Full opinion text
OPINION AND ORDER CRABB, District Judge. This is a civil action brought by plaintiff United States of America against defendant Murphy Oil USA. Inc. to obtain injunctive relief and civil penalties for alleged past and present violations of environmental laws at defendant’s petroleum refinery in Superior, Wisconsin. Plaintiff contends that defendant has violated and is continuing to violate the Clean Air Act, 42 U.S.C. §§ 7401-7671q, the Clean Water Act, 33 U.S.C. §§ 1251-1387. Sub-chapter III of the Resource Conservation and Recovery Act, 42 U.S.C. §§ 6921-6939e, and the Emergency Planning and Community Right-to-Know Act, 42 U.S.C. §§ 6991-6991h. Jurisdiction is present. See 28 U.S.C. §§ 1331, 1345 and 1355; 42 U.S.C. § 7413(b); 33 U.S.C. § 1319(b); 42 U.S.C. §§ 6928(a) and (h) and 6991(e). Some description of the laws alleged to have been violated will provide context for this comprehensive prosecution plaintiff has brought, in which it is alleging 24 separate violations against defendant and in which defendant has asserted eleven affirmative defenses, nine of them against the alleged Clean Air Act violations. The Clean Air Act assigns responsibility to both the state and federal governments for preventing and controlling air pollution. Congress has charged the Environmental Protection Agency with establishing national ambient air quality standards that protect human health and the environment. See 42 -U.S.C. § 7409. Individual states have the opportunity to adopt statutes and regulations to achieve the federally established air quality standards within their borders. See 42 U.S.C. §§ 7407 and 7410. Once approved by plaintiff, these state plans are referred to as “state implementation plans” and are enforceable by both the state and federal governments. See id.; see also 42 U.S.C. § 7413(a) and (b). Plaintiff has approved Wisconsin’s implementation plan for regulating sulfur dioxide, the main air pollutant at issue in this case. As part of their preparation of implementation plans, states must designate those areas in their states in which air quality attains the standards set by the federal government. In those “attainment areas” states must implement and enforce a Prevention of Significant Deterioration program that prescribes a pre-construction review process for large stationary sources of air emissions. In Wisconsin, the Department of Natural Resources has had authority for this review process during all relevant times. The reviewing authority estimates the emissions for a proposed source to determine whether they will lead to a deterioration of the air quality within the attainment area beyond statutorily determined levels. Those sources that will produce such emissions must undergo Prevention of Significant Deterioration review that may require the utilization of best available control technology to control emissions from the proposed new or modified emission source. See 42 U.S.C. § 7475(a)(4). In addition, the Clean Air Act prescribes uniform national standards known as New Source Performance Standards that establish technology-based minimum levels of performance with which certain types of new and modified sources must comply. See 42 U.S.C. § 7411. These standards apply to certain types of new emission sources and the modification of certain types of existing sources. The Clean Water Act has as its goal the restoration and maintenance of the chemical, biological and physical integrity of the nation’s waters. See 33 U.S.C. § 1251(a). It prohibits the discharge of any pollutant into the navigable waters of the United States except in compliance with a National Pollutant Discharge Elimination System permit issued by plaintiff. See 33 U.S.C. § 1342. The Wisconsin Department of Natural Resources administers the permit system within Wisconsin, pursuant to a 1974 memorandum of understanding that gave the state implementation and enforcement authority over the system. Under the Clean Water Act, effluent limitations control particular discharges. Generally, there are two types of limits, categorical limits and water based quality limits. In this case, only water based quality limits are at issue. The Resource Conservation and Recovery Act addresses the problems posed by hazardous waste and attempts to reduce the threat to human health and the environment that such waste poses. The act takes what has been called a “eradle-to-grave” approach, regulating hazardous waste from its initial generation to its ultimate disposal. See, e.g., United States v. Power Engineering Co., 10 F.Supp.2d 1145, 1147 (D.Colo.1998). Plaintiff has authorized the state of Wisconsin to administer and enforce a hazardous waste program. As a generator of hazardous waste, defendant is subject to the act. The Emergency Planning and Community Right-to-Know Act was enacted as independent legislation within the Comprehensive Environmental Response Compensation and Liability Act. The act has two goals: providing local communities with information about potential chemical hazards within their boundaries and encouraging state and local emergency planning for response to spills or releases of toxic or hazardous chemicals. See Steel Co. v. Citizens for a Better Environment, 523 U.S. 83, 86, 118 S.Ct. 1003, 140 L.Ed.2d 210 (1998). The act’s reporting requirements compel users of specified toxic and hazardous chemicals to file annual forms describing such matters as the name and quantity of chemicals on hand, the waste-disposal method employed and the annual quantity released into each environmental medium. See id. at 86-87, 118 S.Ct. 1003; 42 U.S.C. §§ 11022 and 11023. The case is before the court on plaintiffs motion for partial summary judgment on all claims as to liability and defendant’s motion for partial summary judgment dismissing claims 1-5, 7, 8 and 14-21. I conclude that defendant’s motion for partial summary judgment must be denied either because there are material facts in dispute that prevent resolution before trial or because the defenses fail as a matter of law. Central to the first four Clean Air Act claims is plaintiffs allegation that defendant withheld from regulators relevant information concerning its plans to improve its sulfur recovery unit and distillate unifier in 1988 and 1992. It remains unclear exactly what information was withheld, what the relevance of any such information might be and what significance any withheld information might have in light of the frequent inspections the Wisconsin Department of Natural Resources made of the refinery and the numerous discussions they had with defendant’s employees before and during the construction period. Until these matters are resolved at trial, it is not possible to make a final determination of many of the defenses defendant has raised or the first four claims plaintiff has brought. I conclude that plaintiffs motion for partial summary judgment must be denied as to claims one through five, ten, eleven, twelve and thirteen, twenty-two through twenty-four and that it will be granted as to claims six, seven, eight, nine, fourteen, seventeen and eighteen. A ruling will be reserved on claim fifteen, a portion of which has been withdrawn by plaintiff. Claims sixteen, nineteen, twenty and twenty-one are withdrawn by plaintiff. Before setting out the undisputed facts, a few words about the parties’ submissions are in order. First, a party’s proposed findings of fact are supposed to be facts. “Facts” refer to the