BOSTON (CBS) — From the moment that the findings of the Wells report were released last Wednesday, the New England Patriots expressed their displeasure with the methods employed and the conclusions reached in the investigation. That disappointment was compounded significantly after the punishment for Tom Brady was announced on Monday.

And so on Thursday morning, the Patriots released a nearly-20,000-word document which sought to put the Wells report in context.

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The Patriots’ report, compiled by team counsel, began with a very clear message:

“The conclusions of the Wells Report are, at best, incomplete, incorrect and lack context. The Report dismisses the scientific explanation for the natural loss of psi of the Patriots footballs by inexplicably rejecting the Referee’s recollection of what gauge he used in his pregame inspection. Texts acknowledged to be attempts at humor and exaggeration are nevertheless interpreted as a plot to improperly deflate footballs, even though none of them refer to any such plot. There is no evidence that Tom Brady preferred footballs that were lower than 12.5 psi and no evidence anyone even thought that he did. All the extensive evidence which contradicts how the texts are interpreted by the investigators is simply dismissed as ‘not plausible.’ Inconsistencies in logic and evidence are ignored.

These points, and others, are addressed in greater detail in the following Annotations to the Executive Summary of the Wells Report by Daniel L. Goldberg, a senior partner in the Boston office of Morgan Lewis and who represented the Patriots and was present during all of the interviews of Patriots personnel conducted at Gillette Stadium. Our intention is to provide additional context for balance and consideration.”

The Patriots’ first point of contention relates to the measuring of the footballs’ PSI at halftime. The Patriots contend that the methods employed were unsatisfactory, and noted that three of the four Colts’ footballs measured under the allowable PSI limit on one of the gauges used.

The Patriots cite 2003 Nobel Prize winner Roderick MacKinnon’s analysis of the science, which you can read more about here.

The report noted that the two gauges used to measure the footballs varied between .3 and .45 PSI apart from each other.

The report reads:

“Referee Walt Anderson, who was alerted to psi issues before the game, has a detailed recollection of the unrecorded psi levels of the 48 footballs he gauged pre-game — essentially 12.5 for the Patriots footballs and 13.0 or 13.1 for the Colts footballs. His Recollection of those pre-game psi levels is one of the foundations of this report. MR. ANDERSON SPECIFICALLY RECALLS THAT HE USED THE LOGO GAUGE FOR THESE PRE-GAME MEASUREMENTS (pg. 52). (This is the only recollection of Mr. Anderson that the report rejects.) Therefore, the Logo gauge numbers are the correct numbers to use for halftime psi. The investigators did rely on those Logo gauge halftime psi numbers in dealing with the Colts footballs. Using that gauge, all the Colts footballs were within regulation. That justified the officials not adding air to them. However, when assessing the Patriots footballs, the investigators reject Anderson’s best recollection that he used the Logo gauge pre-game, and instead look to the larger psi drop that is shown by the lower psi, non-Logo gauge.”

The Patriots claim that when using one of the gauges — the same gauge used to assess the Colts balls as acceptable — the deflation levels in their footballs can be explained through the Ideal Gas Law.

“With the Logo gauge, 8 of the 11 Patriots footballs are in the Ideal Gas Law range and the average of all 11 Patriots footballs was 11.49 — fully consistent with the Ideal Gas Law’s prediction of exactly what that psi would be. THAT IS, RELYING ON MR. ANDERSON’S BEST RECOLLECTIONS, BASIC SCIENCE FULLY EXPLAINS THE DROP IN PSI OF THE PATRIOTS FOOTBALLS DURING THE FIRST HALF.”

The report continues on the matter:

“There is no rationale for this flip-flopping on whether Mr. Anderson’s recollections were correct. … Perhaps releasing drafts of the consultant’s report, and all communications between the investigators and their consultants regarding the development of their opinions, would shed more light on this so the public can have all relevant information.”

The Patriots continue, saying that the entire investigation was based on unfounded assumptions from the league, which did not understand the science behind air pressure variations when they initiated the official investigation from Paul, Weiss.

