities,’’ — despite his insistence to the contrary. 
 
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 “We found [Brady’s] claims not plausible and contradicted by other evidence,” the NFL’s report said. 
 
 One of the two Patriots workers, a part-time attendant named Jim McNally, described himself in a text recovered by investigators as “the deflator,’’ the report found. 
 
 Brady and the two men appear to have been caught in a web of evidence that ranged from security video footage of McNally suspiciously ducking into a bathroom with a bag full of footballs moments before delivering them to the field, to Brady and the other worker engaging in apparent damage-control calls and texts as soon as reports broke of the purported cheating. 
 
 Continue reading it below 
 
 No other member of the Patriots organization, including owner Robert Kraft and coach Bill Belichick, was implicated as a result of the 15-week inquiry. But the findings cast a cloud over the franchise’s fourth Super Bowl title of the century in February, just as the 2007 Spygate affair tainted previous triumphs. 
 
 NFL Commissioner Roger Goodell, a close friend of Kraft’s, directed Troy Vincent, the league executive in charge of football operations, to consider disciplinary action, which could include a fine or suspension for Brady. 
 
 Kraft, who earlier professed the franchise’s innocence, lambasted the findings, though he said he will not appeal them and will accept any penalties. 
 
 The inquiry centered on allegations that the Patriots used underinflated footballs in January while defeating the Indianapolis Colts, 45-7, in the American Football Conference championship game to advance to the Super Bowl. Brady has said he prefers balls with lower inflation levels because they are easier to grip and throw. 
 
 “To say we are disappointed in the findings, which do not include any incontrovertible or hard evidence of deliberate deflation of footballs at the AFC Championship Game, would be a gross understatement,’’ Kraft said in a statement. “While I respect the independent process of the investigation, the time, effort and resources expended to reach this conclusion are incomprehensible to me.’’ 
 
 The NFL’s findings are based almost entirely on circumstantial evidence, and while investigators appeared to build a persuasive case that inappropriate activity occurred, Kraft suggested there was no smoking gun linking Brady to cheating. 
 
 Brady — who refused to provide his e-mails, text messages, and phone records to league investigators — has not publicly addressed the controversy, which has come to be known as “Deflategate,” since an uncomfortable news conference in January when he was asked directly, “Are you a cheater?’’ 
 
 “I don’t believe so,’’ he replied. “I mean, I feel I always played within the rules.” 
 
 He also rejected the notion that others had acted on his behalf. “I am very comfortable saying nobody did it, as far as I know,” Brady said then. 
 
 Video: Tom Brady says he did not alter the footballs in Colts game 
 
 But his denials in an interview with the NFL investigators ultimately seemed to fall flat. 
 
 “We found [Brady’s] claims not plausible and contradicted by other evidence,” the report said. 
 
 Brady was not available Wednesday. But his father, Tom Brady Sr., was quoted by USA Today as portraying him as a victim of “Framegate.’’ 
 
 “I don’t have any doubt about my son’s integrity — not one bit,” the elder Brady said. “In this country, you’re innocent until proven guilty. It just seems Tommy is now guilty until proven innocent.’’ 
 
 Brady’s next scheduled public appearance is a speaking engagement Thursday at Salem State College. 
 
 The report alleges that McNally, who served as the locker room attendant at Gillette Stadium for NFL officials, and John Jastremski, a Patriots equipment assistant, probably engaged in “a deliberate effort to release air’’ from the footballs after a referee examined them before the game. 
 
 Attempts to reach Jastremski were not successful. When a Boston Globe reporter seeking a comment knocked at McNally’s home in Amherst, N.H., a man standing behind a curtain said, “Get off my land right now.’’ 
 
 The evidence against Brady included text messages between McNally and Jastremski in the three months before the AFC title game. Some texts allegedly implied Brady requested his footballs be deflated below the league’s minimum standard of 12.5 pounds of pressure per square inch. 
 
 Investigators alleged the texts showed Brady was not pleased with the quality of some game balls the attendants had prepared. In one text, McNally complained to Jastremski, “Tom sucks . . . im going [to] make that next ball a [expletive] balloon.’’ 
 
 Jastremski’s alleged reply: “Talked to him last night. He actually brought you up and said you must have a lot of stress trying to get them done.’’ 
 