historical events out of which the dispute arose. Facts are what happened, who did it, when it happened, who made what admissions or representations, what or whom was involved. It is not a “fact” that this court has subject matter jurisdiction over the case, pursuant to 28 U.S.C. § 1331 or any other statute. That is a conclusion of law. Similarly, it is not a fact that notice of the commencement of this action was given to the state of Wisconsin pursuant to 42 U.S.C. § 7412(b). That too is a legal conclusion. The fact or facts are what was done to effect such notice. Did plaintiff send the state a letter? If so, on what date was it sent and what did it say? Counsel should not include excerpts from statutes in their proposed findings of fact; such excerpts are not facts but law and should be saved for discussion in the brief or proposed conclusions of law. Counsel should note that except in unusual circumstances, it is not a material fact that so-and-so testified to such-and-such in a deposition. For example, in a case involving an automobile accident it is not a material fact that John Smith testified in a deposition that the traffic light was green when he entered the intersection. The fact for the trier of fact (or the judge determining the existence or non-existence of disputed material facts) is whether the light was green, not what John Smith said about it. The correct way to propose the fact is, “The traffic light was green when John Smith entered the intersection. See April 2, 2001 deposition of John Smith at 27, Is. 11-22.” Second, it is not necessary to repeat all of the proposed facts in the brief. See Procedures to be Followed on Motions for Summary Judgment ¶ 5. If counsel include facts in a brief, they must take care not to rely on any fact that has not been made the subject of a proposed finding. Moi-eover, if counsel believe it necessary to refer to factual matters, they should cite the proposed finding of fact that supports the assertion of fact, rather than cite a declaration of an expert or a deposition of a witness. Citing a declaration or deposition implies to the factfinder that the factual matter is new and has not been properly proposed as a fact. Counsel should not expect the court to comb through more than 1700 proposed findings of fact and conclusions of law to determine whether a particular factual assertion has been proposed properly. Third, it is definitely not necessary to propose the same fact more than once, even if it relates to more than one claim. Counsel’s practice in this case, along with their unauthorized inclusion of extensive and irrelevant argument in their response to their opponent’s proposed facts, has caused the record in this case to swell to unprecedented proportions. Another word. When a party is asking a court to decide an issue involving scientific and bureaucratic terms that are unfamiliar to lay people, the party should use care to assist the court in understanding the terminology. Above all, it should not use acronyms without explaining what they stand for or employ terms whose meaning a court has no way of learning. (For example, plaintiff has never told the court what a “multimedia” inspection of an oil refinery might be. The Oxford English Dictionary says that “multimedia” designates or pertains to “a form of artistic, educational, or commercial communication in which more than one medium is used.” From the context in which plaintiff uses the word, I doubt that it meant to say that the Environmental Protection Agency representatives went to defendant’s refinery to make a presentation using a number of forms of media.) Defendant’s expert on opacity matters, Thomas Rose, used the term “seact” in a report; (neither the Oxford English Dictionary, Merriam-Webster online nor any specialized engineering dictionary recognizes this word.) Finally, defendant has moved to strike plaintiffs untimely proposed findings of fact and conclusions of law in opposition to defendant’s motion for summary judgment (dkt.# 123). The motion will be granted. The magistrate judge set a deadline of March 23, 2001, for the filing of such submissions, warning the parties that after two previous extensions of time, this deadline was firm. Despite the warning, plaintiffs filing was three days late. From the findings of fact proposed by the parties, I find that the following are material and not disputed. UNDISPUTED FACTS A. Background Plaintiff is the United States of America, suing on behalf of the United States Environmental Protection Agency. (Future references to “plaintiff’ in this opinion will be to the EPA.) Defendant Murphy Oil USA, Inc. is a Delaware corporation that has owned and operated a petroleum refinery in Superior, Wisconsin, since approximately 1950. The refinery is located about 1.5 miles from Lake Superior. It extends over 230 acres and can process an average annual crude capacity of somewhat less than 35,000 barrels a day. Defendant’s refinery uses many processes, including atmospheric distillation, hydrotreating, isomerization, fluidized catalytic cracking, alkylation, catalytic reforming, sulfur recovery and blending operations, among others. Defendant receives crude oil from Canada and North Dakota through the Lakehead Pipeline and refines it into several petroleum derivatives, including at least six types of crude oil with varying sulfur contents. Those with lower sulfur content are identified as sweet crudes; those with higher contents are known as sour crudes. Historically, about 45 to 50% of defendant’s “feed stock” is converted into gasoline. The rest becomes diesel fuel, kerosene, light and heavy oil fuels, propane and butane gas, asphalt and elemental sulfur. B. Clean Air Act Claims (1-6) 1. Claims one to four; preconstruction activities a. Defendant’s sulfur recovery unit Defendant’s sulfur recovery unit was built by another company for a gas plant. Defendant bought it and moved it to Superior, where it was reconstructed for defendant’s use and installed in 1973. The unit uses a vapor-phase catalytic reaction of S02 and H2S to recover sulfur from H2S, a highly toxic gas. The unit converts hydrogen sulfide, or H2S, from the amine section acid gas and from the sour water stripper off-gas into elemental sulfur. The capacity of the sulfur recovery unit to process gas streams is measured in long tons per day. The unit converts hydrogen sulfide into liquid elemental sulfur through a process known as the Claus reaction, which consists of a thermal reactor and two catalytic reactors. The thermal reactor partially burns the hydrogen sulfide. The resulting H2S/S02 mixture is converted to elemental sulfur and recovered in that form in the Claus unit. Residual S02 and other gases (“tail gas”) are routed to the sulfur recovery unit tail gas incinerator and then released into the air. The molten elemental sulfur is transferred to a sulfur pit for storage as a product and then sold commercially. Typically, two-stage Claus sulfur recovery units convert 90 to 95% of the hydrogen sulfide into elemental sulfur. In June 1986, Thomas Graney became Manager of Operations at defendant’s refinery in Superior. In that position, he was responsible for the day-to-day operations of the process units, including the sulfur recovery unit. He does not consider himself an expert in sulfur recovery units. When he began work, the Claus unit was not running well. It was off line much of the time and had frequent mechanical failures. During the