“League personnel, thus, with no basis and no understanding of the effect of temperature on psi, had already prejudged the issues. The Colts footballs also lost psi, but no similar ‘preliminary finding’ was made regarding the Colts. The Wells investigators, then, were hired by the League to investigate an issue that the League had already prejudged. … The January 18 letter to the Patriots also contained two significant misstatements that set a tone for this investigation and were an apparent source of media misreporting: 1) that one of the Patriots footballs was measured at 10.1 psi at halftime, an obvious misstatement; 2) that all of the Colts footballs measured within regulation — another misstatement. The League never corrected this notice in any respect. Why was the League content to have the Patriots dealing with this investigation for months based on inaccurate information?”

The Patriots also contend that the conclusion reached by Wells — that Jastremski and McNally conducted illegal activity — was based mostly on text messages. On that point, the Patriots claim there is no evidence.

“Mr. Jastremski and Mr. McNally were obviously uninhibited texters, sending communications with no thought that anyone else would ever see them. They certainly would not have cursed at the team’s quarterback if they thought their texts would ever see the light of day. Perhaps most revealing, then, is that not a single text states that: (i) Brady wanted footballs set below 12.5 psi; (ii) there was a plan to deflate footballs after the referee inspected them; or (iii) there was any actual such deflation. Nonetheless, the report assumes that every text reference to inflation or deflation of footballs suggests there was a plot to improperly deflate footballs after the referee’s inspection. In reality, there is simply no basis to assume that conclusion.”

Given that the Patriots were busy preparing for the Super Bowl at the time of the investigation, this point of contention is one of their biggest.

“The report treats these inaccuracies as inconsequential (See page 101), when quite the opposite is true; they fueled international media misinformation to the Patriots serious detriment.”

The report explains Brady’s increased communications with equipment assistant John Jastremski, which were considered to be suspicious and damning by Ted Wells’ team.

“[T]he media frenzy over deflated footballs started the day after the AFC Championship Game. Mr. Brady is used to the limelight and to critics; Mr. Jastremski is not. Since Mr. Jastremski prepared the footballs, it was reasonable to expect that this media attention would focus on him. It was also reasonable to expect that (as happened) Mr. Jastremski’s boss would question Mr. Jastremski to see what, if anything, he knew. Mr. Brady’s reaching out to Mr. Jastremski to see how he was holding up in these circumstances is not only understandable, but commendable.”

The rebuttal also asserts that Tom Brady would have no motivation to want the Patriots’ employees to deflate the footballs after the officials set them at 12.5 PSI.

“[Brady’s] performance is, simply, not affected by where the psi of footballs is in that very broad range. This is confirmed by the AFC Championship Game itself. Not only did the Patriots score 28 points in the second half with footballs reinflated significantly above 12.5, but no player or game official noticed that any below-regulation footballs were being used in the first half. Who handled the footballs the most during the first half of the AFC Championship Game? The game officials. They handled Patriots game footballs before and after each of the over 44 offensive Patriots’ plays. They held the footballs. They put them on the ground. They lateraled them. They caught them. They could even compare them with the Colts footballs they also handled.

“No single game official noticed anything different about the footballs. In sum, even those experienced in handling footballs cannot tell if they are at or a psi or two below regulation. The footballs remain firm and hard.”

The Patriots also contend that Ted Wells is not being truthful when he claimed to request a second interview with McNally only after obtaining text message communications between McNally and Jastremski which Wells had previously not possessed.

“[I]nvestigators had all such texts in their possession and available for the questioning.  They apparently just overlooked them,  identifying them now as a matter they wanted to cover in yet another interview. Although asked numerous times for the reason for their request for yet another interview with Mr. McNally, the Wells investigators never stated the reason that now appears evident from the Report:  They had overlooked texts in their earlier interviews and wanted the opportunity to ask about them. This information would have confirmed what is now clear. The request was inconsistent with the interview protocol agreed to at the outset.”

As a result, the Patriots flatly deny charges that they failed to make McNally available for a follow-up interview.

“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 — scarcely an “unanticipated circumstance” calling for yet another interview — and refused to disclose their reason for an additional interview.  There was no refusal to cooperate by the Patriots.”

Likewise, the Patriots denied the assertion that Brady’s gifting of autographs and memorabilia to McNally is evidence that Brady knew of nefarious behavior.

