I can not map EF

I have this entity in my Domain:

    public class CalibrationToolActivePart
        {
            [Key]
            public int CalibrationToolActivePartID { get; set; }

            public int CalibrationToolID { get; set; }

            public int CalibrationToolTypePartID { get; set; }

            public int MeasureUnitID { get; set; }

            [ForeignKey("CalibrationToolID")]
            [ScriptIgnore(ApplyToOverrides=true)]
            public virtual CalibrationTool CalibrationTool { get; set; }

            [ForeignKey("CalibrationToolTypePartID")]
            [ScriptIgnore(ApplyToOverrides = true)]
            public virtual CalibrationToolTypePart CalibrationToolTypePart { get; set; }

            [ForeignKey("MeasureUnitID")]
            [ScriptIgnore(ApplyToOverrides = true)]
            public virtual MeasureUnit MeasureUnit { get; set; }
            public int? ToleranceID { get; set; }
            //TODO: Tolerance outra tabela
            [ForeignKey("ToleranceID")]
            public virtual Tolerance Tolerance { get; set; }

            public bool Active { get; set; }
        }  

And the one that sends the foreign key:

 public class Tolerance
    {
        [Key]
        public int ToleranceID { get; set; }
        [Display(Name = "Nome")]
        [Required(ErrorMessage = "O campo \"Nome\" deve ser preenchido")]
        public string Name { get; set; }
        [Required(ErrorMessage = "O campo \"Tipo\" deve ser selecionado")]
        public int MeasureTypeID { get; set; }
        [ForeignKey("MeasureTypeID")]
        public virtual MeasureType MeasureType { get; set; }
        [Required(ErrorMessage = "O campo \"Unidade\" deve ser selecionado")]
        public int MeasureUnitID { get; set; }
        [ForeignKey("MeasureUnitID")]
        public virtual MeasureUnit MeasureUnit { get; set; }
        [Required(ErrorMessage = "O campo \"Máximo Permitido\" deve ser preenchido")]
        public int CompanyID { get; set; }
        [Required(ErrorMessage = "O campo \"Mínimo\" deve ser preenchido")]
        public double Minimum { get; set; }
        [Required(ErrorMessage = "O campo \"Máximo\" deve ser preenchido")]
        public double Maximum { get; set; }
        public bool Inactive { get; set; }
        [ScriptIgnore(ApplyToOverrides=true)]
        public virtual ICollection<CalibrationToolActivePart> CalibrationToolActiveParts { get; set; }

        public double MaximumAllowed { get; set; }
        [Required(ErrorMessage = "O campo \"Total\" deve ser preenchido")]
        public double Total { get; set; }
    }

The mapper module looks like this:

 internal class CalibrationConfiguration : EntityTypeConfiguration<Calibration>
    {
        public CalibrationConfiguration()
        {
            HasRequired<CalibrationTool>(x => x.CalibrationTool)
                .WithMany(x => x.Calibrations)
                .HasForeignKey(x => x.CalibrationToolID);


            HasMany<File>(x => x.StandardCertificationFiles)
                .WithMany(x => x.Calibrations)
                .Map(m =>
                {
                    m.ToTable("Calibrations_Files");
                    m.MapLeftKey("CalibrationID");
                    m.MapRightKey("FileID");
                });

            HasMany<CalibrationTool>(x => x.CalibrationToolsUsed)
                .WithMany()
                .Map(m =>
                {
                    m.ToTable("Calibrations_CalibrationTools");
                    m.MapLeftKey("CalibrationID");
                    m.MapRightKey("CalibrationToolID");
                });
        }

this is the other one:

 internal class ToleranceConfiguration : EntityTypeConfiguration<Tolerance>
    {
        public ToleranceConfiguration()
        {
            HasMany<CalibrationToolActivePart>(x => x.CalibrationToolActiveParts)
                .WithOptional(x => x.Tolerance)
                .HasForeignKey(x => x.ToleranceID);
        }
    }

I just have to leave N for N and I can not do this, you need more information just to comment what I'm putting.