period 1986-87, Graney retained a firm known as Sulfur Operations Support to help fix the design problems of the sulfur recovery unit. Graney received four letters or reports from Sulfur Operations Support between January 1987 and May 1987, containing analyses of the sulfur plant. The firm’s conclusion was that the combustion chamber of the sulfur recovery unit was too' small. In 1987 and 1988, defendant made physical changes to the sulfur recovery unit at a cost of more than $250,000 by upgrading the primary burner, replacing the catalyst, installing a new and larger combustion chamber, adding an acid gas knock-out drum and a tail gas analyzer, as well as adding a hydrocarbon coalescer in the upstream amine unit and installing a distributed control system. These changes served to improve the reliability of the unit and to improve its sulfur recovery efficiency- On February 18, 1988, the Wisconsin Department of Natural Resources issued a notice of violation to defendant for violating the state’s Statewide Sulfur Dioxide Rule, Wis. Admin. Code § NR 417.07(2)(g), which limited S02 emissions from the Claus sulfur recovery unit to 843 pounds an hour over any tjiree hour period and 6,743 pounds an horn* dyer any 24 hour period. In a February 29,\l988 response to the notice of violation, defendant stated that the modifications to the refinery that it had begun would enable it to be operating the sulfur recovery unit by July 29, 1988 and to demonstrate full compliance with the proposed alternate emission limits no later than September 1988. When the sulfur recovery unit and associated amine system were not operating, sour gases bypassed the sulfur recovery unit and were burned directly without pollution control, causing an increase in sulfur dioxide emissions that in 1988, 1990 and 1991 sometimes exceeded the legal limits under the Wisconsin Administrative Code. On April 8,1988, Department of Natural Resources staff held an enforcement conference with defendant to discuss resolution of the February 18, 1988 notice of violation. Pursuant to the department’s directive, defendant presented a proposal and schedule to undertake various enhancements to the sulfur recovery unit that would reduce sulfur dioxide emissions from the refinery and bring the refinery into compliance with state sulfur dioxide rules. The department found the proposal acceptable for compliance with S02 rules. Mark Miller started working at defendant’s refinery in January 1989 as a process engineer with responsibility for assisting the operations department in improving the running of the refinery process units and the sulfur recovery unit. At the time, defendant was still having problems as a result of the unit’s lack of mechanical reliability. Downtime for the sulfur recovery unit resulted in excessive S02 emissions. Defendant retained Western Research to conduct a comprehensive full performance test on its sulfur recovery unit. Western Research provided a report to defendant before July 14, 1992, the date on which defendant submitted its No. 2 distillate unifier permit application to the Department of Natural Resources. Part of the Western Research work was to prepare a “material balance” of the sulfur recovery test, that is, a summary of the components going into a unit and those leaving the unit. Also, Western Research evaluated the sulfur recovery efficiency of the sulfur recovery unit as of a particular day in October 1989. In its report, it stated that the calculated recovery efficiency was 95.5% and the rated or expected recovery efficiency was 96.2%. On March 18, 1990, the Wisconsin Department of Natural Resources issued another notice of violation to defendant for violating Wis. Admin. Code § NR 417.07(5), which limited S02 emissions from the tail gas incinerator at the sulfur recovery unit to 393.4 pounds an hour. In 1990, defendant retained Becker, Losier & Associates, which subcontracted with E & L Engineering to study possible improvements in the operation of the sulfur recovery unit. Defendant’s process engineer Miller served as defendant’s point of contact with E & L. Earlier, in a report dated September 28, 1989, Walt R. Losier of the firm had reviewed defendant’s sulfur recovery unit problems and had made recommendations for changes to solve the problems. On April 3, 1990, E & L prepared a comparison study of the existing design of the sulfur recovery unit and a future revised design that would add a new 9.0 pound per square inch gauge blower and deeper sulfur seal legs, allowing an increase in acid gas flow equal to 16.0 long tons of sulfur a day. On April 23, 1990, Miller asked E & L to add a new design case to “determine the unit capacity bottlenecks when additional acid gas is brought into the unit.” Defendant was aware that environmental regulations would require it to reduce the amount of sulfur in the distillate (diesel) fuel. In anticipation, it wanted to know what it would take to make the sulfur recovery unit process an extra four long tons of sulfur a day. Defendant knew as early as 1990 that it would have to increase the capacity of the Sulfur recovery unit to produce low sulfur diesel fuel. At the time, the design capacity of the unit was 15.1 long tons a day of sulfur. On May 8, 1990, E & L reviewed the existing sulfur unit design in light of the future requirements for several cases. (The parties seem to use the word “cases” to refer to design alternatives.) Defendant gave serious consideration to only two of the cases, both of which anticipated adding the sour water system off-gas, adding a new combustion air blower and increasing the depth of the sulfur seal legs. One of the cases would have required an 8.0 pound per square inch gauge blower. Instead, defendant purchased two new air combustion blowers, one of 9.0 pounds per square inch gauge and another of 11.5. As of July 26, 1990, defendant had asked E & L to provide 17 to 18 foot sulfur seal legs and determined that the design should be based on the 11.0 pounds per square inch gauge air blower case. Defendant was responsible for obtaining the necessary construction permits. On May 21, 1990, David-Petty, an employee of defendant, wrote to the Wisconsin Department of Natural Resources, asking for a determination whether two proposed alternatives for modification of the existing sulfur recovery unit would trigger the need to comply with New Source Performance Standards. He stated in the letter that the sulfur recovery unit had a nominal design capacity of 14 long tons a day and that ordinarily, New Source Performance Standards do not address Claus units smaller than 20 long tons a day capacity. A department employee, Scott Humrickhouse, replied to defendant’s letter. He noted the reliability problems defendant had had with its sulfur recovery unit and the excessive S02 emissions that were the consequence of the frequent periods of downtime. He listed the alternatives Petty had described in his May 21 letter and said that neither would trigger New Source Performance Standards or Prevention of Significant Deterioration requirements or require a new source air pollution control permit. He asked defendant to submit a plan and schedule for “design, construction and operation of the [sulfur recovery] unit” by July 30, 1990. On July 30, 1990, James Gesick, manager of defendant’s refinery, wrote to the department, stating that defendant agreed to undertake the 1991 sulfur recovery unit improvements and that it had elected