“Such requests are made multiple times almost every day in the team locker room or equipment room, even on game day. Mr. Brady believes he has never turned down such a request. If receiving an autograph from Mr. Brady is evidence that you are being rewarded by him for nefarious conduct, then hundreds or even thousands of people must be part of a scheme of wrongdoing.”

On the point of Brady refusing to turn over his personal cell phone, the Patriots assert than any of his communications with Jastremski could be found on Jastremski’s phone, which Wells had access to, and that no communication ever existed between Brady and McNally.

“The absence of any texting between Mr. Brady and Mr. McNally was further confirmed by the uncontradicted testimony by each of them that they had never spoken to each other on the phone, had never texted each other, and had never even had a substantive in-person conversation with each other. The investigators found no witness who contradicted any of these statements even though they had access to countless people who were in the Patriots locker room area or the player’s bench area where, on game day, Mr. Brady and Mr. McNally were in the same vicinity. The absence of a single witness who observed some substantive conversation, and the absence of texts during what the investigators felt was a critical time, corroborated their statements that they never had any such communications. If any information about texts on Mr. Brady’s phone was really an issue, they could have asked Mr. Brady’s agent (who offered at the end of Brady’s interview to respond to further inquiries) to confirm there were no texts with Mr. McNally.”

“Given the fact that Mr. Jastremski and Mr. McNally had both turned over their phone records, no adverse inferences should be drawn from the fact that Mr. Brady did not make his phone or its contents available.”

“As to the texts, which are discussed later, there is not a single text which refers to a plan to deflate footballs after the referee’s inspection, to having done so, to any Brady instructions to do so, or to any knowledge by Mr. Brady of such conduct. It is pure surmise and speculation that every deflation reference in a text is to improper deflation of footballs after the referee inspected them. In short, there is simply no evidentiary support for the conclusion that Mr. Brady was aware of any actual or even attempted effort to improperly release air from the footballs. All the evidence — as well as logic — is to the contrary.”

The Patriots also addressed Ted Wells’ clear anger expressed on his conference call that he was not happy to have his integrity and objectivity questioned. The Patriots noted that all judges must reveal financial relationships to either party, and that “it is not an attack on the judge’s integrity to expect him or her to do so.”

“The issue that has been raised in the media is whether public acknowledgment and the disclosure of these extensive relationships with the League was appropriate. Such disclosures would help the public better assess the findings regarding League conduct, of which there is not a single critical comment or single suggestion for improvement in the report. No one should take calls for such disclosure personally.”

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With regard to the Wells conclusion that Brady was “at least generally aware” of illegal activities, the Patriots strongly protest.

“The phrasing of this conclusion reflects what a reach it was. Unable to conclude that Mr. Brady had knowledge of, let alone directed, any improper activities, the best the report comes up with is the phrase ‘generally aware.’ As noted above, there is simply no evidentiary basis for this conclusion, let alone for the conclusion that there were any underlying inappropriate activities.”

“The texts that form the heart of this report show two persons with quite uninhibited texting history — and yet NOT A SINGLE TEXT REFERS TO DEFLATING FOOTBALLS TO A LEVEL BELOW REGULATION, TO DEFLATING FOOTBALLS AFTER THE REFEREE’S INSPECTION, OR TO ANY DIRECTIONS FROM MR. BRADY — OR EVEN ANY BELIEF THAT TOM BRADY WOULD PREFER TO USE BELOW REGULATION FOOTBALLS.”

The Patriots fight the contention that McNally “stole” the footballs from the officials’ locker room, noting that he had to navigate a room that was full of NFL employees.

“Mr. McNally, a physically big man, hoisted two large bags of footballs and lumbered past all these League officials and out the door of the Officials’ Locker Room. As is clear from the report, no one objected; no one told him to stop; no one requested that he wait to be accompanied by a League official; no one told him that a League official had to carry the footballs to the field. After he walked past all of these League officials and out the door of the Officials’ Locker Room to the hallway, he then walked past James Daniel, an NFL official and one of the people who had been alerted to the Colts psi concerns pre-game (pg. 45). Mr. Daniel, as seen on the security video, looked at Mr. McNally carrying the bags of footballs toward the field unaccompanied by any League or game official, and made no objection to Mr. McNally continuing unaccompanied to the field. In short, if officials lost track of the location of game footballs, it was not because Mr. McNally stealthily removed them. (Omitted from the investigation were interviews with all those League officials whom Mr. McNally walked past with the bags of footballs on his shoulders.)”