 The report includes numerous text references to McNally allegedly wanting Brady to sign memorabilia in exchange for deflating balls. 
 
 “Remember to put a couple sweet pig skins ready for tom to sign,” McNally allegedly texted Jastremski. 
 
 The report states, “Taking the text messages as a whole, Brady is a constant reference point in the discussions between McNally and Jastremski about inflation, deflation, needles, and 18 items to be received by McNally.’’ 
 
 Citing videotape evidence and witness interviews, the report alleges that McNally inappropriately removed the Patriots game balls from the officials locker room before the AFC title game and carried them into a restroom near the entrance to the field. He allegedly locked the door and remained there for about 1 minute and 40 seconds before he delivered the balls to the field. 
 
 A scientific consultant hired by the NFL investigators simulated the time it would take to reduce the pressure in 13 footballs by using a needle, and the time was “well under one minute and forty seconds,’’ according to the findings. 
 
 The report states that Colts general manager Ryan Grigson alerted the NFL before the game to be aware of the Patriots possibly deflating footballs. And after one of Brady’s passes was intercepted in the first half, the Colts tested the ball and told officials it was underinflated. 
 
 That prompted the officials to test 11 of the Patriots footballs at halftime, and each one was found to be inflated below the league minimum, the report states. Four Colts balls were tested and deemed legal. 
 
 Soon after the first news stories about the Patriots’ alleged wrongdoing broke on Jan. 19, Brady and Jastremski engaged in a number of telephone and text communications investigators cite as additional evidence that Brady was aware of the inappropriate activity. 
 
 Brady and Jastremski had not communicated by phone or text for more than six months before then. But at 7:26 a.m. on Jan. 19, the morning after the AFC title game, they spoke by phone for the first of six times over the next three days, their conversations lasting a total of more than 55 minutes. 
 
 The report alleges Brady also invited Jastremski to his office at Gillette Stadium, and investigators said Brady sent Jastremski text messages apparently aimed at calming him. “You good Jonny boy?’’ one text from Brady allegedly read. “Still nervous; so far so good though,’’ Jastremski wrote back, according to the report. 
 
 Brady and Jastremski then allegedly contradicted each other in interviews with investigators. Brady, while denying any knowledge or involvement in wrongdoing, told the investigators he did not know McNally’s name or his game-day duties. 
 
 However, Jastremski told investigators Brady did know McNally’s name and his game-day responsibilities, the report states. In addition, McNally was said to have told NFL security officials that Brady personally told him which inflation level he preferred for his footballs. 
 
 Investigators complained the Patriots refused to make McNally available for a final interview on “important topics,’’ a complaint that Kraft said “offended’’ him. “What the report fails to mention is that he had already been interviewed four times and we felt the fifth request was excessive for a part-time game-day employee who has a full-time job with another employer,’’ Kraft said. 
 
 Regarding the number of times McNally was interviewed, the report states only that the team counsel refused to make McNally available for “a follow-up interview” regarding what investigators deemed “important topics.” 
 
 The investigation, led by Theodore V. Wells Jr., a private attorney commissioned by the NFL, included analysis by scientific consultants who concluded that no other factor such as weather caused the Patriots’ balls to deflate. 
 
 Kraft took exception to the finding that weather played no role. “Based on the explanations I have heard and the studies that have been done, I don’t know how the science of atmospheric conditions can be refuted or how conclusions to the contrary can be drawn without some definitive evidence,’’ he said. 
 
 Investigators interviewed more than 65 witnesses, including Belichick.
– Tom Brady appealed his four-game suspension over under-inflated footballs with about an hour to spare before today's 5pm deadline, reports AP. The NFL Players Association filed the paperwork on his behalf. The Patriots, meanwhile, issued a detailed rebuttal to the league report on the scandal, saying its conclusions are "at best, incomplete, incorrect and lack context." One notable part: Referring to texts between team employees Jim McNally and John Jastremski, the Patriots say there's no proof they were talking about deflating footballs, reports the Boston Globe. Instead, McNally's "deflator" nickname referred to weight loss, says the team: "Mr. Jastremski would sometimes work out and bulk up—he is a slender guy and his goal was to get to 200 pounds. Mr. McNally is a big fellow and had the opposite goal: to lose weight. 'Deflate' was a term they used to refer to losing weight."