to separate the amine and sulfur recovery systems. He provided a detailed schedule for completion and he noted that defendant was undertaking the work on the understanding derived from the department’s 1990 Applicability Determination that the work would not trigger either New Source Pollution Standards or Prevention of Significant Deterioration requirements. On October 16, 1990, Ron Anderson, Gesick’s replacement, wrote to Humrickhouse, stating that defendant’s plan should eliminate the reliability problems experienced in the past. In a letter dated October 16, 1990, defendant informed the department again of its intention to proceed with the sulfur recovery unit improvements and to provide periodic updates to regulators. On September 21,1990, plaintiff issued a finding of violation to defendant for violating the New Source Pollution Standards by an unrelated process unit (a heater) at defendant’s refinery. On November 13, 1990, plaintiff held a “Section 113” conference with defendant to discuss the finding of a violation. During the conference, defendant stated that because of mechanical problems with its sulfur recovery unit, it was constructing a modification to the unit under the guidance of the Wisconsin Department of Natural Resources and that the project was not subject to New Source Pollution Standards. In response to a request by plaintiff, defendant sent Sylvia Lopez, an air engineer employed by plaintiff, copies of the correspondence between defendant and the Wisconsin Department of Natural Resources in 1990, concerning the modifications to be made to the sulfur recovery unit. On January 24, 1991, Lopez and Jeff Trevino, a lawyer for plaintiff, gave preliminary confirmation to the Department of Natural Resources’ position that defendant’s construction of its second alternative plan for the sulfur recovery unit was not subject to New Source Pollution Standards and did not require construction or operation permits. After receiving the 1990 Applicability Determination, defendant began construction on the 1991 sulfur recovery unit project and began providing both plaintiff and the Department of Natural Resources with periodic progress reports. In April 1993, after the project was completed, the department inspected the refinery, including the sulfur recovery unit, and found “some improvement to the operation” during the preceding year. The author added, “The rebuild of this unit has proved to be very helpful.” This report was provided to plaintiffs Region 5 office. Among the activities associated with the 1991 sulfur recovery unit project was the rerouting of sour gas generated by a device called the sour water stripper to the sulfur recovery unit for pollution control purposes. Before this project was undertaken, defendant had sent the sour water stripper gas to an incinerator where sulfur byproducts from its combustion were discharged directly into the atmosphere without the benefit of a pollution control device. Defendant told the Department of. Natural Resources about the planned rerouting in a letter dated November 2, 1990. The re-routing resulted in a reduction of approximately one ton a day of sulfur emissions from the refinery. The other modifications that defendant made to the sulfur recovery unit in 1991 included replacing the 9 foot sulfur seal legs with deeper 18 foot legs; installing a new and larger sulfur pit; installing two new ah' combustion blowers, one 9.0 pounds per square inch and one 11.5 pounds per square inch; replacing and increasing the heat exchange surface of the waste heat boiler, enlarging the condenser surface area on the sulfur recovery unit. Also, by 1991, defendant had eliminated the use of hot gas bypass on the sulfur recovery unit. On March 23, 1998, United States Environmental Protection Agency Region 5 issued defendant a request pursuant to 42 U.S.C. § 7414, asking for information about the “design capacity” and “maximum operating capacity” of defendant’s sulfur recovery unit and for any date on which defendant had increased those capacities. Defendant responded that before 1991, the unit’s capacity was estimated to be 14.0 long tons a day and that modifications made in 1991 had increased the design capacity by 0.4 long tons a day over the original design, for a total capacity of 14.4 long tons of sulfur a day after the renovation. Plaintiff determined that defendant’s sulfur recovery unit was not subject to the requirements of the Clean Air Act’s New Source Performance Standards. During a 1998 National Enforcement Investigations Center inspection of defendant, plaintiffs inspectors reviewed defendant’s annual sulfur production records from 1990 to 1997. From this review, they came to believe that sulfur production had exceeded the 20 long tons a day level during October 1996. Plaintiffs National Enforcement Investigations Center included the sulfur production data in its final inspection report, dated November 1998, and provided the information to Region 5 and the Wisconsin Department of Natural Resources. The information triggered an investigation into the history of the modifications to defendant’s sulfur recovery unit. In late October 1998, Department of Natural Resources employees Steve Dunn and Dan Rosenthal began to investigate the capacity of defendant’s unit. The department turned over the results of the investigation to plaintiff, which determined that defendant had provided inaccurate responses in the past regarding the unit’s capacity. b. Defendant’s No. 2 distillate unifier After undertaking the sulfur recovery unit improvements in 1988 and 1991, defendant considered improving its No. 2 distillate unifier to allow it to produce diesel products with lower sulfur content. On April 20, 1992, Mark Miller sought regulatory guidance from Dan Rosenthal, the local Wisconsin Department of Natural Resources compliance engineer. Defendant described the proposed project and provided a schedule for completion of the project. Miller wrote that “[t]he sulfur production and S02 emissions are based on 90 percent sulfur recovery efficiency. The unit normally operates at a higher recovery efficiency (approximately 93-95%).” On April 22, 1992, Manager of Operations Graney wrote to his supervisor, W.E. Heck, reporting that Rosenthal had told Miller that the incremental feed to the sulfur recovery unit from the No. 2 distillate unifier project would require an air permit application. Graney noted that “pre-permit construction variance may not be allowed if we have to do a [Prevention of Significant Deterioration] permit.” Defendant obtained a pre-construction permit. Additionally, Rosenthal told Miller that the No. 2 distillate unifier project would be subject to the Prevention of Significant Deterioration requirements, which would require air dispersion modeling and best available control technology analysis for the sulfur recovery unit. As of May 1992, defendant was working within a tight time frame to get the No. 2 distillate unifier project completed. Defendant wanted to start producing low sulfur diesel fuel by August 1, 1993. Graney thought the need for Wisconsin Department of Natural Resources approval before construction began was a good reason to avoid the Prevention of Significant Deterioration rules. On May 29, 1992, approximately two months before defendant submitted the No. 2 distillate unifier permit application, Miller advised Graney that the heat recovery unit tubes were leaking diethylamine into the Claus