“Even after halftime, when obvious attention was being paid to game footballs and psi issues by League and game officials, who took control of the footballs at halftime, the security video shows Mr. McNally, with no objection, taking the footballs from the Officials’ Locker Room back to the field totally unaccompanied by any League or Game official. Mr. McNally’s removal of the footballs from the Officials’ Locker Room before the game began was simply not unauthorized, unknown, unusual, or in violation of some protocol or instruction. The report nonetheless portrays Mr. McNally’s departure from the Officials’ Locker Room before the game as a step in secretly taking the footballs for nefarious reasons.”

“When the NFC Championship Game ended abruptly in overtime, someone in the Officials’ Locker Room sitting area said “we’re back on.” Mr. McNally then stood up, put the two bags of footballs on his shoulders, and proceeded past all of these NFL personnel and game officials (see pgs. 54-55) to the door of the Officials’ Locker Room sitting room (described in the report as a “large sitting room” — pg. 54). This was not some clandestine departure — it was in clear view of all those League officials. Once the footballs are taken to the field they are to be taken to the area adjacent to the replay booth. The outdoor security camera shows that is exactly what Mr. McNally did. Anyone actually concerned about the location of the game footballs could simply have checked that location. The security video shows Mr. Anderson coming out to the field and going there. Not surprisingly, he found Mr. McNally was there with the bags of footballs. No one then reprimanded Mr. McNally for having taken the footballs without permission or accompaniment, although the report would have one now believe that officials thought Mr. McNally had done something wrong by taking the footballs himself. No official chastised him; no one re-checked football psi; no official suggested using the back-up footballs. Mr. McNally’s departure from the sitting room in the Officials’ Locker Room, and his walk from there towards the field, are all on the security video. His walk was not in any way hurried or furtive or secretive. Nothing about his activities supports a conclusion that he was carrying out a secret plan to deflate footballs.”

With regard to the Wells reports’ assertion that 12 footballs can be deflated by 1 PSI in 1 minute and 40 seconds, the Patriots counsel notes that it was a very inexact experiment, one that does not prove anything.

“[T]he experiment nonetheless assumed a plan to release an inconsequential amount of air. There is no indication in the report of the size, agility or age of those who raced to complete the task as quickly as possible — and hence no real assessment of whether a person of Mr. McNally’s age and physical characteristics could have accomplished this task, which would involve taking the footballs out of the bag, putting them on the floor (which happens to be sloped, increasing the level of difficulty if footballs were laid out on the floor), carefully controlling them to be sure not to deflate any football twice, returning them to the bag, unlocking the door and leaving. In all events, there was good reason for Mr. McNally to stop in the bathroom, since his sideline duties require he be on the field the entire first half.”

In a point that was almost instantly mocked on social media, the Patriots claim that McNally referring to himself as the “deflator” was a reference to him losing weight.

“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. One can specifically see this use of the term in a Nov. 30, 2014 text from Mr. McNally to Mr. Jastremski: ‘deflate and give somebody that jacket.'”

The Patriots also deny that McNally telling Jastremski “I’m not going to ESPN … yet,” was a joke that McNally would not tattle on Jastremski for stealing items from the equipment room.

“The May 2014 McNally text reference to ‘not going to espn’ follows his request for ‘new kicks,’ and 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.’ The Wells investigators had this text long before their interviews with Mr. McNally and Mr. Jastremski. Had they asked Mr. McNally or Mr. Jastremski about this text when they interviewed each for a full day using four lawyers, they would have learned this.

“Certainly there is no way one could reasonably base conclusions that a scheme existed and was implemented to improperly deflate footballs based on these texts, particularly where ball tampering at the AFC Championship Game is belied by science, would have been illogical in concept and improbable in practice, and where it would, if anything, had disserved the quarterback.”