side of the process during the September 13, 1989 stack test. Miller told Graney he believed that, although four stack tests were conducted, the sulfur recovery unit was running well only during the stack test of October 31, 1989. When defendant amended its No. 2 distillate unifier permit application, defendant wrote that both it and the Department of Natural Resources had “agreed that the basis for setting the baseline emissions will be to utilize the total sulfur shipped out of the plant. However, to utilize this figure, a calculation/assumption on the sulfur recovery efficiency must be made. This calculation/assumption has been on the basis of two stack tests cited in # 2 above [those performed on September 13, 1989 and October 31, 1989].” In a letter dated September 28, 1989, Walt Losier noted that during the first site visit in mid-September 1989, the tail gas in the sulfur unit had a very low ratio of H2S to S02. Defendant anticipated that the ratio would improve once the ‘Western R & D unit” was operating satisfactorily and the sample system changed and that it would give an efficiency of sulfur recovery from the acid gas in the range of 90 to 92%. The May 15,1992 letter from Becker provided defendant with current sulfur recovery efficiency information of 95 to 96%. Becker estimated the ten percent sulfur loading capacity of the sulfur recovery unit and the available sulfur capacity of the unit, noting that a higher sulfur input would not decrease overall efficiency. On July 6, 1992, Miller wrote to the Department of Natural Resources about defendant’s project to produce low sulfur diesel fuel, stating that “both the increased feed rate and sulfur dioxide emissions are well within the maximum design capacity of the [sulfur recovery unit].” He estimated that the current daily maximum of sulfur was 14 long tons a day, with a maximum design of 19 long tons a day for the sulfur feed and a projected daily maximum sulfur feed of 17 long tons a day. He wrote that in his opinion the project was exempt as a specified change in operation because changes in sulfur removal at the No. 2 distillate unifier resulted in an increase in sulfur production that did not exceed the operating capacity of the sulfur recovery unit. Defendant met with department staff on July 8, 1992, to discuss the proposal and the potential need for a permit. The department sought regulatory guidance and an opinion from plaintiff (although it continued to insist that defendant have a state permit). Region 5 told the department that a Prevention of Significant Deterioration permit was needed unless defendant was to “net out” or restrict emissions through a “synthetic minor permit.” On July 14, 1992, defendant submitted a permit application seeking authorization to modify its No. 2 distillate unifier. At the request of the Wisconsin Department of Natural Resources, defendant amended its application to obtain a “synthetic minor permit.” As part of the No. 2 distillate unifier permit application, ■ defendant had to show what the actual S02 emissions were before the project and what they would be after the project. Defendant chose to use a baseline period of August 1, 1989 to August 1, 1991, and a baseline recovery efficiency of 90% taken from the October 31, 1989 stack test. Defendant contended that it had improved the sulfur recovery unit recovery efficiency from 90% to 98% and took credit for emission reductions. It contended also that the distillate unifier project would result in a net decrease of 22 tons a year of S02 emissions. On September 17, 1992, refinery manager Ron Anderson sent the Department of Natural Resources a letter revising the No. 2 distillate unifier permit application and specifically revising the baseline recovery efficiency estimates by claiming a pre-project recovery efficiency of 86% for the period before the 1991 sulfur recovery unit modification rather than the 90% recovery efficiency for the entire period submitted in the original No. 2 distillate unifier permit application. In connection with its permit application, neither Graney nor Mark Miller provided the 1987 analyses of the sulfur recovery unit defendant had received from Sulfur Operations Support. On November 13, 1992, after an extensive exchange of correspondence and various meetings, the department issued defendant Air Permit No. 92-POY. The department determined that the modifications involving the No. 2 distillate unifier would be exempt from Prevention of Significant Deterioration review because defendant had agreed to abide by synthetic minor permit limitations that restricted emissions from the refinery to levels below Prevention of Significant Deterioration applicability thresholds. The department concluded that the proposed change would be minor because the increase of sulfur dioxide emissions would be less than 40 tons a year. The department stated in the permit that the project would not trigger Prevention of Significant Deterioration review or other requirements. It mailed copies of the permit to solicit comments from various interested parties, including plaintiff. The cover letter advised recipients that they had 30 days in which to appeal the decision if they objected to it. During the 30-day appeal period, plaintiffs Region 5 inspectors toured the refinery to inspect air pollution sources at the refinery and determine compliance with all applicable air rules. Plaintiffs staff discussed the sulfur recovery unit, the No. 2 distillate project and the air permit, No. 92-POY. Plaintiff never filed an appeal or any other objection to the issuance of the permit. During 1992, defendant constructed a new amine tower for separating hydrogen and H2S at the refinery’s No. 2 distillate unifier. Between 1992 and 1993, defendant increased the reactor size of the No. 2 distillate unifier. Six years later, in a 1998 inspection of defendant, plaintiff concluded that defendant’s sulfur recovery unit had a sulfur input capacity of greater than 20 long tons a day. Plaintiff undertook further investigation and subsequently issued a finding of violation to defendant on November 25, 1998, alleging that defendant was in violation of New Source Pollution Standards Subpart J. On September 29, 2000, plaintiff issued a notice of violation to defendant for its alleged failure to provide all relevant information in support of a permit application. At all times relevant to this suit, the state of Wisconsin had the- authority to issue Prevention of Significant Deterioration permits. Defendant first discussed the No. 2 distillate unifier project with Department of Natural Resources staff in April 1992, only six months after defendant’s completion of the sulfur recovery unit modifications. The Department of Natural Resources did not treat the modifications as one project. In September 1988, the Department of Natural Resources began enforcing the 393 pounds an hour limitation as an enforceable limit for S02 emissions from the sulfur recovery unit. 2. Settlement with state In December 1992, the state of Wisconsin initiated an enforcement action against defendant, alleging various violations of Wisconsin statutes and the Wisconsin Administrative Code that are part of the approved state implementation plan. The department provided plaintiff with a copy of its complaint on the day it was filed in Circuit Court for Douglas County. After extensive negotiations, the parties resolved the claims raised in the action by a stipulation for settlement that was entered as a judgment in the circuit court on August 19, 1994. Plaintiff was not a party to the action, but it was involved in discussions with the state regarding the settlement and followed the progress of the action and the negotiations closely during the three years the action was pending. It intended to file an action of its own if the state litigation was not resolved promptly. On February 6, 1991, Wisconsin Department of Natural Resources Engineer Dan Rosenthal toured the Superior Refinery and met with Jim Kowitz, Refinery Manager. During the tour, Rosenthal expressed the department’s intention to resolve “all outstanding air issues at the Spooner [enforcement action] meeting.” On December 7, 1992, plaintiff inspected defendant’s refinery, including the sulfur recovery unit, with the stated purpose “... to inspect air pollution sources at Murphy Oil to determine compliance with all applicable air rules.” During the inspection, plaintiff asked about defendant’s sulfur recovery unit operations, compliance with S02 emission limits and the state Air Permit, No. 92-POY-094. Plaintiff discussed amine unit operations, the past and present methods of monitoring the hydrogen sulfide/sulfur dioxide ratio and the applicable S02 emission limitation for the sulfur recovery unit. The department provided plaintiff with a draft of the 1994 stipulation, which included the release language absolving defendant of liability for “any violation concerning emissions of sulfur dioxide or hydrogen sulfide which may have occurred within six years of this Stipulation and which emissions [defendant] had previously reported to the DNR.” Plaintiff wanted to be sure that the stipulation would not release defendant from potential enforcement actions involving Resource Conservation and Recovery Act violations. Following the settlement, defendant spent $25 million on pollution control projects at the refinery. The parties’ settlement included the following provision: Compliance with the terms of this stipulation shall constitute full satisfaction and release of [defendant’s] ... liability for civil forfeitures or penalties and/or criminal liability for any and all violations alleged in the Complaint filed herein, the referral letter (with attachments) from the secretary of the Department of Natural Resources ... to the Attorney General dated August 9, 1991, attached hereto as Exhibit A ... and any violation concerning emissions of sulfur dioxide or hydrogen sulfide which may have occurred within six years of the date of this stipulation and which emissions [defendant] has previously reported to the DNR. Between 1988 and 1993, defendant reported to the Department of Natural Resources all sulfur dioxide emissions from its refinery, including those from the sulfur recovery unit. • Exhibit A of the 1994 settlement agreement includes the following paragraph in Section B, Air Management Operations: [Defendant’s] sulfur recovery process has been [sic] source of concern for several years. Initially, the primary problem was the unit’s lack of efficiency. It removed less HS2 than it was designed to remove. When this problem was eventually solved, another became evident — because of its poor design, the unit needs frequent repairs which necessitates taking it off-line. During these times, sour gas gets burned and excess S02 gets emitted. 3. Claim five: opacity reading During the 1990s, plaintiffs National Environmental Investigation Center conducted “multimedia” compliance inspections of all petroleum refineries within Region 5, including one at defendant’s refinery from May 26 to June 4, 1998 and from June 15 to June 19, 1998. Before the inspection, plaintiff issued defendant a document request, asking that certain information be available for on-site review. The engineers reviewed the documents, asked for additional ones and had copies made of certain documents for later review. Preliminarily, the engineers made numerous findings of “noncompliance and areas of concern” and met with defendant’s personnel at the end of the inspection to inform them of the potential findings. On July 31,1998, plaintiff issued a notice of violation for violation of the “fugitive source rules” and violation of the opacity limit of 40% from the stack of the four steam generating boilers. Stationary sources can discharge visible emissions into the atmosphere that are usually in the shape of a plume. Plaintiff conducts visible emission readings in accordance with U.S. EPA Reference Method 9 to determine opacity, that is, the degree to which emissions reduce the transmission of light and obscure the view of an object in the background. The opacity can be determined by a qualified, trained observer using certain procedures set forth in Reference Method 9. Defendant operates four steam generating boilers that are vented to a single stack. The boilers produce 150 pound steam that is used at times for fueling some of the refinery processes. In 1998, the boilers were fueled by refinery fuel gas and No. 6 fuel oil. While plaintiff was conducting an inspection of defendant’s refinery during the period June 15 to June 19, 1998, two of its employees, Margaret Sieffert and Spiros Bourgikos, noticed a dark plume' rising from the stack from the four steam generating boilers. The two decided it was appropriate to conduct visible emissions readings under the circumstances, although they had not planned on doing so and Seiffert did not have a Visible Emissions Observations Form with her. Nevertheless, she conducted observations of the smoke for 37 minutes on June 17. Her-observations revealed six-minute opacity readings as high as 63%. When Sieffert made her observations, she did not record all of the items of information required for visual observations and she did not use a compass to determine directions. When she returned to her office five days later, she copied data onto a form. In doing so, she erred in placing a North arrow on the required sketch and when she described directions in the written part of the form. Several years later, she prepared a new sketch to depict what she believes was her true position in relation to the plume, wind direction and relative position of the sun. 4. Claim six: volatile organic compounds At a refinery, fugitive emissions can leak from system components that are in volatile organic compounds service, such as valves, flanges, pumps, compressors, sampling systems, open-ended lines and pressure relief valves. “Fugitive emissions” are emissions from any emission point within a facility other than a flue or a stack. A “volatile organic compound” is any organic compound that participates in atmospheric photochemical reactions. Defendant’s refinery contains at least 6,640 system volatile organic compound components. Defendant has an established leak detection and repair program to monitor volatile organic compound components at the refinery. From June 15 through June 19, 1998, National Environmental Investigations Center inspectors visited the refinery to' conduct an unannounced inspection of defendant’s leak detection and repair program and to test for leaks and emissions of volatile organic compounds. Plaintiff noted 16 separate instances between June 15 and June 19, 1998, when open lines at defendant’s refinery were not sealed with a second valve, a blind flange, a plug or a cap. Plaintiff identified 76 components not repaired in 15 days. It found at least 49 separate, observed