The Patriots say that McNally’s and Jastremski’s texts about inflating the footballs to a “balloon” were obvious jokes, as McNally would never actually have an opportunity to insert air into the footballs.

“In short, the report ignores the description of an unstated meaning to these texts which disregards their content and obvious hyperbole. The problems with relying on text messages to derive meaning are well known. They do not convey tone of voice. They are not well-suited for humor or sarcasm. Shorthand expressions or terms routinely used by those sending texts to each other may not be understood or appreciated. How many people have sent a joking text which could be misinterpreted if read cold by a third person? … Although the report recognized the texts between Mr. Jastremski and Mr. McNally were filled with hyperbole and attempts at humor, it arbitrarily decided where the joking ended and what the jokes referred to.”

Ted Wells said this week that Jastremski saying “he” was thinking about the stress that McNally had to “get them done” had to have referred to illegally manipulating footballs. However, the Patriots allege that Jastremski was referring to a friend, who was aware of McNally’s issues selling his family’s season tickets.

“As Mr. McNally explained, his sister is in charge of the family’s long-held Patriots seasons tickets, and she has developing health issues. Keeping track of what was being done with the tickets when not being used by the family was getting stressful. Using the team’s Ticket Exchange program provides no opportunity for reselling tickets at a profit, but using services like StubHub can result in season ticket revocations. These issues had been discussed by Mr. McNally with Mr. Jastremski and shared with Mr. Jastremski’s friend, who stayed over at Mr. Jastremski’s house the night of the Jets game and knew of Mr. McNally’s family issues with his tickets. In conversation that evening, he expressed concern to Mr. Jastremski about Mr. McNally’s situation and shared information about another friend who had similar stress about reselling tickets. That was the conversation that Mr. Jastremski explained the text was referring to. After the conversation with Mr. Jastremski’s friend was explained by Mr. Jastremski, the investigators did not request the opportunity to interview the Mr. Jastremski friend to determine whether any such conversation had in fact happened. The Patriots tracked down Mr. Jastremski’s friend, who is a professional fraud investigator and whose livelihood depends on his honesty. They arranged for a telephone interview with the investigators in which the individual explained in great detail the timing (the night of the Jets game), place (Mr. Jastremski’s house) and content of the conversation (dealing with Mr. McNally’s sister, suffering some early onset memory loss, trying to sell the family game tickets). The investigators, rather than take further steps to check out this information, simply chose to disbelieve input that did not square with their conclusions.”

“Mr. Brady, when asked about this text, said that not only did he never have any such conversation with Mr. Jastremski but that, at the time, he did not even know how footballs got from the Officials’ Locker Room to the field — whether game officials took them, whether League officials took them, etc. That is simply not a matter he needs to focus on as the game is about to start.  In sum, the keystone link that the investigators rely on to implicate Mr. Brady is that he is the individual being referred to in this text as “him” and “he” even though all four people in any way involved in or related to this text have rebutted this interpretation. The investigators made up their minds that “him” and “he” referred to Mr. Brady, and dismissed all contradictory evidence as ‘not plausible.'”

The Patriots also claim that the pair’s reference to a “needle” only references the need to supply the officials with needles in the locker room.

“There is simply no basis to conclude, as the report does, that every reference to a needle refers to a needle to be used for the purpose of deflating footballs after the referee’s inspection.”

The Patriots pointed out that the Colts violated an NFL rule by inserting a gauge into the intercepted football on the sideline.

“The Colts, with advance concerns about psi, did not take the issue to the referee. They took the matter into their own hands and had an intern gauge the football. (pg. 63) This conduct was in violation of Rule 2. Nowhere does the Report identify this conduct as a violation of the Rule.”

The report reiterates many times that the only record of request from Brady to anybody about PSI came after the Week 7 Jets game, when officials pumped balls up to 16 PSI, and they only involved Brady requesting balls be set at 12.5 PSI.

“There is no evidence that Mr. Brady ever expressed a desire for footballs lower than 12.5, ever asked to practice with footballs set at lower than 12.5, or ever felt he would be advantaged in any way by using a football set under 12.5. Quite to the contrary, what Mr. Brady explained to the investigators is that the consistency of the footballs and their tactile feel are most important to him, and he cannot even tell the difference if a football is within regulation or a psi or so above or below regulation.”