instances between June 15 and June 19, 1998, when pipeline valves or pressure relief valves in gaseous service were not visibly marked. It identified at least 16 occasions in 1995, 15 occasions in 1996 and 10 occasions in 1997 when leaking components at 10,000 ppm or greater were not fixed within 15 days. Plaintiffs inspectors used Foxboro OVA-108 monitoring instruments, which are portable leak detection and repair instruments. The inspectors calibrated the instruments each morning before using them. They recorded on data sheets the monitoring results for each component monitored. Plaintiffs inspectors focused on valve evaluation. Plaintiffs inspectors identified 73 leaking valves among the approximately 2,700 valves in the nine process units monitored by plaintiff and by defendant’s contractor. Defendant’s contractor identified only 37 leaking valves among the more than 6,640 valves in the nine process units defendant and plaintiff monitored. Plaintiffs inspection took place within 10 days of defendant’s monitoring. Defendant’s contractor found leaks in .56% of the valves; plaintiffs inspectors found 2.7%. For the first two days of the inspection, defendant’s monitoring contractor confirmed each of the leaking valves the inspectors identified. The contractor chose not to participate in the final day of monitoring. C. Clean Water Act Claims (7-13) 1. Claims seven to nine: National Pollutant Discharge Elimination System Defendant discharges treated wastewa-ter from a discharge point, identified as Outfall 001, into Newton Creek, a shallow drainage ditch that flows eventually into Lake Superior. On June 29, 1993, the Wisconsin Department of Natural Resources issued defendant Wisconsin Pollutant Discharge Elimination System Permit No. WI-0003085-5, which contained specified effluent limitations, monitoring requirements and other terms and conditions for defendant’s discharges into Newton Creek. On August 27, 1993, defendant petitioned for a review of the permit. Among other things, defendant challenged (1) the department’s reliance on a chloride limit that had not been promulgated as an administrative rule as required by Sub-chapter II of Wis. Stat. ch. 227; (2) the department’s decision to maintain a discharge point at Newton Creek and its failure to take into account the default mixing formula in establishing the water quality based effluent limitations; and (3) the department’s derivation of the water quality criteria under Ch. NR 105 that resulted in effluent limitations for a number of substances, including selenium. In an alternative challenge, defendant requested a variance to the petition. On August 2, 1994, the department modified Permit No. WI-0003085-5, partially approving defendant’s request for a variance to water quality standards. The modified permit contained specified effluent limitations, monitoring requirements and other terms and conditions for defendant’s discharges into Newton Creek. In a letter to defendant dated August 2, 1994, the department wrote The modification of Wisconsin Pollutant Discharge Elimination System (WPDES) Permit No. WI-0003085-5, initiated by the Department on June 17, 1994, has been processed. This modification incorporates revised effluent limitations, and associated conditions,'based on variances to water quality standards .... The parameters for which the Department modified limits include total recoverable ... selenium ... and chlorides. The permit, which is attached, replaces the original permit issued on June 29, 1993. Please replace the original permit with the attached modified permit. All discharges from this facility and actions or reports relating thereto shall be in accordance with the terms and conditions of the original permit, as modified. On August 16, 1999, the department issued defendant Permit No. WI-003085-6, which replaced Permit No. WI-0003085-5. The department never addressed defendant’s petition for review of Permit No. WI-0003085-5. Beginning December 1, 1995, the modified permit required defendant to meet certain effluent limitations, including the following: Defendant’s modified permit expired on March 31, 1998. Defendant’s timely application for renewal of its permit extended the expiration date of its modified permit, pending the department’s final determination whether to renew the permit. Defendant continued to operate under its modified permit until August 15, 1999; its new permit became effective on August 16, 1999. Defendant’s discharge monitoring reports show that its discharge of chlorides through Outfall 001 exceeded the permissible weekly average contained in its modified permit for the following periods: March 8-14, 1996; March 22-28, 1997; and April 1-7, 1997. Defendant’s discharge monitoring reports show that its discharge of selenium through Outfall 001 exceeded the permissible weekly average contained in its modified permit for the following periods: July 29-31, 1996; February 8-14 and 15-21,1998. The modified permit required defendant to monitor its discharge of Outfall 001 for phosphorous each month beginning December 1, 1995. Defendant was required to limit its discharge of phosphorous to an average of 1 mg/L per month beginning April 1, 1997, if its discharge of phosphorous exceeded 60 pounds in any of the 12 months for which representative phosphorous samples were reported before January 1, 1997. Under defendant’s modified permit, compliance with the 1 mg/L limitation was determined on the basis of a rolling 12-month average. Defendant’s discharge monitoring report in November 1996 showed a phosphorous discharge for the preceding month of approximately 132 pounds, which triggered the 1 mg/L limitation. Defendant’s discharge monitoring reports show that the rolling 12-month average calculated for April and May 1998 of its discharge of phosphorous through Outfall 001 exceeded the 1 mg/L limitation contained in its modified permit. Under defendant’s modified permit, a value calculated under the rolling 12-month average in excess of the 1 mg/L limitation is equivalent to an exceedance of a monthly average limitation. 2. Claims ten to thirteen: spill containment and countermeasure plan In 1998, an environmental engineer with the National Environmental Investigation Center, inspected defendant’s facility and was given a copy of defendant’s 1996 spill prevention control and countermeasure plan. In 1998, the plan provided for future installation of a sufficient diked secondary containment area to a volume equal to the capacity of the largest tank plus sufficient freeboard for precipitation and provided for the installation of adequate secondary containment for slop oil tanks S-l and S-2 and the common diked area for Tanks 21, 22 and 23. In response to spills of petroleum compounds at tanks S-l and S-2, defendant had proposed installation of containment areas around tanks S-l and S-2 but such containment areas were not required by federal statute or regulation. Defendant delayed installation of the secondary containment structure around tanks S-l and S-2 until it knew that such structures would not interfere with any of the department’s future investigatory or remedial efforts. At the time of the inspection in 1998, the Wisconsin Department of Natural Resources had not notified defendant that the site would be closed (meaning no further remedial action was anticipated). At the time of the inspection in 1998, defendant had not provided a sufficient secondary containment area for slop