The Patriots also contend that there is no evidence of Brady offering autographed goods being offered as a means to reward McNally for doing something illegal.

“Construing texts in this fashion is another demonstration that all information was filtered through the assumption that there was wrongdoing. Texts are interpreted to fit the conclusion. They do not drive the conclusion.”

The Wells investigation concluded that when Brady said he did not know McNally personally, the quarterback was lying. The Patriots contend that there is no evidence to suggest Brady was lying.

“Other than pleasantries that might have been exchanged in passing in the locker room or equipment room area (Mr. Brady exchanges those pleasantries with most people he comes in contact with, as could have been readily confirmed by the investigators) and Mr. McNally’s recollection of asking Mr. Brady to sign some autographs, there is not even a single communication between them — oral, written, text, email, etc. — which exists or which a single witness identified. Indeed, Mr. McNally felt he needed to ask for permission to get the autographs on the day he thought could be Mr. Brady’s last game of the season — that is how non-existent any relationship with Mr. Brady was.”

Another very noteworthy point came in the Patriots’ request for Ted Wells to investigate a prior report of Colts ball boys possessing needles on the sideline.

“Evidence was also provided [by the Patriots] that Indianapolis ball boys, in a prior season, had been seen by Jacksonville personnel with ball needles hidden under their long sleeves.”

The Patriots note that their own legal counsel was denied their requests to be present during Wells’ interviews with NFL personnel, and they also note that they were not provided with documentation of the halftime measurements until March 23.

“It was provided then only on the condition that it not be disclosed and, particularly, that it not be disclosed to the media until the final report was issued. This condition was imposed in the face of the extensively reported misinformation about halftime football psi that the League had refused to correct. One can only speculate why it was so important for the League that the accurate halftime information be withheld from the public until it was ultimately part of a report that downplayed the science and instead relied on selective texts.”

With regard to not making McNally available to be interviewed, the Patriots note that McNally interviewed with NFL security three times without a Patriots employee present, and NFL investigators originally did not even ask for his phone.

“At his third interview with League Security personnel, he was subjected to very aggressive questioning and demeaning assertions that he was lying when he denied any knowledge of improper football deflation.  This approach to the issues by League personnel was consistent with their prejudgments of wrongdoing by the Patriots.  Notwithstanding that he had already been interviewed three times, when Mr. Wells asked to interview him again, the Patriots agreed to facilitate that fourth interview.  That agreement was based on an explicit understanding reached with the Wells investigators: barring unanticipated circumstances, individuals would only be interviewed by the Wells investigators one time.

“Based on this understanding, the Patriots asked Mr. McNally, a game day only employee with whom the team had no ongoing employment relationship, to leave his full-time, out-of-state job in order to be available for an interview at the stadium.  Prior to the interview, the Patriots prevailed upon Mr. McNally to allow his personal phone to be checked for any relevant information, all of which was provided to the Wells investigators before the interview.  The investigators therefore had all of Mr. Jastremski’s texts (which were provided three weeks before Mr. McNally was interviewed) as well as Mr. McNally’s phone records.  The Wells investigators brought four lawyers to the McNally interview.  They spent the entire day with him.  He gave over seven hours of testimony.  He answered every question.  Among other things, the Wells investigators inquired at length about texts with Mr. Jastremski.  Having taken a day off work, he was willing to stay as long as it took to finish.  The interview did not end until the investigation team exhausted every topic and question they had.

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“Thus, when subsequently asked for what would have been a fifth interview of Mr. McNally, Patriots counsel wanted to understand what unanticipated circumstances warranted this, including whether the interview would be limited to matters that were simply not available to the investigators during Mr. McNally’s prior interview.  The Patriots advised the investigators of their reluctance to have Mr. McNally back yet again, particularly given the media harassment he and his family had suffered as a result of prior leaks of Mr. McNally’s name and hometown.  The distress to him and his family caused by the ensuing media attention was described in detail to the investigators.  With this background, there was a high hurdle before the Patriots would ask Mr. McNally to appear yet again for what would be his fifth interview, and a particular desire to be sure that the standard for another interview — unanticipated circumstances — was met.”