oil tanks S-l and S-2. After the department gave verbal notification that the site would be closed in September 1999, defendant constructed secondary containment around tanks S-l and S-2. . In 1997, defendant increased the height of the dike walls surrounding Tanks 21, 22 and 23. After the 1998 investigation, defendant verified the volume of the secondary containment area for Tank 57 and found it to be sufficient under the plan. Defendant’s spill prevention control and countermeasure plan was certified by a professional engineer on April 4, 1996. Defendant amended its plan in November 1996 and June 1997 but the amendments were not certified by a professional engineer. During the three years following the April 1996 certification, defendant eliminated potential spill sources and updated its list of potential spill sources. Defendant did not get its 1996 plan recer-tified after it had made changes to its list of potential spill sources. The spill prevention control and countermeasure plan “record of changes” form dated April 2000 indicates that pages 14-6 through 14 — 41 of the plan were amended in 1997. Although not documented on the record of changes form, pages 14-1 through 14-5 of the plan were amended in November 1996. At the time of the 1998 inspection, the 1996 plan consisted of amended pages 14-1 through 14-41. D. Resource Conservation and Recovery Act Claims (H-21) Defendant generates hazardous waste as a byproduct of its manufacturing processes at various locations throughout the refinery. From May 26 to June 4, 1998 and from June 15 to June 19, 1998, inspectors from plaintiffs National Enforcement Investigations Center conducted an environmental inspection of the refinery to determine defendant’s compliance with various environmental statutes and regulations. Linda TeKrony conducted the Resource Conservation and Recovery Act portion of the inspection. TeKrony toured the facility and reviewed records and documents. In response to a question about the location of defendant’s laboratory waste materials, TeKrony was shown two locations where non-chlorinated solvents were being accumulated in brown glass bottles. One bottle was open and located under a fume hood; the other was positioned to collect additional waste from analytical equipment. Neither bottle was labeled to identify the contents. Defendant generates hazardous waste at its wastewater treatment plant in the form of sludge, which is processed to remove recoverable oil, leaving thickener sludge containing hazardous solids. Defendant’s wastewater treatment plant collects these solids and pipes them to a thickener tank. Thereafter, the sludge that accumulates is pumped out into large containers and from those containers into 55-gallon drums that are disposed of off-site. On May 28, 1998, TeKrony observed four 55-gallon drums in defendant’s wash pad area that were being used to accumulate hazardous wastes, including contaminated gravel, oily pads and rags and wash pad sludges. All of the drums were labeled as hazardous waste and all had covers in place but none of the covers was secured by its barrel cover locking ring. Defendant’s recorded inspections of the “less-than-90-day” hazardous wastes are organized by waste stream, with each waste stream’s weekly inspections entered on a separate sheet beginning from the date of their initial accumulation. Seven of these weekly inspections were not recorded. However, some of the seven missing inspection records were for waste stream inspections that would have occurred in the same week. TeKrony reviewed all hazardous and nonhazardous waste manifests and associated land disposal restriction notifications for off-site shipments of defendant’s waste sent to each treatment or storage facility during the period January 1994 through May 1998. On 21 occasions between December 1995 and May 1998, land disposal restriction notices failed to identify all hazardous waste numbers applicable to the thickener sludge. In. October 1995, a land disposal restriction notice that defendant submitted to a treatment or storage facility did not identify all hazardous waste numbers applicable to the heat exchanger bundle cleaning sludge. On fifteen additional occasions, between December 1995 and May 1998, land disposal restriction notices that defendant submitted to a treatment or storage facility did not include the EPA hazardous waste numbers, the manifest number associated with the shipment or the contaminants subject to treatment. On four occasions between January 1994 and May 1998, defendant failed to maintain for a period of three years copies of its land disposal restriction notifications submitted to a treatment or storage facility with shipments of its hazardous waste. On December 18, 2000, the state of Wisconsin filed suit against defendant in the Circuit Court for Douglas County, Wisconsin, alleging several claims under the Resource Conservation and Recovery Act similar to those asserted by plaintiff in this case. The state asked for a stay in the state court action pending resolution of this action. E. Claims 22-2p. Emergency Planning and Community Right-to-Know Claims During the years 1994 to 1996, defendant manufactured, processed or otherwise used at its refinery the toxic chemicals ethylbenzene, toluene, xylene (mixed isomers), benzene, 1,2,4-trimethylbenzene, cyclohexane, ammonia, ethylene, hydrogen cyanide, hydrogen fluoride, propylene and diethanolamine. Defendant submitted Form R reports documenting its use of these toxic chemicals to the Environmental Protection Agency and the Wisconsin Department of Natural Resources for the years 1994, 1995 and 1996. In its Form R reports, defendant reported its storage tank air emissions as “fugitive” emissions for the toxic chemicals ethylbenzene, toluene, xylene (mixed isomers), benzene, 1,2,4-trimethylbenzene and cyclohexane. It did not report the emissions for these chemicals as’“stack” air releases. Fugitive emissions tend to be diffuse and multi-directional; stack emissions are typically released through vents or other openings in a single direction. Defendant’s storage tanks have floating roofs that adjust to the level of their liquid contents. When the liquid is pumped out of the storage tank, the roof lowers, leaving behind traces of the liquid on the tank walls. Under its tank operating permits, defendant was required to control fugitive emissions by installing a welded internal floating roof and double wiper seals in each tank. [In claims 23 and 24, the parties dispute certain statutory obligations defendant had under the Emergency Planning and Community Rightr-to-Know Act. Plaintiff asserts that defendant was required to prepare and maintain its threshold “calculations” and defendant argues that it was required to maintain its threshold “determinations.” Without deciding the issue, I use the term “determination” throughout the fact section because that term is used in the relevant provision, 40 C.F.R. § 372.10(a).] In support of its 1994 Form R report, defendant was required to prepare and retain its threshold determinations for a period of three years for many toxic chemicals, including ammonia, ethylene, formaldehyde, hydrogen cyanide, hydrogen fluoride, propylene and diethanolamine. For its 1995 Form R report, defendant was required to prepare and retain its determinations for the following toxic chemicals, among others: ethylene, formaldehyde, hydrogen cyanide, propylene and diethanolamine. For its 1996 Form R